Deoxyribonucleic acid (; DNA) is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms (with the exception of RNA viruses). The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information. Along with RNA and proteins, DNA is one of the three major macromolecules that are essential for all known forms of life.

DNA consists of two long polymers of simple units called nucleotides, with backbones made of sugars and phosphate groups joined by ester bonds. These two strands run in opposite directions to each other and are therefore anti-parallel. Attached to each sugar is one of four types of molecules called nucleobases (informally, ''bases''). It is the sequence of these four nucleobases along the backbone that encodes information. This information is read using the genetic code, which specifies the sequence of the amino acids within proteins. The code is read by copying stretches of DNA into the related nucleic acid RNA in a process called transcription.

Within cells DNA is organized into long structures called chromosomes. During cell division these chromosomes are duplicated in the process of DNA replication, providing each cell its own complete set of chromosomes. Eukaryotic organisms (animals, plants, fungi, and protists) store most of their DNA inside the cell nucleus and some of their DNA in organelles, such as mitochondria or chloroplasts. In contrast, prokaryotes (bacteria and archaea) store their DNA only in the cytoplasm. Within the chromosomes, chromatin proteins such as histones compact and organize DNA. These compact structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed.

Properties

DNA is a long polymer made from repeating units called nucleotides. As first discovered by James D. Watson and Francis Crick, the structure of DNA of all species comprises two helical chains each coiled round the same axis, and each with a pitch of 34 Ångströms (3.4 nanometres) and a radius of 10 Ångströms (1.0 nanometres). According to another study, when measured in a particular solution, the DNA chain measured 22 to 26 Ångströms wide (2.2 to 2.6 nanometres), and one nucleotide unit measured 3.3 Å (0.33 nm) long. Although each individual repeating unit is very small, DNA polymers can be very large molecules containing millions of nucleotides. For instance, the largest human chromosome, chromosome number 1, is approximately 220 million base pairs long.

In living organisms DNA does not usually exist as a single molecule, but instead as a pair of molecules that are held tightly together. These two long strands entwine like vines, in the shape of a double helix. The nucleotide repeats contain both the segment of the backbone of the molecule, which holds the chain together, and a nucleobase, which interacts with the other DNA strand in the helix. A nucleobase linked to a sugar is called a nucleoside and a base linked to a sugar and one or more phosphate groups is called a nucleotide. Polymers comprising multiple linked nucleotides (as in DNA) is called a polynucleotide.

The backbone of the DNA strand is made from alternating phosphate and sugar residues. The sugar in DNA is 2-deoxyribose, which is a pentose (five-carbon) sugar. The sugars are joined together by phosphate groups that form phosphodiester bonds between the third and fifth carbon atoms of adjacent sugar rings. These asymmetric bonds mean a strand of DNA has a direction. In a double helix the direction of the nucleotides in one strand is opposite to their direction in the other strand: the strands are ''antiparallel''. The asymmetric ends of DNA strands are called the 5′ (''five prime'') and 3′ (''three prime'') ends, with the 5' end having a terminal phosphate group and the 3' end a terminal hydroxyl group. One major difference between DNA and RNA is the sugar, with the 2-deoxyribose in DNA being replaced by the alternative pentose sugar ribose in RNA.

The DNA double helix is stabilized primarily by two forces: hydrogen bonds between nucleotides and base-stacking interactions among the aromatic nucleobases. In the aqueous environment of the cell, the conjugated π bonds of nucleotide bases align perpendicular to the axis of the DNA molecule, minimizing their interaction with the solvation shell and therefore, the Gibbs free energy. The four bases found in DNA are adenine (abbreviated A), cytosine (C), guanine (G) and thymine (T). These four bases are attached to the sugar/phosphate to form the complete nucleotide, as shown for adenosine monophosphate.

The nucleobases are classified into two types: the purines, A and G, being fused five- and six-membered heterocyclic compounds, and the pyrimidines, the six-membered rings C and T. A fifth pyrimidine nucleobase, uracil (U), usually takes the place of thymine in RNA and differs from thymine by lacking a methyl group on its ring. Uracil is not usually found in DNA, occurring only as a breakdown product of cytosine. In addition to RNA and DNA a large number of artificial nucleic acid analogues have also been created to study the proprieties of nucleic acids, or for use in biotechnology.

Grooves

Twin helical strands form the DNA backbone. Another double helix may be found by tracing the spaces, or grooves, between the strands. These voids are adjacent to the base pairs and may provide a binding site. As the strands are not directly opposite each other, the grooves are unequally sized. One groove, the major groove, is 22 Å wide and the other, the minor groove, is 12 Å wide. The narrowness of the minor groove means that the edges of the bases are more accessible in the major groove. As a result, proteins like transcription factors that can bind to specific sequences in double-stranded DNA usually make contacts to the sides of the bases exposed in the major groove. This situation varies in unusual conformations of DNA within the cell ''(see below)'', but the major and minor grooves are always named to reflect the differences in size that would be seen if the DNA is twisted back into the ordinary B form.

Base pairing

In a DNA double helix, each type of nucleobase on one strand normally interacts with just one type of nucleobase on the other strand. This is called complementary base pairing. Here, purines form hydrogen bonds to pyrimidines, with A bonding only to T, and C bonding only to G. This arrangement of two nucleotides binding together across the double helix is called a base pair. As hydrogen bonds are not covalent, they can be broken and rejoined relatively easily. The two strands of DNA in a double helix can therefore be pulled apart like a zipper, either by a mechanical force or high temperature. As a result of this complementarity, all the information in the double-stranded sequence of a DNA helix is duplicated on each strand, which is vital in DNA replication. Indeed, this reversible and specific interaction between complementary base pairs is critical for all the functions of DNA in living organisms. The two types of base pairs form different numbers of hydrogen bonds, AT forming two hydrogen bonds, and GC forming three hydrogen bonds (see figures, left). DNA with high GC-content is more stable than DNA with low GC-content. Although it is often stated that this is due to the added stability of an additional hydrogen bond, this is incorrect. DNA with high GC-content is more stable due to intra-strand base stacking interactions.

As noted above, most DNA molecules are actually two polymer strands, bound together in a helical fashion by noncovalent bonds; this double stranded structure (dsDNA) is maintained largely by the intrastrand base stacking interactions, which are strongest for G,C stacks. The two strands can come apart - a process known as melting - to form two ss DNA molecules. Melting occurs when conditions favor ssDNA; such conditions are high temperature, low salt and high pH (low pH also melts DNA, but since DNA is unstable due to acid depurination, low pH is rarely used). The stability of the dsDNA form depends not only on the GC-content (% G,C basepairs) but also on sequence (since stacking is sequence specific) and also length (longer molecules are more stable). The stability can be measured in various ways; a common way is the "melting temperature", which is the temperature at which 50% of the ds molecules are converted to ss molecules; melting temperature is dependent on ionic strength and the concentration of DNA. As a result, it is both the percentage of GC base pairs and the overall length of a DNA double helix that determine the strength of the association between the two strands of DNA. Long DNA helices with a high GC-content have stronger-interacting strands, while short helices with high AT content have weaker-interacting strands. In biology, parts of the DNA double helix that need to separate easily, such as the TATAAT Pribnow box in some promoters, tend to have a high AT content, making the strands easier to pull apart.

In the laboratory, the strength of this interaction can be measured by finding the temperature required to break the hydrogen bonds, their melting temperature (also called ''T_m'' value). When all the base pairs in a DNA double helix melt, the strands separate and exist in solution as two entirely independent molecules. These single-stranded DNA molecules (''ssDNA'') have no single common shape, but some conformations are more stable than others.

Sense and antisense

A DNA sequence is called "sense" if its sequence is the same as that of a messenger RNA copy that is translated into protein. The sequence on the opposite strand is called the "antisense" sequence. Both sense and antisense sequences can exist on different parts of the same strand of DNA (i.e. both strands contain both sense and antisense sequences). In both prokaryotes and eukaryotes, antisense RNA sequences are produced, but the functions of these RNAs are not entirely clear. One proposal is that antisense RNAs are involved in regulating gene expression through RNA-RNA base pairing.

A few DNA sequences in prokaryotes and eukaryotes, and more in plasmids and viruses, blur the distinction between sense and antisense strands by having overlapping genes. In these cases, some DNA sequences do double duty, encoding one protein when read along one strand, and a second protein when read in the opposite direction along the other strand. In bacteria, this overlap may be involved in the regulation of gene transcription, while in viruses, overlapping genes increase the amount of information that can be encoded within the small viral genome.

Supercoiling

DNA can be twisted like a rope in a process called DNA supercoiling. With DNA in its "relaxed" state, a strand usually circles the axis of the double helix once every 10.4 base pairs, but if the DNA is twisted the strands become more tightly or more loosely wound. If the DNA is twisted in the direction of the helix, this is positive supercoiling, and the bases are held more tightly together. If they are twisted in the opposite direction, this is negative supercoiling, and the bases come apart more easily. In nature, most DNA has slight negative supercoiling that is introduced by enzymes called topoisomerases. These enzymes are also needed to relieve the twisting stresses introduced into DNA strands during processes such as transcription and DNA replication.

Alternate DNA structures

DNA exists in many possible conformations that include A-DNA, B-DNA, and Z-DNA forms, although, only B-DNA and Z-DNA have been directly observed in functional organisms. The conformation that DNA adopts depends on the hydration level, DNA sequence, the amount and direction of supercoiling, chemical modifications of the bases, the type and concentration of metal ions, as well as the presence of polyamines in solution.

The first published reports of A-DNA X-ray diffraction patterns— and also B-DNA used analyses based on Patterson transforms that provided only a limited amount of structural information for oriented fibers of DNA. An alternate analysis was then proposed by Wilkins ''et al.'', in 1953, for the ''in vivo'' B-DNA X-ray diffraction/scattering patterns of highly hydrated DNA fibers in terms of squares of Bessel functions. In the same journal, James D. Watson and Francis Crick presented their molecular modeling analysis of the DNA X-ray diffraction patterns to suggest that the structure was a double-helix.

Although the `B-DNA form' is most common under the conditions found in cells, it is not a well-defined conformation but a family of related DNA conformations that occur at the high hydration levels present in living cells. Their corresponding X-ray diffraction and scattering patterns are characteristic of molecular paracrystals with a significant degree of disorder.

Compared to B-DNA, the A-DNA form is a wider right-handed spiral, with a shallow, wide minor groove and a narrower, deeper major groove. The A form occurs under non-physiological conditions in partially dehydrated samples of DNA, while in the cell it may be produced in hybrid pairings of DNA and RNA strands, as well as in enzyme-DNA complexes. Segments of DNA where the bases have been chemically modified by methylation may undergo a larger change in conformation and adopt the Z form. Here, the strands turn about the helical axis in a left-handed spiral, the opposite of the more common B form. These unusual structures can be recognized by specific Z-DNA binding proteins and may be involved in the regulation of transcription.

Alternate DNA chemistry

For a number of years exobiologists have proposed the existence of a shadow biosphere, a postulated microbial biosphere of Earth that uses radically different biochemical and molecular processes than currently known life. One of the proposals was the existence of lifeforms that use arsenic instead of phosphorus in DNA.

A December 2010 NASA press conference stated that the bacterium GFAJ-1, which has evolved in an arsenic-rich environment, is the first terrestrial lifeform found which may have this ability. The bacterium was found in Mono Lake, east of Yosemite National Park. GFAJ-1 is a rod-shaped extremophile bacterium in the family Halomonadaceae that, when starved of phosphorus, may be capable of incorporating the usually poisonous element arsenic in its DNA. This discovery may lend weight to the long-standing idea that extraterrestrial life could have a different chemical makeup from life on Earth. The research was carried out by a team led by Felisa Wolfe-Simon, a geomicrobiologist and geobiochemist, a Postdoctoral Fellow of the NASA Astrobiology Institute with Arizona State University. This finding has, however, faced strong criticism from the scientific community; scientists have argued that there is no evidence that arsenic is actually incorporated into biomolecules. Independent conformation of this finding has also not yet been possible.

Quadruplex structures

At the ends of the linear chromosomes are specialized regions of DNA called telomeres. The main function of these regions is to allow the cell to replicate chromosome ends using the enzyme telomerase, as the enzymes that normally replicate DNA cannot copy the extreme 3′ ends of chromosomes. These specialized chromosome caps also help protect the DNA ends, and stop the DNA repair systems in the cell from treating them as damage to be corrected. In human cells, telomeres are usually lengths of single-stranded DNA containing several thousand repeats of a simple TTAGGG sequence.

These guanine-rich sequences may stabilize chromosome ends by forming structures of stacked sets of four-base units, rather than the usual base pairs found in other DNA molecules. Here, four guanine bases form a flat plate and these flat four-base units then stack on top of each other, to form a stable ''G-quadruplex'' structure. These structures are stabilized by hydrogen bonding between the edges of the bases and chelation of a metal ion in the centre of each four-base unit. Other structures can also be formed, with the central set of four bases coming from either a single strand folded around the bases, or several different parallel strands, each contributing one base to the central structure.

In addition to these stacked structures, telomeres also form large loop structures called telomere loops, or T-loops. Here, the single-stranded DNA curls around in a long circle stabilized by telomere-binding proteins. At the very end of the T-loop, the single-stranded telomere DNA is held onto a region of double-stranded DNA by the telomere strand disrupting the double-helical DNA and base pairing to one of the two strands. This triple-stranded structure is called a displacement loop or D-loop.

Branched DNA

In DNA fraying occurs when non-complementary regions exist at the end of an otherwise complementary double-strand of DNA. However, branched DNA can occur if a third strand of DNA is introduced and contains adjoining regions able to hybridize with the frayed regions of the pre-existing double-strand. Although the simplest example of branched DNA involves only three strands of DNA, complexes involving additional strands and multiple branches are also possible. Branched DNA can be used in nanotechnology to construct geometric shapes, see the section on uses in technology below.

Vibration

DNA may carry out low-frequency collective motion as observed by the Raman spectroscopy and analyzed with a quasi-continuum model.

Chemical modifications

Base modifications

The expression of genes is influenced by how the DNA is packaged in chromosomes, in a structure called chromatin. Base modifications can be involved in packaging, with regions that have low or no gene expression usually containing high levels of methylation of cytosine bases. For example, cytosine methylation, produces 5-methylcytosine, which is important for X-chromosome inactivation. The average level of methylation varies between organisms – the worm ''Caenorhabditis elegans'' lacks cytosine methylation, while vertebrates have higher levels, with up to 1% of their DNA containing 5-methylcytosine. Despite the importance of 5-methylcytosine, it can deaminate to leave a thymine base, so methylated cytosines are particularly prone to mutations. Other base modifications include adenine methylation in bacteria, the presence of 5-hydroxymethylcytosine in the brain, and the glycosylation of uracil to produce the "J-base" in kinetoplastids.

Damage

DNA can be damaged by many sorts of mutagens, which change the DNA sequence. Mutagens include oxidizing agents, alkylating agents and also high-energy electromagnetic radiation such as ultraviolet light and X-rays. The type of DNA damage produced depends on the type of mutagen. For example, UV light can damage DNA by producing thymine dimers, which are cross-links between pyrimidine bases. On the other hand, oxidants such as free radicals or hydrogen peroxide produce multiple forms of damage, including base modifications, particularly of guanosine, and double-strand breaks. A typical human cell contains about 150,000 bases that have suffered oxidative damage. Of these oxidative lesions, the most dangerous are double-strand breaks, as these are difficult to repair and can produce point mutations, insertions and deletions from the DNA sequence, as well as chromosomal translocations.

Many mutagens fit into the space between two adjacent base pairs, this is called ''intercalation''. Most intercalators are aromatic and planar molecules; examples include ethidium bromide, daunomycin, and doxorubicin. In order for an intercalator to fit between base pairs, the bases must separate, distorting the DNA strands by unwinding of the double helix. This inhibits both transcription and DNA replication, causing toxicity and mutations. As a result, DNA intercalators are often carcinogens, and benzo[''a'']pyrene diol epoxide, acridines, aflatoxin and ethidium bromide are well-known examples. Nevertheless, due to their ability to inhibit DNA transcription and replication, other similar toxins are also used in chemotherapy to inhibit rapidly growing cancer cells.

Biological functions

DNA usually occurs as linear chromosomes in eukaryotes, and circular chromosomes in prokaryotes. The set of chromosomes in a cell makes up its genome; the human genome has approximately 3 billion base pairs of DNA arranged into 46 chromosomes. The information carried by DNA is held in the sequence of pieces of DNA called genes. Transmission of genetic information in genes is achieved via complementary base pairing. For example, in transcription, when a cell uses the information in a gene, the DNA sequence is copied into a complementary RNA sequence through the attraction between the DNA and the correct RNA nucleotides. Usually, this RNA copy is then used to make a matching protein sequence in a process called translation, which depends on the same interaction between RNA nucleotides. In alternative fashion, a cell may simply copy its genetic information in a process called DNA replication. The details of these functions are covered in other articles; here we focus on the interactions between DNA and other molecules that mediate the function of the genome.

Genes and genomes

Genomic DNA is tightly and orderly packed in the process called DNA condensation to fit the small available volumes of the cell. In eukaryotes, DNA is located in the cell nucleus, as well as small amounts in mitochondria and chloroplasts. In prokaryotes, the DNA is held within an irregularly shaped body in the cytoplasm called the nucleoid. The genetic information in a genome is held within genes, and the complete set of this information in an organism is called its genotype. A gene is a unit of heredity and is a region of DNA that influences a particular characteristic in an organism. Genes contain an open reading frame that can be transcribed, as well as regulatory sequences such as promoters and enhancers, which control the transcription of the open reading frame.

In many species, only a small fraction of the total sequence of the genome encodes protein. For example, only about 1.5% of the human genome consists of protein-coding exons, with over 50% of human DNA consisting of non-coding repetitive sequences. The reasons for the presence of so much noncoding DNA in eukaryotic genomes and the extraordinary differences in genome size, or ''C-value'', among species represent a long-standing puzzle known as the "C-value enigma". However, DNA sequences that do not code protein may still encode functional non-coding RNA molecules, which are involved in the regulation of gene expression. Some noncoding DNA sequences play structural roles in chromosomes. Telomeres and centromeres typically contain few genes, but are important for the function and stability of chromosomes. An abundant form of noncoding DNA in humans are pseudogenes, which are copies of genes that have been disabled by mutation. These sequences are usually just molecular fossils, although they can occasionally serve as raw genetic material for the creation of new genes through the process of gene duplication and divergence.

Transcription and translation

A gene is a sequence of DNA that contains genetic information and can influence the phenotype of an organism. Within a gene, the sequence of bases along a DNA strand defines a messenger RNA sequence, which then defines one or more protein sequences. The relationship between the nucleotide sequences of genes and the amino-acid sequences of proteins is determined by the rules of translation, known collectively as the genetic code. The genetic code consists of three-letter 'words' called ''codons'' formed from a sequence of three nucleotides (e.g. ACT, CAG, TTT).

In transcription, the codons of a gene are copied into messenger RNA by RNA polymerase. This RNA copy is then decoded by a ribosome that reads the RNA sequence by base-pairing the messenger RNA to transfer RNA, which carries amino acids. Since there are 4 bases in 3-letter combinations, there are 64 possible codons ($4^3$ combinations). These encode the twenty standard amino acids, giving most amino acids more than one possible codon. There are also three 'stop' or 'nonsense' codons signifying the end of the coding region; these are the TAA, TGA and TAG codons.

Replication

Cell division is essential for an organism to grow, but, when a cell divides, it must replicate the DNA in its genome so that the two daughter cells have the same genetic information as their parent. The double-stranded structure of DNA provides a simple mechanism for DNA replication. Here, the two strands are separated and then each strand's complementary DNA sequence is recreated by an enzyme called DNA polymerase. This enzyme makes the complementary strand by finding the correct base through complementary base pairing, and bonding it onto the original strand. As DNA polymerases can only extend a DNA strand in a 5′ to 3′ direction, different mechanisms are used to copy the antiparallel strands of the double helix. In this way, the base on the old strand dictates which base appears on the new strand, and the cell ends up with a perfect copy of its DNA.

Interactions with proteins

All the functions of DNA depend on interactions with proteins. These protein interactions can be non-specific, or the protein can bind specifically to a single DNA sequence. Enzymes can also bind to DNA and of these, the polymerases that copy the DNA base sequence in transcription and DNA replication are particularly important.

DNA-binding proteins

Structural proteins that bind DNA are well-understood examples of non-specific DNA-protein interactions. Within chromosomes, DNA is held in complexes with structural proteins. These proteins organize the DNA into a compact structure called chromatin. In eukaryotes this structure involves DNA binding to a complex of small basic proteins called histones, while in prokaryotes multiple types of proteins are involved. The histones form a disk-shaped complex called a nucleosome, which contains two complete turns of double-stranded DNA wrapped around its surface. These non-specific interactions are formed through basic residues in the histones making ionic bonds to the acidic sugar-phosphate backbone of the DNA, and are therefore largely independent of the base sequence. Chemical modifications of these basic amino acid residues include methylation, phosphorylation and acetylation. These chemical changes alter the strength of the interaction between the DNA and the histones, making the DNA more or less accessible to transcription factors and changing the rate of transcription. Other non-specific DNA-binding proteins in chromatin include the high-mobility group proteins, which bind to bent or distorted DNA. These proteins are important in bending arrays of nucleosomes and arranging them into the larger structures that make up chromosomes.

A distinct group of DNA-binding proteins are the DNA-binding proteins that specifically bind single-stranded DNA. In humans, replication protein A is the best-understood member of this family and is used in processes where the double helix is separated, including DNA replication, recombination and DNA repair. These binding proteins seem to stabilize single-stranded DNA and protect it from forming stem-loops or being degraded by nucleases.

In contrast, other proteins have evolved to bind to particular DNA sequences. The most intensively studied of these are the various transcription factors, which are proteins that regulate transcription. Each transcription factor binds to one particular set of DNA sequences and activates or inhibits the transcription of genes that have these sequences close to their promoters. The transcription factors do this in two ways. Firstly, they can bind the RNA polymerase responsible for transcription, either directly or through other mediator proteins; this locates the polymerase at the promoter and allows it to begin transcription. Alternatively, transcription factors can bind enzymes that modify the histones at the promoter; this will change the accessibility of the DNA template to the polymerase.

As these DNA targets can occur throughout an organism's genome, changes in the activity of one type of transcription factor can affect thousands of genes. Consequently, these proteins are often the targets of the signal transduction processes that control responses to environmental changes or cellular differentiation and development. The specificity of these transcription factors' interactions with DNA come from the proteins making multiple contacts to the edges of the DNA bases, allowing them to "read" the DNA sequence. Most of these base-interactions are made in the major groove, where the bases are most accessible.

DNA-modifying enzymes

Nucleases and ligases

Nucleases are enzymes that cut DNA strands by catalyzing the hydrolysis of the phosphodiester bonds. Nucleases that hydrolyse nucleotides from the ends of DNA strands are called exonucleases, while endonucleases cut within strands. The most frequently used nucleases in molecular biology are the restriction endonucleases, which cut DNA at specific sequences. For instance, the EcoRV enzyme shown to the left recognizes the 6-base sequence 5′-GAT|ATC-3′ and makes a cut at the vertical line. In nature, these enzymes protect bacteria against phage infection by digesting the phage DNA when it enters the bacterial cell, acting as part of the restriction modification system. In technology, these sequence-specific nucleases are used in molecular cloning and DNA fingerprinting.

Enzymes called DNA ligases can rejoin cut or broken DNA strands. Ligases are particularly important in lagging strand DNA replication, as they join together the short segments of DNA produced at the replication fork into a complete copy of the DNA template. They are also used in DNA repair and genetic recombination.

Topoisomerases and helicases

Topoisomerases are enzymes with both nuclease and ligase activity. These proteins change the amount of supercoiling in DNA. Some of these enzymes work by cutting the DNA helix and allowing one section to rotate, thereby reducing its level of supercoiling; the enzyme then seals the DNA break. Other types of these enzymes are capable of cutting one DNA helix and then passing a second strand of DNA through this break, before rejoining the helix. Topoisomerases are required for many processes involving DNA, such as DNA replication and transcription.

Helicases are proteins that are a type of molecular motor. They use the chemical energy in nucleoside triphosphates, predominantly ATP, to break hydrogen bonds between bases and unwind the DNA double helix into single strands. These enzymes are essential for most processes where enzymes need to access the DNA bases.

Polymerases

Polymerases are enzymes that synthesize polynucleotide chains from nucleoside triphosphates. The sequence of their products are copies of existing polynucleotide chains – which are called ''templates''. These enzymes function by adding nucleotides onto the 3′ hydroxyl group of the previous nucleotide in a DNA strand. As a consequence, all polymerases work in a 5′ to 3′ direction. In the active site of these enzymes, the incoming nucleoside triphosphate base-pairs to the template: this allows polymerases to accurately synthesize the complementary strand of their template. Polymerases are classified according to the type of template that they use.

In DNA replication, a DNA-dependent DNA polymerase makes a copy of a DNA sequence. Accuracy is vital in this process, so many of these polymerases have a proofreading activity. Here, the polymerase recognizes the occasional mistakes in the synthesis reaction by the lack of base pairing between the mismatched nucleotides. If a mismatch is detected, a 3′ to 5′ exonuclease activity is activated and the incorrect base removed. In most organisms, DNA polymerases function in a large complex called the replisome that contains multiple accessory subunits, such as the DNA clamp or helicases.

RNA-dependent DNA polymerases are a specialized class of polymerases that copy the sequence of an RNA strand into DNA. They include reverse transcriptase, which is a viral enzyme involved in the infection of cells by retroviruses, and telomerase, which is required for the replication of telomeres. Telomerase is an unusual polymerase because it contains its own RNA template as part of its structure.

Transcription is carried out by a DNA-dependent RNA polymerase that copies the sequence of a DNA strand into RNA. To begin transcribing a gene, the RNA polymerase binds to a sequence of DNA called a promoter and separates the DNA strands. It then copies the gene sequence into a messenger RNA transcript until it reaches a region of DNA called the terminator, where it halts and detaches from the DNA. As with human DNA-dependent DNA polymerases, RNA polymerase II, the enzyme that transcribes most of the genes in the human genome, operates as part of a large protein complex with multiple regulatory and accessory subunits.

Genetic recombination

A DNA helix usually does not interact with other segments of DNA, and in human cells the different chromosomes even occupy separate areas in the nucleus called "chromosome territories". This physical separation of different chromosomes is important for the ability of DNA to function as a stable repository for information, as one of the few times chromosomes interact is during chromosomal crossover when they recombine. Chromosomal crossover is when two DNA helices break, swap a section and then rejoin.

Recombination allows chromosomes to exchange genetic information and produces new combinations of genes, which increases the efficiency of natural selection and can be important in the rapid evolution of new proteins. Genetic recombination can also be involved in DNA repair, particularly in the cell's response to double-strand breaks.

The most common form of chromosomal crossover is homologous recombination, where the two chromosomes involved share very similar sequences. Non-homologous recombination can be damaging to cells, as it can produce chromosomal translocations and genetic abnormalities. The recombination reaction is catalyzed by enzymes known as recombinases, such as RAD51. The first step in recombination is a double-stranded break either caused by an endonuclease or damage to the DNA. A series of steps catalyzed in part by the recombinase then leads to joining of the two helices by at least one Holliday junction, in which a segment of a single strand in each helix is annealed to the complementary strand in the other helix. The Holliday junction is a tetrahedral junction structure that can be moved along the pair of chromosomes, swapping one strand for another. The recombination reaction is then halted by cleavage of the junction and re-ligation of the released DNA.

Evolution

DNA contains the genetic information that allows all modern living things to function, grow and reproduce. However, it is unclear how long in the 4-billion-year history of life DNA has performed this function, as it has been proposed that the earliest forms of life may have used RNA as their genetic material. RNA may have acted as the central part of early cell metabolism as it can both transmit genetic information and carry out catalysis as part of ribozymes. This ancient RNA world where nucleic acid would have been used for both catalysis and genetics may have influenced the evolution of the current genetic code based on four nucleotide bases. This would occur, since the number of different bases in such an organism is a trade-off between a small number of bases increasing replication accuracy and a large number of bases increasing the catalytic efficiency of ribozymes.

However, there is no direct evidence of ancient genetic systems, as recovery of DNA from most fossils is impossible. This is because DNA will survive in the environment for less than one million years and slowly degrades into short fragments in solution. Claims for older DNA have been made, most notably a report of the isolation of a viable bacterium from a salt crystal 250 million years old, but these claims are controversial.

On August 8, 2011, a report, based on NASA studies with meteorites found on Earth, was published suggesting building blocks of DNA (adenine, guanine and related organic molecules) may have been formed extraterrestrially in outer space.

Uses in technology

Genetic engineering

Methods have been developed to purify DNA from organisms, such as phenol-chloroform extraction, and to manipulate it in the laboratory, such as restriction digests and the polymerase chain reaction. Modern biology and biochemistry make intensive use of these techniques in recombinant DNA technology. Recombinant DNA is a man-made DNA sequence that has been assembled from other DNA sequences. They can be transformed into organisms in the form of plasmids or in the appropriate format, by using a viral vector. The genetically modified organisms produced can be used to produce products such as recombinant proteins, used in medical research, or be grown in agriculture.

Forensics

Forensic scientists can use DNA in blood, semen, skin, saliva or hair found at a crime scene to identify a matching DNA of an individual, such as a perpetrator. This process is formally termed DNA profiling, but may also be called "genetic fingerprinting". In DNA profiling, the lengths of variable sections of repetitive DNA, such as short tandem repeats and minisatellites, are compared between people. This method is usually an extremely reliable technique for identifying a matching DNA. However, identification can be complicated if the scene is contaminated with DNA from several people. DNA profiling was developed in 1984 by British geneticist Sir Alec Jeffreys, and first used in forensic science to convict Colin Pitchfork in the 1988 Enderby murders case.

People convicted of certain types of crimes may be required to provide a sample of DNA for a database. This has helped investigators solve old cases where only a DNA sample was obtained from the scene. DNA profiling can also be used to identify victims of mass casualty incidents. On the other hand, many convicted people have been released from prison on the basis of DNA techniques, which were not available when a crime had originally been committed.

Bioinformatics

Bioinformatics involves the manipulation, searching, and data mining of biological data, and this includes DNA sequence data. The development of techniques to store and search DNA sequences have led to widely applied advances in computer science, especially string searching algorithms, machine learning and database theory. String searching or matching algorithms, which find an occurrence of a sequence of letters inside a larger sequence of letters, were developed to search for specific sequences of nucleotides. The DNA sequenced may be aligned with other DNA sequences to identify homologous sequences and locate the specific mutations that make them distinct. These techniques, especially multiple sequence alignment, are used in studying phylogenetic relationships and protein function. Data sets representing entire genomes' worth of DNA sequences, such as those produced by the Human Genome Project, are difficult to use without the annotations that identify the locations of genes and regulatory elements on each chromosome. Regions of DNA sequence that have the characteristic patterns associated with protein- or RNA-coding genes can be identified by gene finding algorithms, which allow researchers to predict the presence of particular gene products and their possible functions in an organism even before they have been isolated experimentally. Entire genomes may also be compared which can shed light on the evolutionary history of particular organism and permit the examination of complex evolutionary events.

DNA nanotechnology

DNA nanotechnology uses the unique molecular recognition properties of DNA and other nucleic acids to create self-assembling branched DNA complexes with useful properties. DNA is thus used as a structural material rather than as a carrier of biological information. This has led to the creation of two-dimensional periodic lattices (both tile-based as well as using the "DNA origami" method) as well as three-dimensional structures in the shapes of polyhedra. Nanomechanical devices and algorithmic self-assembly have also been demonstrated, and these DNA structures have been used to template the arrangement of other molecules such as gold nanoparticles and streptavidin proteins.

History and anthropology

Because DNA collects mutations over time, which are then inherited, it contains historical information, and, by comparing DNA sequences, geneticists can infer the evolutionary history of organisms, their phylogeny. This field of phylogenetics is a powerful tool in evolutionary biology. If DNA sequences within a species are compared, population geneticists can learn the history of particular populations. This can be used in studies ranging from ecological genetics to anthropology; For example, DNA evidence is being used to try to identify the Ten Lost Tribes of Israel.

DNA has also been used to look at modern family relationships, such as establishing family relationships between the descendants of Sally Hemings and Thomas Jefferson. This usage is closely related to the use of DNA in criminal investigations detailed above. Indeed, some criminal investigations have been solved when DNA from crime scenes has matched relatives of the guilty individual.

History of DNA research

DNA was first isolated by the Swiss physician Friedrich Miescher who, in 1869, discovered a microscopic substance in the pus of discarded surgical bandages. As it resided in the nuclei of cells, he called it "nuclein". In 1878, Albrecht Kossel isolated the non-protein component of "nuclein", nucleic acid, and later isolated its five primary nucleobases. In 1919, Phoebus Levene identified the base, sugar and phosphate nucleotide unit. Levene suggested that DNA consisted of a string of nucleotide units linked together through the phosphate groups. However, Levene thought the chain was short and the bases repeated in a fixed order. In 1937 William Astbury produced the first X-ray diffraction patterns that showed that DNA had a regular structure.

In 1927 Nikolai Koltsov proposed that inherited traits would be inherited via a "giant hereditary molecule" which would be made up of "two mirror strands that would replicate in a semi-conservative fashion using each strand as a template". In 1928, Frederick Griffith discovered that traits of the "smooth" form of the ''Pneumococcus'' could be transferred to the "rough" form of the same bacteria by mixing killed "smooth" bacteria with the live "rough" form. This system provided the first clear suggestion that DNA carries genetic information—the Avery–MacLeod–McCarty experiment—when Oswald Avery, along with coworkers Colin MacLeod and Maclyn McCarty, identified DNA as the transforming principle in 1943. DNA's role in heredity was confirmed in 1952, when Alfred Hershey and Martha Chase in the Hershey–Chase experiment showed that DNA is the genetic material of the T2 phage.

In 1953, James D. Watson and Francis Crick suggested what is now accepted as the first correct double-helix model of DNA structure in the journal ''Nature''. Their double-helix, molecular model of DNA was then based on a single X-ray diffraction image (labeled as "Photo 51") taken by Rosalind Franklin and Raymond Gosling in May 1952, as well as the information that the DNA bases are paired — also obtained through private communications from Erwin Chargaff in the previous years. Chargaff's rules played a very important role in establishing double-helix configurations for B-DNA as well as A-DNA.

Experimental evidence supporting the Watson and Crick model were published in a series of five articles in the same issue of ''Nature''. Of these, Franklin and Gosling's paper was the first publication of their own X-ray diffraction data and original analysis method that partially supported the Watson and Crick model; this issue also contained an article on DNA structure by Maurice Wilkins and two of his colleagues, whose analysis and ''in vivo'' B-DNA X-ray patterns also supported the presence ''in vivo'' of the double-helical DNA configurations as proposed by Crick and Watson for their double-helix molecular model of DNA in the previous two pages of ''Nature''. In 1962, after Franklin's death, Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine. However, Nobel rules of the time allowed only living recipients, but a vigorous debate continues on who should receive credit for the discovery.

In an influential presentation in 1957, Crick laid out the central dogma of molecular biology, which foretold the relationship between DNA, RNA, and proteins, and articulated the "adaptor hypothesis". Final confirmation of the replication mechanism that was implied by the double-helical structure followed in 1958 through the Meselson–Stahl experiment. Further work by Crick and coworkers showed that the genetic code was based on non-overlapping triplets of bases, called codons, allowing Har Gobind Khorana, Robert W. Holley and Marshall Warren Nirenberg to decipher the genetic code. These findings represent the birth of molecular biology.

See also

References

Further reading

Judson, Horace F. 1979. ''The Eighth Day of Creation: Makers of the Revolution in Biology''. Touchstone Books, ISBN 0-671-22540-5. 2nd edition: Cold Spring Harbor Laboratory Press, 1996 paperback: ISBN 0-87969-478-5.

, first published in October 1974 by MacMillan, with foreword by Francis Crick;the definitive DNA textbook,revised in 1994 with a 9 page postscript

Micklas, David. 2003. ''DNA Science: A First Course''. Cold Spring Harbor Press: ISBN 978-0879696368

Rosenfeld, Israel. 2010. ''DNA: A Graphic Guide to the Molecule that Shook the World''. Columbia University Press: ISBN 978-0231142717

Schultz, Mark and Zander Cannon. 2009. ''The Stuff of Life: A Graphic Guide to Genetics and DNA''. Hill and Wang: ISBN 0809089475

Watson, James D. 2004. ''DNA: The Secret of Life''. Random House: ISBN 978-0099451846

External links

DNA binding site prediction on protein

DNA coiling to form chromosomes

DNA the Double Helix Game From the official Nobel Prize web site

DNA under electron microscope

Dolan DNA Learning Center

Double Helix: 50 years of DNA, ''Nature''

Double Helix 1953–2003 National Centre for Biotechnology Education

Francis Crick and James Watson talking on the BBC in 1962, 1972, and 1974

Genetic Education Modules for Teachers—''DNA from the Beginning'' Study Guide

Guide to DNA cloning

DNA from the Beginning Another DNA Learning Center site on DNA, genes, and heredity from Mendel to the human genome project.

DNA Lab, demonstrates how to extract DNA from wheat using readily available equipment and supplies.

Rosalind Franklin's contributions to the study of DNA

The Register of Francis Crick Personal Papers 1938 – 2007 at Mandeville Special Collections Library, University of California, San Diego

U.S. National DNA Day—watch videos and participate in real-time chat with top scientists

Clue to chemistry of heredity found The New York Times June 1953. First American newspaper coverage of the discovery of the DNA structure

An Introduction to DNA and Chromosomes from HOPES: Huntington's Disease Outreach Project for Education at Stanford

Category:Genetics Category:Helices Category:Scattering

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Coordinates	15°48′00″N47°54′00″N
Name	Thomas Jefferson
Alt	Portrait of Thomas Jefferson by Rembrandt Peale.
Office	3rd President of the United States
Vicepresident	Aaron BurrGeorge Clinton
Term start	March 4, 1801
Term end	March 4, 1809
Predecessor	John Adams
Successor	James Madison
Office2	2nd Vice President of the United States
President2	John Adams
Term start2	March 4, 1797
Term end2	March 4, 1801
Predecessor2	John Adams
Successor2	Aaron Burr
Office3	1st United States Secretary of State
President3	George Washington
Term start3	March 22, 1790
Term end3	December 31, 1793
Predecessor3	John Jay (Acting)
Successor3	Edmund Randolph
Ambassador from4	United States
Country4	France
Nominator4	Congress of the Confederation
Term start4	May 17, 1785
Term end4	September 26, 1789
Predecessor4	Benjamin Franklin
Successor4	William Short
Office5	Delegate to the Congress of the Confederationfrom Virginia
Term start5	November 1, 1783
Term end5	May 7, 1784
Predecessor5	James Madison
Successor5	Richard Henry Lee
Office6	2nd Governor of Virginia
Term start6	June 1, 1779
Term end6	June 3, 1781
Predecessor6	Patrick Henry
Successor6	William Fleming
Office7	Delegate to the Second Continental Congressfrom Virginia
Term start7	June 20, 1775
Term end7	September 26, 1776
Predecessor7	George Washington
Successor7	John Harvie
Birth date	April 13, 1743
Birth place	Shadwell, Virginia
Death date	July 04, 1826
Death place	Charlottesville, Virginia, United States
Party	Democratic-Republican Party
Spouse	Martha Wayles
Children	MarthaJaneMaryLucyLucy Elizabeth
Alma mater	College of William and Mary
Profession	PlanterLawyerTeacher
Religion	''See article''
Signature	Thomas Jefferson Signature.svg }}

Thomas Jefferson (April 13, 1743 – July 4, 1826) was the principal author of the Declaration of Independence (1776) and the third President of the United States (1801–1809). He was an influential Founding Father, and an exponent of Jeffersonian democracy. Jefferson envisioned America as a great "Empire of Liberty" that would promote republicanism.

At the beginning of the American Revolution, Jefferson served in the Continental Congress, representing Virginia. He then served as the wartime Governor of Virginia (1779–1781), barely escaping capture by the British in 1781. Just after the war ended, from mid-1784 Jefferson served as a diplomat, stationed in Paris, initially as a commissioner to help negotiate commercial treaties. In May 1785, he became the United States Minister to France. He was the first United States Secretary of State (1790–1793). During the administration of President George Washington, Jefferson advised against a national bank and the Jay Treaty. Upon leaving office, with his close friend James Madison he organized the Democratic-Republican Party to oppose Treasury Secretary Alexander Hamilton's policies, especially his desire to create a national bank. He and Madison secretly wrote the Kentucky and Virginia Resolutions, which attempted to nullify the Alien and Sedition Acts and formed the basis of States' rights.

Elected president in what he called the Revolution of 1800, he oversaw a peaceful transition in power, purchased the vast Louisiana Territory from France (1803), and sent the Lewis and Clark Expedition (1804–1806) to explore the new west. He decided to allow slavery in the acquired territory, which laid the foundation for the crisis of the Union a half century later. His second term was beset with troubles at home, such as the failed treason trial of his former Vice President Aaron Burr, and escalating trouble with Britain. Jefferson always distrusted Britain as a threat to American values. With Britain at war with Napoleon, he tried aggressive economic warfare, however his embargo laws stopped American trade, hurt the economy, and provoked a furious reaction in the Northeast.

Jefferson was part of the Virginia planter elite. He was a loving husband to his wife Martha, who died in childbirth, and an affectionate father to their children. As a tobacco planter, Jefferson owned hundreds of slaves throughout his life; he held views on the racial inferiority of Africans common at the time. Most historians believe that after his wife died, Jefferson had an intimate relationship for nearly four decades with Martha's half-sister, his mixed-race slave Sally Hemings; and fathered her six children. He freed the four surviving Hemings children when they came of age.

A leader in The Enlightenment, Jefferson was a polymath who spoke five languages and was deeply interested in science and political philosophy. While not an orator he was an indefatigable letter writer and was acquainted with many influential people in America and Europe. His views on slavery were complex, and changed over the course of his life,. He was a leading American opponent of the international slave trade, and presided over its abolition in 1807. Jefferson is typically rated by historical scholars as one of the greatest U.S. presidents, though in recent decades scholars have tended to be more negative.

Early life and education

Family

The third of ten children, Thomas Jefferson was born on April 13, 1743) into the Randolph family that linked him to some of the most prominent individuals in Virginia. His mother was Jane Randolph, daughter of Isham Randolph of Dungeness, a ship's captain and sometime planter, first cousin to Peyton Randolph, and granddaughter of wealthy English and Scottish gentry. Jefferson's father was Peter Jefferson, a planter and major slaveholder, and a surveyor in Albemarle County (Shadwell, then Edge Hill, Virginia). He was of possible Welsh descent, although this remains unclear. When Colonel William Randolph, an old friend of Peter Jefferson, died in 1745, Peter assumed executorship and personal charge of William Randolph's estate in Tuckahoe as well as his infant son, Thomas Mann Randolph, Jr. That year the Jeffersons relocated to Tuckahoe, where they would remain for the next seven years before returning to their home in Albemarle in 1752. Peter Jefferson was appointed to the colonelcy of the county, an important position at the time. After he died in 1757, his son Thomas Jefferson inherited his estate, including about 50 slaves. They comprised the core of his labor force when he started to build Monticello as a young man.

When Thomas Jefferson was 22, his oldest sister Jane died at the age of 25 on October 1, 1765. He fell into a period of deep mourning, as he was already saddened by the absence of his sisters Mary, who had been married several years to Thomas Bolling, and Martha, who had wed in July to Dabney Carr. Both had moved to their husbands' residences. Only Jefferson's younger siblings Elizabeth, Lucy, and the two toddlers, were at home. He drew little comfort from the younger ones, as they did not provide him with the same intellectual stimulation as the older sisters had.

Education

In 1752, Jefferson began attending a local school run by a Scottish Presbyterian minister. At the age of nine, Jefferson began studying Latin, Greek, and French; he learned to ride horses, and began to appreciate the study of nature. He studied under the Reverend James Maury from 1758 to 1760 near Gordonsville, Virginia. While boarding with Maury's family, he studied history, science and the classics.

At age 16, Jefferson entered the College of William & Mary in Williamsburg, and first met the law professor George Wythe, who became his influential mentor. For two years he studied mathematics, metaphysics, and philosophy under Professor William Small, who introduced the enthusiastic Jefferson to the writings of the British Empiricists, including John Locke, Francis Bacon, and Isaac Newton. He also improved his French, Greek, and violin. A diligent student, Jefferson displayed an avid curiosity in all fields and graduated in 1762 with highest honors. Jefferson read law while working as a law clerk for Wythe. During this time, he also read a wide variety of English classics and political works. Jefferson was admitted to the Virginia bar five years later in 1767.

Throughout his life, books played a vital role in Jefferson's education. Even during the American Revolution and while minister to France, Jefferson collected and accumulated thousands of books for his library at Monticello. A significant portion of Jefferson's library was also bequeathed to him in the will of George Wythe who himself had an extensive library. Always eager for more knowledge, Jefferson's education would continue throughout most of his life. Jefferson once stated, "I cannot live without books." By 1815, his library included 6,487 books, which he then sold to the Library of Congress to replace the collection destroyed in the War of 1812.

Career

Jefferson handled many cases as a lawyer in colonial Virginia, and was very active from 1768 to 1773. Jefferson's client list included members of the Virginia's elite families, including members of his mother's family, the Randolphs.

In 1768 Thomas Jefferson started the construction of Monticello, a neoclassical mansion. Since childhood, Jefferson had always wanted to build a beautiful mountaintop home within sight of Shadwell. Jefferson fell greatly in debt by spending lavishly over the years on Monticello in what was a continuing project to create a neoclassical environment, based on his study of the architect Andrea Palladio and the classical orders.

Besides practicing law, Jefferson represented Albemarle County in the Virginia House of Burgesses beginning on May 11, 1769 and ending June 20, 1775. Wythe also served at the same time. Following the passage of the Coercive Acts by the British Parliament in 1774, he wrote a set of resolutions against the acts, which were expanded into ''A Summary View of the Rights of British America'', his first published work. Previous criticism of the Coercive Acts had focused on legal and constitutional issues, but Jefferson offered the radical notion that the colonists had the natural right to govern themselves. Jefferson also argued that Parliament was the legislature of Great Britain only, and had no legislative authority in the colonies. The paper was intended to serve as instructions for the Virginia delegation of the First Continental Congress, but Jefferson's ideas proved to be too radical for that body.

Marriage and family

In 1772, at age 28 Jefferson married the 23-year-old widow Martha Wayles Skelton. They had six children, only two of whom survived to adulthood. Only their oldest daughter Martha lived beyond age 25.

# Martha Washington Jefferson (1772–1836), who married Thomas Mann Randolph, Jr., future governor of Virginia. They had twelve children, eleven of whom survived to adulthood. # Jane Jefferson (1774–1775) # stillborn or unnamed son (1777) # Mary Wayles Jefferson (1778–1804), called Polly, married her cousin John Wayles Eppes, son of Martha's sister, Elizabeth Wayles Eppes. Mary died at age 25 after the birth of her third child; only their son Francis W. Eppes survived to adulthood. Jefferson made his grandson Francis Eppes the designated heir of Poplar Forest, originally intended for Mary. In 1829 Francis Eppes moved to Florida, where he had a cotton plantation until the Civil War. # Lucy Elizabeth Jefferson (1780–1781) # Lucy Elizabeth Jefferson (1782–1785); it was customary to name subsequent children after one who had died, particularly when the family was also trying to pass down family names. The second Lucy died while Jefferson was in Paris, prompting him to have his youngest living daughter Polly sent to him; she was then age nine.

Mrs. Jefferson died on September 6, 1782, a few months after the birth of her last child. He was at his wife's bedside when she died. Jefferson was deeply upset after her death, and often rode on secluded roads to mourn for his wife.

Jefferson never remarried, as he had promised his wife. However, historians believe that while he was in Paris as the US minister, he began a relationship about 1789 with his young mixed-race slave Sally Hemings, who had accompanied his youngest daughter there. She became pregnant and according to her son's memoir, agreed to return to the US with Jefferson if he would free her children. The first child died soon after their return. He fathered five more children with her, four of whom survived to adulthood.

Jefferson never responded to reports or rumors about his relationship with her; his daughter and oldest grandson Thomas Jefferson Randolph denied it. In fact Randolph noted the Hemings' children's strong resemblance to his grandfather, but he told the historian Henry Randall that Jefferson's nephew Peter Carr was the father. Based on this family testimony and Jefferson's discretion, his descendants and various historians denied Jefferson's paternity for nearly 200 years.

The matter was eventually settled (to the satisfaction of most historians) when a 1998 DNA study showed a match between the Jefferson male line and Eston Hemings' descendants and additional research was done. The Thomas Jefferson Foundation (TJF), which runs Monticello, conducted an independent historic review in 2000, as did the National Genealogical Society; both were among those who concluded that Jefferson was likely the father. As the Monticello Website says:

"Through his celebrity as the eloquent spokesman for liberty and equality as well as the ancestor of people living on both sides of the color line, Jefferson has left a unique legacy for descendants of Monticello's enslaved people as well as for all Americans."

In the antebellum period, the Hemingses would have been called a "shadow family". Hemings was three-fourths white and a half-sister to Jefferson's late wife, as her father was also John Wayles. Wayles had six children by his 12-year liaison with his slave Betty Hemings; the youngest was Sally. As the historians Philip D. Morgan and Joshua D. Rothman have written, there were numerous interracial relationships in the Wayles-Hemings-Jefferson families, Albemarle County and Virginia, often with multiple generations repeating the pattern.

Hemings' children were seven-eighths European in ancestry and legally white according to Virginia law of the time. (The "one-drop rule" did not become law until 1924.) Four survived to adulthood:

William Beverley,

Harriet Hemings,

Madison Hemings and

Thomas Eston Hemings.

All but Madison eventually identified as white and lived as adults in white communities. Jefferson freed them as they came of age, the first two informally by letting them "escape," and the last two in his will.

Political career from 1775 to 1800

Drafting a declaration

Jefferson served as a delegate to the Second Continental Congress beginning in June 1775, soon after the outbreak of the American Revolutionary War. He didn't know many people in the congress, but sought out John Adams, who along with his cousin Samuel had emerged as leaders of the convention. Jefferson and Adams there established a friendship that would last the rest of their lives, and was the direct cause of Jefferson's role in drafting the declaration. When Congress began considering a resolution of independence in June 1776, Adams saw to it that Jefferson was appointed to the five-man committee that was to prepare a declaration to accompany the resolution. The committee, after discussing the general outline that the document should follow, decided that Jefferson would write the first draft. The committee in general, and Jefferson in particular, thought Adams should write the document. Adams persuaded the committee to choose Jefferson, who was not thrilled with the assignment, and promised to consult with Jefferson personally. Jefferson had limited time for writing over the next seventeen days, and wrote the draft quickly. Jefferson completed a draft in consultation with other committee members, drawing on his own proposed draft of the Virginia Constitution, George Mason's draft of the Virginia Declaration of Rights, and other sources. The other committee members made various changes, most notably Jefferson had written, "We hold these truths to be sacred and un-deniable..." Franklin changed it to, "We hold these truths to be self-evident." A final draft incorporating these alterations was presented to the Congress on June 28, 1776. The title of the document was "A Declaration by the Representatives of the United States of America, in General Congress assembled."

After voting in favor of the resolution of independence on July 2, Congress turned its attention to the declaration. Over three days of fiery debate, Congress made changes in wording and deleted nearly a fourth of the text, most notably a passage critical of the slave trade, all changes that Jefferson resented. During the three day debate Jefferson spoke not a word for or against any of the revisions. On July 4, 1776, the wording of the Declaration of Independence was ratified. Before the signing a prayer was said and in silence the delegates to the convention applied their signature to the document. The Declaration would eventually become Jefferson's major claim to fame, and his eloquent preamble became an enduring statement of human rights. Jefferson remained at the convention for several more months, though the rest of his time in Philadelphia was uneventful.

State legislator

In September 1776, Jefferson returned to Virginia and was elected to the new Virginia House of Delegates for Albemarle County. He served there from September 26, 1776 – June 1, 1779. During his term in the House, Jefferson set out to reform and update Virginia's system of laws to reflect its new status as a democratic state. He drafted 126 bills in three years, including laws to abolish primogeniture, establish freedom of religion, and streamline the judicial system. In 1778, Jefferson's "Bill for the More General Diffusion of Knowledge" and subsequent efforts to reduce clerical control led to some small changes at William and Mary College. While in the state legislature Jefferson proposed a bill to eliminate capital punishment in Virginia for all crimes except murder and treason. His effort to end the death penalty law was defeated.

Governor of Virginia

In 1779, at the age of thirty-six, Jefferson was elected Governor of Virginia and served from 1779–1781. At this time the now united colonies were in the middle of the American Revolutionary War with Britain. Georgia had fallen helpless into the hands of the British, South Carolina was invaded, and Charleston threatened. In his capacity as Governor Jefferson made efforts to prepare Richmond for attack by moving all arms, military supplies and records from Richmond to a foundry located five miles outside of town. General Benedict Arnold, who had switched to the British side in 1780, learned of this transfer and moved to capture the foundry. Jefferson then attempted to devise a way to move the supplies to Westham, seven miles to the north, but he was too late. Arnold's troops burned the foundry before returning to Richmond, where they burned much of the city the following morning. Jefferson at later points in his political career was criticized, especially by his political opponents, for failing to defend Richmond during this time.

In January of 1781, Benedict Arnold led an armada of British ships and with 1600 British regulars conducted raids along the James River. Later he would join Lord Cornwallis, whose troops were marching across Virginia from the south. In advance, Cornwallis dispatched a cavalry force commanded by Banastre Tarleton on a secret expedition to Monticello to capture then Governor Jefferson. Quickly making his way at night, Tarleton hoped to catch Jefferson by surprise, however in the midst of the activity and havoc of the invasion an action by a young Virginian named Jack Jouett, a captain in the Virginia militia, thwarted the British capture of Virginia's governor. Jouett had spotted the assembly and departure of Tarleton and his men and making his way to Monticello, by way of various back roads of which he was familiar, arrived at Monticello in time to warn Jefferson, members of the Virginia Assembly and citizens at large. With little warning Jefferson and his family fled and managed to escape, leaving his home to be captured by British troops. A detachment of Cornwallis' troops, in their march north from the Carolinas, seized the estate along with another plantation which Jefferson owned on the James River. British troops destroyed all his crops, burnt his barns and fences, drove off the cattle, seized all usable horses, cut the throats of the colts, and after setting fires left the plantation a smoldering, blackened waste. Twenty-seven slaves were also captured to which Jefferson later replied.. "Had he carried off the slaves to give them freedom, he would have done right."

As governor in 1780, he transferred the state capital from Williamsburg to Richmond. He continued to advocate educational reforms at the College of William and Mary, including the nation's first student-policed honor code. In 1779, at Jefferson's behest, William and Mary appointed George Wythe to be the first professor of law in an American university. Many people disliked his tenure, and he did not win office again in Virginia. However, in 1783 he was appointed to Congress by the state legislature.

Notes on the State of Virginia

In the Fall of 1780, Gov. Thomas Jefferson was given a list of 22 questions, by Secretary of the French legation to the United States François Marbois, intended to gather pertinent information on the American colonies. Jefferson's responses to Marbois' "Queries" would become known as ''Notes on the State of Virginia''. Jefferson, scientifically trained, was a member of the American Philosophical Society and had extensive knowledge of western lands from Virginia to Illinois. In a course of 5 years, Jefferson enthusiastically devoted his intellectual energy to the book, which discussed contemporary scientific knowledge, and Virginia's history, politics, and ethnography. Jefferson was aided by Thomas Walker, George R. Clark, and U.S. geographer Thomas Hutchins. The book was first published in France in 1785 and in England in 1787.

Member of Congress

Virginia appointed Jefferson to its delegation to the Congress of the Confederation in 1783. As a member of the committee formed to set foreign exchange rates, he recommended that American currency should be based on the decimal system; his plan was adopted. Jefferson also recommended setting up the Committee of the States, to function as the executive arm of Congress. The plan was adopted but failed in practice. He resigned from Congress when he was appointed minister to France in May 1784.

Minister to France

Jefferson was minister to France from 1785 to 1789, a peaceful time in Europe. When the French Foreign minister Count de Vergennes commented to Jefferson, "You replace Monsieur Franklin I hear", Jefferson replied, "I ''succeed'' him, no man can ''replace'' him.

He enjoyed the architecture, arts, and the salon culture of Paris. He often dined with many of the city's most prominent people, but sided with the revolutionaries in 1789 French Revolution. While in Paris, Jefferson corresponded with a number of individuals who had important roles in events leading up to the French Revolution. These included marquis de Lafayette and comte de Mirabeau, a popular pamphleteer who repeated ideals that had been the basis for the American Revolution.

Jefferson brought some of his slaves to serve the household, including James Hemings for training as a French chef. After his youngest daughter died, he requested that a young woman slave accompany his daughter Polly to France. Sally Hemings was chosen to travel with Polly, and lived with the Jefferson household for about two years in Paris. The historian Annette Gordon-Reed suggests that Jefferson began his long-term relationship with Hemings while in Paris; as was recounted by their son Madison Hemings in his 1873 memoir. There are no direct written accounts from Sally Hemings.

Secretary of State

In September of 1789 Jefferson returned to America from France with his daughter. Immediately upon his return President Washington wrote to him urging him to accept a seat in his Cabinet as Secretary of State. After a brief conference Jefferson accepted the appointment.

As George Washington's Secretary of State, (1790–1793) Jefferson and Alexander Hamilton argued over national fiscal policy, especially the funding of the debts of the war. Jefferson later compared Hamilton and the Federalists with "Royalism", and stated the "Hamiltonians were panting after...crowns, coronets and mitres." Due to their opposition to Hamilton, Jefferson and James Madison founded and led the Democratic-Republican Party. He worked with Madison and his campaign manager John J. Beckley to build a nationwide network of Republican allies. Jefferson's political actions, and his attempt to undermine Hamilton, nearly led George Washington to dismiss Jefferson from his cabinet. Though Jefferson left the cabinet voluntarily, Washington never forgave him, and never spoke to him again.

The French minister said in 1793: "Senator Morris and Secretary of the Treasury Hamilton...had the greatest influence over the President's mind, and that it was only with difficulty that he [Jefferson] counterbalanced their efforts." Jefferson supported France against Britain when they fought in 1793. Jefferson believed that political success at home depended on the success of the French army in Europe. The French minister in 1793, Edmond-Charles Genêt, caused a crisis when he tried to influence public opinion in appealing to the people, something Jefferson tried to stop.

Break from office

Jefferson retired to Monticello in late 1793 where he continued to oppose the policies of Hamilton and Washington. However, the Jay Treaty of 1794, led by Hamilton, brought peace and trade with Britain while Madison, with strong support from Jefferson, wanted, "to strangle the former mother country" without going to war. "It became an article of faith among Republicans that 'commercial weapons' would suffice to bring Great Britain to any terms the United States chose to dictate."

Even during the violence of the Reign of Terror, Jefferson refused to disavow the revolution because "To back away from France would be to undermine the cause of republicanism in America."

Election of 1796 and Vice Presidency

As the Democratic-Republican candidate in 1796 he lost to John Adams, but had enough electoral votes to become Vice President (1797–1801). As one of the chief duties of a Vice president is presiding over the Senate, Jefferson was concerned about the lack of rules governing this body, often leaving matters to the discretion of the presiding officer. Jefferson once wrote: ''"It is now so long since I have acted in the legislative line that I am entirely rusty in the Parliamentary rules of procedure.”'' Jefferson spent much of his time researching procedures and rules for governing bodies years before taking office. As a student he had transcribed notes on British parliamentary law into a manual he would later refer to as his ''Parliamentary Pocket Book''. Jefferson had also served on the committee appointed to draw up the rules of order for the Continental Congress in 1776. As Vice President he was more than qualified to bring reform to Senatorial procedural matters, and now prompted by the immediate need for such rules of order he would write his 'A Manual of Parliamentary Practice.' a document which the House of Representatives follow to the present day.

With the Quasi-War underway, the Federalists under John Adams started rebuilding the military, levied new taxes, and enacted the Alien and Sedition Acts. Jefferson believed that the Alien and Sedition Acts were an effort to suppress Democratic-Republicans rather than dangerous enemy aliens, although the acts later expired. Jefferson and Madison rallied support by anonymously writing the Kentucky and Virginia Resolutions, which declared that the federal government had no right to exercise powers not specifically delegated to it by the states. Though the resolutions followed the "interposition" approach of James Madison, Jefferson advocated nullification and at one point drafted a threat for Kentucky to secede. Jefferson's biographer Dumas Malone argued that this might have gotten Jefferson impeached for treason, had his actions become known at the time. In writing the Kentucky Resolutions, Jefferson warned that, "unless arrested at the threshold," the Alien and Sedition Acts would "necessarily drive these states into revolution and blood." Historian Ron Chernow says of this "he wasn't calling for peaceful protests or civil disobedience: he was calling for outright rebellion, if needed, against the federal government of which he was vice president." Jefferson "thus set forth a radical doctrine of states' rights that effectively undermined the constitution." Chernow argues that neither Jefferson nor Madison sensed that they had sponsored measures as inimical as the Alien and Sedition Acts themselves. Historian Garry Wills argued "Their nullification effort, if others had picked it up, would have been a greater threat to freedom than the misguided [alien and sedition] laws, which were soon rendered feckless by ridicule and electoral pressure" The theoretical damage of the Kentucky and Virginia resolutions was "deep and lasting, and was a recipe for disunion". George Washington was so appalled by them that he told Patrick Henry that if "systematically and pertinaciously pursued", they would "dissolve the union or produce coercion". The influence of Jefferson's doctrine of states' rights reverberated right up to the Civil War and beyond. Future president James Garfield, at the close of the Civil War, said that Jefferson's Kentucky Resolution "contained the germ of nullification and secession, and we are today reaping the fruits".

According to historian Ron Chernow, during the Quasi-War Jefferson engaged in a "secret campaign to sabotage Adams in French eyes". He held four confidential talks with French consul Joseph Letombe in the spring of 1797. In his private meetings with Letombe, Jefferson attacked Adams, predicted that he would only serve one term and encouraged France to invade England. Jefferson also advised Letombe to stall any American envoys sent to Paris by instructing them to "listen to them and then drag out the negotiations at length and mollify them by the urbanity of the proceedings." This toughened the tone that the French government adopted with the new Adams Administration. Due to pressure against the Adams Administration on behalf of the French government from Jefferson and his supporters, congress released the papers in connection with the XYZ Affair, which rallied support from Jefferson and the French government to Adams.

Election of 1800

Working closely with Aaron Burr of New York, Jefferson rallied his party, attacking the new taxes especially, and ran for the Presidency in 1800. Before the passage of the Twelfth Amendment, a problem with the new union's electoral system arose.

Hamilton convinced his party that Jefferson would be a lesser political evil than Burr and that such scandal within the electoral process would undermine the new constitution. On February 17, 1801, after thirty-six ballots, the House elected Jefferson President and Burr Vice President.

Jefferson owed his election victory to the South's inflated number of Electors, which counted slaves under the three-fifths compromise. After his election in 1800, some called him the "Negro President", with critics like the ''Mercury and New-England Palladium of Boston'' stating that Jefferson had the gall to celebrate his election as a victory for democracy when he won "the temple of Liberty on the shoulders of slaves."

Presidency 1801–1809

Thomas Jefferson took the oath of office on March 4, 1801, at a time when partisan strife between the Democratic-Republican and Federalist parties was growing to alarming proportions. Regarded by his supporters as the 'People's President' news of Jefferson's election was well received in many parts of the new country and was marked by celebrations throughout the Union. He was sworn in by Chief Justice John Marshall at the new Capitol in Washington DC. In contrast to the preceding president John Adams, Jefferson exhibited a dislike of formal etiquette. Unlike Washington, who arrived at his inauguration in a stagecoach drawn by six cream colored horses, Jefferson arrived alone on horseback without guard or escort. He was dressed plainly and after dismounting, retired his own horse himself.

As a result of his two predecessors, as well as the state of events in Europe, Jefferson inherited the presidency with relatively few urgent problems. Though he and his supporters initially wanted to dismantle several of the accomplishments of his two predecessors, notably the national bank, military, and federal taxation system, his treasury secretary persuaded him not to. In his second term, Jefferson's popularity suffered because the problems he faced, most notably those caused by the wars in Europe, became more difficult to solve. With the Battle of Austerlitz in 1805, Napoleon became more aggressive than ever; most of Jefferson's attempts to negotiate with him were unsuccessful during his second term. Jefferson's presidency is remembered for four major events. First came the purchase of the Louisiana territory from France in 1803, which doubled the size of the United States. A second accomplishment was the defeat of Mediterranean Sea pirates in the First Barbary War. The third occurred during Jefferson's second term, when he proposed legislation (approved by Congress) outlawing the importation of African slaves, as of the earliest date permitted by the U.S. Constitution. The fourth was the Embargo Act of 1807. Due to political attacks against him, in particular those by Alexander Hamilton and his supporters, he used the Alien and Sedition Acts to counter some of these political adversaries. His second term was more troubled than his first term, in part due to growing aggression on the part of Napoleon. Disliking the Jay Treaty, Jefferson instead passed the Embargo Act of 1807 which caused widespread economic problems while not accomplishing its goals, thus hurting his popularity.

Administration, Cabinet and Supreme Court appointments

{{infobox u.s. cabinet |align	left |clearyes |NameJefferson
President	Thomas Jefferson |President start1801 |President end1809
Vice president	Aaron Burr |Vice President start1801 |Vice President end1805
Vice president 2	George Clinton |Vice President start 21805 |Vice President end 21809
State	James Madison |State start1801 |State end1809
Treasury	Samuel Dexter |Treasury date1801
Treasury 2	Albert Gallatin |Treasury start 21801 |Treasury end 21809
War	Henry Dearborn |War start1801 |War end1809
Justice	Levi Lincoln, Sr. |Justice start1801 |Justice end1804
Justice 2	John Breckinridge |Justice start 21805 |Justice end 21806
Justice 3	Caesar A. Rodney |Justice start 31807 |Justice end 31809
Navy	Benjamin Stoddert |Navy date1801
Navy 2	Robert Smith |Navy start 21801 |Navy end 21809 }}

Associate Justice

William Johnson – 1804

Henry Brockholst Livingston – 1807

Thomas Todd – 1807

States admitted to the Union:

Ohio – March 1, 1803

First Barbary War

When Jefferson became president in 1801, the United States was at the time paying $80,000 to the Barbary states as a 'tribute' for protection against North African piracy. For decades, the pirates had been capturing American ships and crew members and demanding huge ransoms for their release. Before Independence, from 1775 until 1783, American merchant ships were protected from the Barbary pirates by the naval and diplomatic influence of Great Britain. When the American Revolution began, American ships were protected by the 1778 alliance with France, which required the French nation to protect "American vessels and effects against all violence, insults, attacks ...". On December 20, 1777, Morocco's Sultan Mohammed III declared that the American merchant ships would be under the protection of the sultanate and could thus enjoy safe passage into the Mediterranean and along the coast. The Moroccan-American Treaty of Friendship stands as the U.S.'s oldest non-broken friendship treaty. The one with Morocco has been the longest-lasting treaty with a foreign power.

After the United States gained independence, it had to protect its own merchant vessels. It also had to pay $80,000 as tribute to the Barbary states, as did Britain and France at this time. When Tripoli made new demands on the new President for a prompt payment of $225,000 and an annual payment of $25,000, Jefferson refused and decided it would be easier to fight the pirates than to continue to pay bribes. On May 10, 1801, the pasha of Tripoli declared war on the United States and the First Barbary War began. As secretary of state and vice president, Jefferson had opposed funds for a Navy to be used for anything more than a coastal defense, however the continued pirate attacks on American shipping interests in the Atlantic and Mediterranean and the systematic kidnapping of American crew members could no longer be ignored. President Jefferson ordered a fleet of naval vessels to various points in the Mediterranean. He forced Tunis and Algiers into breaking their alliance with Tripoli which ultimately forced it out of the fight. Jefferson also ordered five separate naval bombardments of Tripoli, which restored peace in the Mediterranean for a while.

Louisiana Purchase

In 1803 the United States under Jefferson bought the Louisiana Territory from France, doubling the size of the United States. As the exact boundaries of the territory were unsettled, England and Spain continued to make claims to parts of the territory until the time of president James Polk. Most of France's wealth in the New World came from their plantations in Caribbean. When France lost control of these countries a couple of years earlier, the Louisiana territory ceased to be of any value to France, who at the time was escalating its war against the rest of Europe. Jefferson sent James Monroe and Robert R. Livingston to Paris in 1802 to purchase the city of New Orleans and adjacent coastal areas. At the request of Jefferson, a French noblemen named Pierre Samuel du Pont de Nemours, having close ties with both Jefferson and Napoleon, also helped negotiate the purchase with France. Napoleon offered to sell the entire territory for a price of $15 million, which Treasury Secretary Albert Gallatin financed easily. Jefferson acted contrary to his usual requirement of explicit Constitutional authority and the Federalists criticized him for acting without that authority, but most thought that this opportunity could not be missed. On December 20, 1803 the French flag was lowered in New Orleans and the U.S. flag raised, symbolizing the transfer of the Louisiana territory from France to the United States.

Politically, the Louisiana Purchase would prove to be one of the most consequential executive decisions in American history, although it wouldn't be finally secured until England and Mexico gave up their claims to it during the presidency of James Polk. Without realizing it at the time Jefferson had purchased one of the largest fertile tracts of land on the planet. The purchase also changed the new nation's national security strategy by removing French imperial ambitions in America. Opinions vary among historians as to who was the principal player in the purchase, some believing it was Napoleon, while others give credit to Jefferson, his secretary of state James Madison, and his negotiator James Monroe. Others agree with Alexander Hamilton, Jefferson's arch rival, and attribute it to "dumb luck". Still others concur that it was all of these things. Historian George Herring has said that while this was somewhat the result of Jefferson and Madison's "shrewd and sometimes belligerent diplomacy", that it "is often and rightly regarded as a diplomatic windfall-the result of accident, luck, and the whim of Napoleon Bonaparte".

Lewis and Clark Expedition

Jefferson had an avid interest in the sciences and had long entertained ideas of exploring the American frontier before Louisiana was purchased from France. As such Jefferson was a member of the American Philosophical Society, founded in Philadelphia in 1743 by Benjamin Franklin, and served as its President from 1797 to 1815. By the turn of the 19th century, the society was well established and staffed, and equipped for research. Jefferson made use of its resources by sending Meriwether Lewis to Philadelphia in 1803 for instruction at the Society in botany, mathematics, surveying, astronomy, chemistry and map making, among other subjects. On January 18, 1803, Jefferson sent a confidential letter to Congress asking for $2,500 to fund an expedition through the West; on February 28, 1803, Congress appropriated the necessary funds.

In 1804 Jefferson appointed Meriwether Lewis and William Clark as leaders of the expedition (1804–1806), which explored the Louisiana Territory and beyond, producing a wealth of scientific and geographical knowledge, and ultimately contributing to the European-American settlement of the West. Knowledge of the western part of the continent had been scant and incomplete, limited to what had been learned from trappers, traders, and explorers. This was the first official American military expedition to the Pacific Coast. Lewis and Clark, for whom the expedition became known, recruited the 45 men to accompany them, and spent a winter training them for the effort.

The expedition had several goals, including finding a "direct & practicable water communication across this continent, for the purposes of commerce" (the long-sought Northwest Passage). They were to follow and map the rivers, and collect scientific data. Jefferson wanted to establish a US claim of "discovery" of the Pacific Northwest by mapping and documenting a United States presence there before Europeans could get a chance to claim the land. The expedition reached the Pacific Ocean by November 1805. With its return in 1806, it had fulfilled Jefferson's hopes by amassing much new data about the topographical features of the county and its natural resources, with details on the flora and fauna, as well as the many Indian tribes of the West with which he hoped to increase trading.

Jefferson also commissioned the Pike Expedition to explore the central region of the Louisiana Purchase, and the Red River Expedition, which was less successful.

West Point

Ideas for a national institution for military education were founded during the American Revolution, but it wasn't until 1802 when Jefferson, following the advice of George Washington, John Adams and others, finally convinced Congress to authorize the funding and building of the United States Military Academy at West Point on the Hudson River in New York. On March 16, 1802, Jefferson signed the Military Peace Establishment Act, directing that a corps of engineers be established and "stationed at West Point in the state of New York, and shall constitute a Military Academy." The Act would provide well-trained officers for a professional army. The officers would be reliable republicans rather than a closed elite as in Europe, for the cadets were to be appointed by Congressmen, and thus exactly reflect the nation's politics. In May 1801 Secretary of War Henry Dearborn announced that the president had "decided in favor of the immediate establishment of a military school at West Point and also on the appointment of Major Jonathan Williams", grandnephew of Benjamin Franklin, to direct "the necessary arrangements, at that place for the commencement of the school." On July 4, 1802, the US Military Academy at West Point formally commenced its role as an institution for scientific and military learning.

In 1807, the United States Congress, acting on Jefferson's request, passed the Act Prohibiting Importation of Slaves. Jefferson signed the act and it went into effect January 1, 1808, the earliest date permitted by the United States Constitution for any law regulating slavery. The act made international import and export of slaves a crime with severe punishments; it did not apply to the internal slave trade.

Embargo

The Embargo Act was passed in 1807 to maintain American neutrality in the Napoleonic Wars. Jefferson hoped to avoid national humiliation on the one hand, and war on the other. In the event he got both war and national humiliation; the economy of the entire Northeast suffered severely, the president was vehemently denounced,, and his party lost support. Instead of retreating Jefferson sent federal agents to secretly track down smugglers and violators.

The embargo was a financial disaster because the Americans could not export, while widespread disregard of the law meant enforcement was difficult. For the most part it effectively throttled American overseas trade. All areas of the United States suffered. In commercial New England and the Middle Atlantic states, ships rotted at the wharves, and in the agricultural areas, particularly in the South, farmers and planters could not dispose of their crops. Jefferson's Secretary of the Treasury Albert Gallatin was against the entire embargo, foreseeing correctly the impossibility of enforcing the policy and the negative public reaction. "As to the hope that it may...induce England to treat us better," wrote Gallatin to Jefferson shortly after the bill had become law, "I think is entirely groundless...government prohibitions do always more mischief than had been calculated; and it is not without much hesitation that a statesman should hazard to regulate the concerns of individuals as if he could do it better than themselves."

Jefferson placed himself in a strange position with his embargo policy. Though he had so frequently argued for as small a federal government as possible, he now found the national government assuming extraordinary police powers in an attempt to enforce his policy. The presidential election of 1808, which James Madison won, showed that the Federalists were regaining strength, and helped to convince Congress that the Embargo would have to be repealed. Shortly before leaving office, in March 1809, Jefferson signed the repeal of the disastrous Embargo. In its place the Nonintercourse Act was enacted which proved no more effective than the Embargo, and it proved impossible to prevent American vessels from trading with the European belligerents once they had left American ports. Jefferson increasingly believed the problem was the greedy traders and merchants who lacked republican virtue by not complying.

Historians have generally given Jefferson poor marks on his embargo policy. Cogliano (2008) notes that the failure of the Embargo "reinforced the view that Jefferson had been lucky rather than adroit during the earlier negotiations." Doron Ben Atar (1993) argued that Jefferson's commercial and foreign policies were misguided, ineffective and harmful to American interests. Kaplan (1957) argued that the War of 1812 was the logical extension of his embargo, and that by entering the Napoleonic Wars on anti-British side, the United States deprived itself of the advantages of neutrality. Kaplan adds, "The results were a personal disaster for Jefferson and general malaise and confusion for the nation."Bradford Perkins (1980) concluded Jefferson was on this issue, "a wavering, miscalculating, and self-deluding man."

Other involvements

He obtained the repeal of some federal taxes in his bid to rely more on customs revenue. He pardoned several people imprisoned under the Alien and Sedition Acts, passed in John Adams' term. He repealed the Judiciary Act of 1801 and removed nearly all of Adams' "midnight judges" from office, which led to the Supreme Court deciding the important case of ''Marbury v. Madison''. He also signed into law a bill that officially segregated the US postal system by not allowing blacks to carry mail.

Father of a university

After leaving the Presidency, Jefferson continued to be active in public affairs. He wanted to found a new institution of higher learning, specifically one free of church influences, where students could specialize in many new areas not offered at other universities. Jefferson believed educating people was a good way to establish an organized society. He believed such schools should be paid for by the general public, so less wealthy people could be educated as students. A letter to Joseph Priestley, in January 1800, indicated that he had been planning the University for decades before its founding.

In 1819 he founded the University of Virginia. Upon its opening in 1825, it was the first university to offer a full slate of elective courses to its students. One of the largest construction projects to that time in North America, the university was notable for being centered about a library rather than a church. No campus chapel was included in Jefferson's original plans. Until his death, Jefferson invited students and faculty of the college to his home.

Jefferson is widely recognized for his planning of the University grounds. Its innovative design was an expression of his aspirations for both state-sponsored education and an agrarian democracy in the new Republic. His educational idea of creating specialized units of learning is expressed in the configuration of his campus plan, which he called the "Academical Village". Individual academic units were defined as distinct structures, represented by Pavilions, facing a grassy quadrangle. Each Pavilion housed classroom, faculty office, and residences. Though distinctive, each is visually equal in importance, and they are linked with a series of open-air arcades that are the front facades of student accommodations. Gardens and vegetable plots are placed behind and surrounded by serpentine walls, affirming the importance of the agrarian lifestyle.

His highly ordered site plan establishes an ensemble of buildings surrounding a central rectangular quadrangle, named The Lawn, which is lined on either side with the academic teaching units and their linking arcades. The quad is enclosed at one end with the library, the repository of knowledge, at the head of the table. The remaining side opposite the library remained open-ended for future growth. The lawn rises gradually as a series of stepped terraces, each a few feet higher than the last, rising up to the library set in the most prominent position at the top, while also suggesting that the Academical Village facilitates easier movement to the future.

Stylistically, Jefferson was a proponent of the Greek and Roman styles, which he believed to be most representative of American democracy by historical association. Each academic unit is designed with a two story temple front facing the quadrangle, while the library is modeled on the Roman Pantheon. The ensemble of buildings surrounding the quad is an unmistakable architectural statement of the importance of secular public education, while the exclusion of religious structures reinforces the principle of separation of church and state. The campus planning and architectural treatment remains today as a paradigm of building of structures to express intellectual ideas and aspirations. A survey of members of the American Institute of Architects identified Jefferson's campus as the most significant work of architecture in America.

The University was designed as the capstone of the educational system of Virginia. In his vision, any citizen of the state could attend school with the sole criterion being ability.

Slavery

Biographers such as Dumas Malone and Merrill Peterson have portrayed Jefferson as anti-slavery in that he hated slavery, opposed it as an institution, tried to end it in the territories, and successfully criminalized the international slave trade in 1807. However, historians such as David Brion Davis and Paul Finkelman, have noted his failure to free slaves he owned, even at his death. His views, like most of his contemporaries, changed over time. Earlier in his life he opposed slavery as an institution and said he wanted it to end, though later he became a stronger defender of the institution, and increasingly articulated defenses for the institution predicated on his views of racial inferiority. Regardless, he depended on enslaved labor to support his household and his plantations. His first public attack on slavery came in 1774; when he was chosen in 1776 to draft the Declaration of Independence, his opposition to slavery was well known. Junius P. Rodriguez says, "All aspects of Jefferson's public career suggest an opposition to slavery." Peter Onuf points to "his well-known opposition to slavery, most famously expressed in... his ''Notes on the state of Virginia'' (1785). Jefferson called slavery an "abominable crime," and a "moral depravity". David Brion Davis said that by 1784 Jefferson was "one of the first statesman in any part of the world to advocate concrete measures for restricting and eradicating Negro slavery." But Davis also noted that after the planter returned to the US from France in 1789, "the most remarkable thing about Jefferson's stand on slavery is his immense silence." Paul Finkelman noted Jefferson's lack of action after this date in terms of correcting or ending the institution. He said Jefferson's greatest failing was "his inability to join the best of his generation in fighting slavery and in his working instead to prevent any significant change in America's racial status quo."

In his first draft of the Declaration of Independence, Jefferson condemned the British crown for the slave trade. He also condemned the King for "inciting American Negroes to rise in arms against their masters", related to the Crown's promise of freedom for slaves who fought for the British in the Revolution. At the request of delegates from South Carolina and Georgia, this language was dropped from the Declaration.

From the mid-1770s, Jefferson advocated a plan of gradual emancipation, in Virginia, by which children of slaves would be freed. But he did not advance legislation for it while in the assembly. During the 1770s as a Virginia legislator, Jefferson also wrote bills to prevent free blacks from living in or moving into Virginia, and to punish interracial relations. Jefferson believed that free blacks should be deported and replaced with white settlers. He feared free blacks would encourage a rebellion by slaves against whites. He proposed policies to prepare slaves for freedom: education, emancipation, and transportation of the freedmen to Africa.

In 1778 Jefferson pushed a bill through the Virginia legislature—one of the first of its kind in modern history—to ban further importation of slaves into the state. Davis says that abolitionists assumed "that an end to slave imports would lead automatically to the amelioration and gradual abolition of slavery." Many slave owners opposed the international slave trade, while still supporting slavery. Ending the importation benefited slaveholders because it increased the value of slaves and decreased the chances of slave rebellion associated with new arrivals.

As a Virginia legislator, Jefferson failed to lead on gradual emancipation and discouraged efforts to include it in law. After he left the Assembly, in 1782 Virginia "easily adopted a law allowing private manumission." Maryland and Delaware passed similar laws as part of the post-Revolutionary War trend toward increased freedoms. In the two decades after the Revolution, in Virginia the number of free blacks climbed from less than one percent in 1782, to 4.2 percent in 1790, and 7.2 percent in 1810. In Delaware, three-quarters of blacks were free by 1810. In these two decades, numerous slaveholders were moved by ideals to free their slaves, either during their lives or by deed of will. In this period, Jefferson nominally freed only two slaves: he allowed Robert Hemings to purchase his freedom at market rates in 1794; and he freed his younger brother James Hemings in 1796, after requiring him to train his brother Peter for three years as a chef.

In 1784, Jefferson wrote an ordinance banning slavery in all the nation's territories (not just the Northwest), but it failed by one vote. While he was in France as US minister, the US Congress adopted a version that banned slavery in the Northwest Territory (north of the Ohio River). He was a leader in abolishing the international slave trade, both for Virginia (1778) and the nation as a whole (1808).

During his presidential term, Jefferson was disappointed that the younger generation was making no move to abolish slavery, but he kept silent. In December 1806 in his presidential message to Congress, he called for a law to ban the international slave trade as required by the U.S. Constitution. He denounced the trade as "violations of human rights which have been so long continued on the unoffending inhabitants of Africa, in which the morality, the reputation, and the best interests of our country have long been eager to proscribe." Jefferson signed the bill passed by Congress, and the international trade became illegal in January 1808. By that time only South Carolina had been officially importing slaves. Illegal smuggling continued for decades.

Views of slaves and blacks

Jefferson inherited slaves as a child, and owned upwards of 700 different people at one time or another. The historian Herbert E. Sloan says that Jefferson's debt prevented his freeing his slaves, but Finkelman says that freeing slaves was "not even a mildly important goal" of Jefferson, who preferred to spend lavishly on luxury goods like wine and French chairs.

As was typical of planters, Jefferson made decisions about breaking up families when he gave slaves to his sisters and daughters as wedding presents. He considered children over the age of 10 or 12, when they began working on the plantation, as ready to leave their families. For instance, he gave the 14-year-old Betsy Hemmings and 30 other slaves to his daughter Mary Jefferson Eppes and her husband on the occasion of her marriage. From 1784-1794, he gave away or sold 161 slaves from Monticello.

Isaac Jefferson learned tinsmithing and nailmaking while held as a slave by Jefferson. Born into slavery in 1775, in 1847 he was interviewed as a free man by the author and historian Charles Campbell. The material remained unpublished until 1951 when Raymond Logan edited it into ''Memoirs of a Monticello Slave''. Isaac Jefferson's account provided valuable details to historians about daily life and family relationships at Monticello.

According to the historian Stephen Ambrose: "Jefferson, like all slaveholders and many others, regarded Negroes as inferior, childlike, untrustworthy and, of course, as property." He believed they were inferior to whites in reasoning, mathematical comprehension, and imagination. Jefferson thought these "differences" were "fixed in nature" and was not dependent on their freedom or education. He thought such differences created "innate inferiority of Blacks compared to Whites". In ''Notes on the State of Virginia'', Jefferson claimed that blacks prefer the beauty of whites over other blacks, and cited "the preferences of the Orangutan for the black woman over those of his own species".

Jefferson did not believe that African Americans could live in American society as free people together with whites. For a long-term solution, he thought that slaves should be freed after reaching maturity and having repaid their owner's investment; afterward, he thought they should be sent to African colonies in what he considered "repatriation", despite their being American-born. Otherwise, he thought the presence of free blacks would encourage a violent uprising by slaves' looking for freedom. Jefferson expressed his fear of slave rebellion: "We have the wolf by the ears; and we can neither hold him, nor safely let him go. Justice is in one scale, and self-preservation in the other."

In 1809, he wrote to Abbé Grégoire, whose book argued against Jefferson's claims of black inferiority in ''Notes on the State of Virginia''. Jefferson said blacks had "respectable intelligence", but did not alter his views. In August 1814 the planter Edward Coles and Jefferson corresponded about Coles' ideas on emancipation. Jefferson urged Coles not to free his slaves, but the younger man took all his slaves to the Illinois and freed them, providing them with land for farms.

Interests, activities, inventions, and improvements

Jefferson was a farmer, with a lifelong interest in mechanical innovations, new crops, soil conditions, and scientific agricultural techniques. He took special interest in his gardens. His main cash crop was tobacco, but its price was usually low and it was rarely profitable. He tried to achieve self-sufficiency with wheat, vegetables, flax, corn, hogs, sheep, poultry and cattle to feed and clothe his family, slaves and white employees, but he had cash flow problems and was always in debt.

Jefferson had a love for reading and collected thousands of books in his personal library. Jefferson stated that he could not "live without books" and that he had a "canine appetite for reading." By 1815, his library included 6,487 books, which he sold to the Library of Congress to replace the smaller collection destroyed in the War of 1812. In honor of Jefferson's contribution, the library's website for federal legislative information was named THOMAS. In 2007, Jefferson's two-volume 1764 edition of the Qur'an was used by Rep. Keith Ellison for his swearing in to the House of Representatives. In February 2011 the ''New York Times'' reported that a part of Jefferson's retirement library, containing 74 volumes with 28 book titles, was discovered at Washington University in St. Louis.

Jefferson was an accomplished architect who helped popularize the Neo-Palladian style in the United States. Modern scholarship indicates that hemp was a secondary crop at Monticello, but there is no evidence that Jefferson used the plant for smoking. Jefferson was interested in birds and wine, and was a noted gourmet. Jefferson was a prolific writer. He learned Gaelic to translate Ossian, and sent to James Macpherson for the originals.

Jefferson invented many small practical devices and improved contemporary inventions. These include the design for a revolving book-stand to hold five volumes at once to be viewed by the reader. Another was the "Great Clock", powered by the Earth's gravitational pull on Revolutionary War cannonballs. Its chime on Monticello's roof could be heard as far as the University of Virginia. Louis Leschot, a machinist, aided Jefferson with the clock. Jefferson invented a 15 cm long coded wooden cypher wheel, mounted on a metal spindle, to keep secure State Department messages while he was Secretary of State. The messages were scrambled and unscrambled by 26 alphabet letters on each circular segment of the wheel. He improved the moldboard plow and the polygraph, in collaboration with Charles Willson Peale.

Political philosophy and views

Jefferson idealized the independent yeoman as the best exemplar of republican virtues, distrusted cities and financiers, and favored states' rights and a strictly limited federal government, though he suspended his qualms to buy Louisiana. Jefferson detested the European system of established churches and called for a wall of separation between church and state; he helped disestablish the Anglican Church in Virginia, and was the author of the Virginia Statute for Religious Freedom (1779, 1786). Jefferson sponsored Jeffersonian democracy; his Democratic-Republican Party, dominated American politics for 25 years.

Jefferson was a leader in developing republicanism in the United States. He insisted that the British aristocratic system was inherently corrupt and that Americans' devotion to civic virtue required independence. Jefferson's vision was that of an agricultural nation of yeoman farmers minding their own affairs.

Jefferson's republican political principles were heavily influenced by the Country Party of 18th century British opposition writers. He was influenced by John Locke (particularly relating to the principle of inalienable rights).

Jefferson had a decided dislike and distrust of banks and bankers and opposed borrowing from banks because he believed it created long-term debt as well as monopolies, and inclined the people to dangerous speculation, as opposed to productive labor on the farm.

Jefferson believed that each man has "certain inalienable rights". He defines the right of "liberty" by saying, "Rightful liberty is unobstructed action according to our will within limits drawn around us by the equal rights of others..." A proper government, for Jefferson, is one that not only prohibits individuals in society from infringing on the liberty of other individuals, but also restrains itself from diminishing individual liberty.

Like almost all political thinkers of his day Jefferson did not support gender equality, and opposed female involvement in politics, saying that "our good ladies ... are contented to soothe and calm the minds of their husbands returning ruffled from political debate."

Democracy

There is no dispute that Jefferson is a major iconic figure in the emergence of democracy—he was the "agrarian democrat" who shaped the thinking of his nation and the world. As historian Vernon Louis Parrington concluded in 1927: :"Far more completely than any other American of his generation he embodied the idealisms of the great revolution -- its faith in human nature, its economic individualism, its conviction that here in America, through the instrumentality of political democracy, the lot of the common man should somehow be made better." Jefferson's concepts of democracy were rooted in The Enlightenment, as Peter Onuf has stressed. He envisioned democracy an expression of society as a whole, calling for national self-determination, cultural uniformity, and based upon the education of the all the people. The emphasis on uniformity allowed no opportunity for a multiracial republic in which some groups were not fully assimilated into the identical republican values. Onuf argues that Jefferson was unable and unwilling to abolish slavery until a such demand could issue naturally from the sensibilities of the entire people. Gordon Wood (2009) concluded that Jefferson personified American ideals: "His ideas about liberty and democracy left such a deep imprint on the future of his country that, despite persistent attempts to discredit his reputation, as long as there is a United States he will remain the supreme spokesman for the nation's noblest ideals and highest aspirations." Public education and a free press was essential to a democratic nation: "If a nation expects to be ignorant and free it expects what never was and never will be....The people cannot be safe without information. Where the press is free, and every man able to read, all is safe.

Foreign policy

According to Tucker and Hendrickson (1992) Jefferson believed America "was the bearer of a new diplomacy, founded on the confidence of a free and virtuous people, that would secure ends based on the natural and universal rights of man, by means that escaped war and its corruptions." Jefferson sought a radical break from the traditional European emphasis on "reason of state" (which could justify any action) and the traditional priority of foreign policy and the needs of the ruling family over the needs of the people.

Jefferson envisaged America becoming the world's great "empire of liberty"--that is, the model for democracy and republicanism. He identified his nation as a beacon to the world, for, he said on departing the presidency in 1809, America was: :"Trusted with the destinies of this solitary republic of the world, the only monument of human rights, and the sole depository of the sacred fire of freedom and self-government, from hence it is to be lighted up in other regions of the earth, if other regions of the earth shall ever become susceptible of its benign influence."

He saw Britain as America's great enemy because it was the base for successful aristocracy and antipathy to democracy, while France, at least in the early stages of the French Revolution, appeared to Jefferson to be an ideal solution to Europe's malaise. He said, "The liberty of the whole world was depending on the issue of the contest." He never wanted war. The paradox was that Britain was much more powerful and was the leading trading partner of the U.S., so that the sort of economic warfare he proposed would hurt the American economy.

Rebellion

In the 1780s Jefferson saw occasional upheaval as a natural event. In a letter to James Madison on January 30, 1787, Jefferson wrote, "A little rebellion, now and then, is a good thing, and as necessary in the political world as storms in the physical...It is a medicine necessary for the sound health of government." Similarly, in a letter to Abigail Adams on February 22, 1787 he wrote, "The spirit of resistance to government is so valuable on certain occasions that I wish it to be always kept alive. It will often be exercised when wrong, but better so than not to be exercised at all." Concerning Shays' Rebellion after he had heard of the bloodshed, on November 13, 1787 Jefferson wrote to William S. Smith, John Adams' son-in-law, "What signify a few lives lost in a century or two? The tree of liberty must from time to time be refreshed with the blood of patriots and tyrants. It is its natural manure." In another letter to William S. Smith during 1787, Jefferson wrote: "And what country can preserve its liberties, if the rulers are not warned from time to time, that this people preserve the spirit of resistance? Let them take arms."

Religion

Jefferson rejected the orthodox Christianity of his day and was especially hostile to the Catholic Church as he saw it operate in France. Throughout his life Jefferson was intensely interested in theology, biblical study, and morality. As a landowner he played a role in governing his local Episcopal Church; in terms of belief he was inclined toward the religious philosophy of Christianity:

In private letters, Jefferson refers to himself as "Christian" (1803): "To the corruptions of Christianity I am, indeed, opposed; but not to the genuine precepts of Jesus himself. I am a Christian, in the only sense in which he wished any one to be; sincerely attached to his doctrines, in preference to all others; ascribing to himself every human excellence....

Jefferson believed in the moral teachings of Christ and edited a compilation of Christ's teachings leaving out the miracles. Jefferson was firmly anticlerical saying that in "every country and every age, the priest has been hostile to liberty. He is always in alliance with the despot...they have perverted the purest religion ever preached to man into mystery and jargon, unintelligible to all mankind, and therefore the safer for their purposes."

Jefferson rejected the idea of immaterial beings and considered the idea of an immaterial Creator a heresy introduced into Christianity. He held to the view that God was a material being, stating in a letter to John Adams that "[t]o talk of immaterial existences is to talk of nothings." He, instead, held to a belief that all things that existed were material, including God. In the same letter to Adams he continues: "At what age of the Christian church this heresy of immaterialism, this masked atheism, crept in, I do not know. But a heresy it certainly is. Jesus taught nothing of it. He told us indeed that 'God is a spirit,' but he has not defined what a spirit is, nor said that it is not matter. And the antient fathers generally, if not universally, held it to be matter: light and thin indeed, an etherial gas; but still matter."

Native American policy

Between 1776 and 1779, while governor of Virginia during the Revolutionary War, Jefferson recommended forcibly moving Cherokee and Shawnee tribes that fought on the British side to lands west of the Mississippi River. Later, Jefferson was the first President to propose the idea of Indian Removal. He laid out an approach to Indian removal in a series of private letters that began in 1803 (for example, see letter to William Henry Harrison below). His first such act as president was to make a deal with the state of Georgia: if Georgia were to release its legal claims to discovery in lands to its west, the U.S. military would help forcefully expel the Cherokee people from Georgia. At the time, the Cherokee Nation had a treaty with the United States government which guaranteed its people the right to their lands, which was violated by Jefferson's deal with Georgia.

Acculturation and assimilation

Jefferson's original plan was for Natives to give up their own cultures, religions, and lifestyles in favor of western European culture, Christian religion, and a European-style agricultural lifestyle.

Jefferson believed that their assimilation into the European-American economy would make them more dependent on trade with white Americans, and would eventually thereby be willing to give up land that they would otherwise not part with, in exchange for trade goods or to resolve unpaid debts. In an 1803 letter to William Henry Harrison, Jefferson wrote:

:To promote this disposition to exchange lands, which they have to spare and we want, for necessaries, which we have to spare and they want, we shall push our trading uses, and be glad to see the good and influential individuals among them run in debt, because we observe that when these debts get beyond what the individuals can pay, they become willing to lop them off by a cession of lands.... In this way our settlements will gradually circumscribe and approach the Indians, and they will in time either incorporate with us as citizens of the United States, or remove beyond the Mississippi. The former is certainly the termination of their history most happy for themselves; but, in the whole course of this, it is essential to cultivate their love. As to their fear, we presume that our strength and their weakness is now so visible that they must see we have only to shut our hand to crush them, and that all our liberalities to them proceed from motives of pure humanity only. Should any tribe be foolhardy enough to take up the hatchet at any time, the seizing the whole country of that tribe, and driving them across the Mississippi, as the only condition of peace, would be an example to others, and a furtherance of our final consolidation.

Forced Indian relocation

With the colonial and native civilizations in collision compounded by British incitement of Indian tribes and mounting hostilities between the two peoples quick measures were resorted to so as to avert another major conflict and measures were taken to forcefully relocate the various Indian tribes to points further west. Jefferson relates his feelings of the affair in a letter to Alexander von Humboldt in 1813:

:You know, my friend, the benevolent plan we were pursuing here for the happiness of the aboriginal inhabitants in our vicinities. We spared nothing to keep them at peace with one another. To teach them agriculture and the rudiments of the most necessary arts, and to encourage industry by establishing among them separate property. In this way they would have been enabled to subsist and multiply on a moderate scale of landed possession. They would have mixed their blood with ours, and been amalgamated and identified with us within no distant period of time. On the commencement of our present war, we pressed on them the observance of peace and neutrality, but the interested and unprincipled policy of England has defeated all our labors for the salvation of these unfortunate people. They have seduced the greater part of the tribes within our neighborhood, to take up the hatchet against us, and the cruel massacres they have committed on the women and children of our frontiers taken by surprise, will oblige us now to pursue them to extermination, or drive them to new seats beyond our reach.

Jefferson believed assimilation was best for Native Americans; second best was removal to the west. The worst possible outcome would happen if Native Americans attacked the whites. He told his Secretary of War, General Henry Dearborn (who was the primary government official responsible for Indian affairs): "if we are constrained to lift the hatchet against any tribe, we will never lay it down until that tribe is exterminated, or driven beyond the Mississipi."

Death

Jefferson' health began to deteriorate by July 1825, and by June 1826 he was confined to bed. His death was from natural causes, a combination of illnesses and conditions including uremia, severe diarrhea, and pneumonia. Jefferson died on July 4, 1826, the fiftieth anniversary of the Declaration of Independence, and a few hours before John Adams.

Though born into a wealthy slave-owning family, Jefferson had many financial problems, and died deeply in debt. He gave instructions for disposal of his assets in his Will and after his death, his possessions (including the persons he held as slaves) were sold off in public auctions starting in 1827, Monticello itself was sold in 1831. Thomas Jefferson is buried in the family cemetery at Monticello. The cemetery only is now owned and operated by the Monticello Association, a separate lineage society that is not affiliated with the Thomas Jefferson Foundation that runs the estate.

Jefferson wrote his own epitaph, which reads:

Legacy

Memorials and Honors

Jefferson has been memorialized in many ways, including buildings, sculptures, and currency. The Jefferson Memorial was dedicated in Washington, D.C. on April 13, 1943, the 200th anniversary of Jefferson's birth. The interior of the memorial includes a statue of Jefferson and engravings of passages from his writings. Most prominent are the words which are inscribed around the monument near the roof: "I have sworn upon the altar of god eternal hostility against every form of tyranny over the mind of man".

Thomas Jefferson has been honored on U.S. postage since the first Jefferson postage stamp was released in 1856. Jefferson was the second president to be featured on U.S. Postage. His portrait appears on the U.S. $2 bill, nickel, and the $100 Series EE Savings Bond, and a Presidential Dollar which released into circulation on August 16, 2007.

His original tombstone, now a cenotaph, is located on the campus in the University of Missouri's [[David R. Francis Quadrangle| Quadrangle]]. A life mask of Jefferson was created by John Henri Isaac Browere in the 1820s.

Jefferson, together with George Washington, Theodore Roosevelt and Abraham Lincoln, was chosen by sculptor Gutzon Borglum and approved by President Calvin Coolidge to be depicted in stone at the Mount Rushmore Memorial. Other memorials to Jefferson include the commissioning of the National Oceanic and Atmospheric Administration ship ''Thomas Jefferson'' in Norfolk, Virginia on July 8, 2003, in commemoration of his establishment of a Survey of the Coast, the predecessor to NOAA's National Ocean Service; and the placement of a bronze monument in Jefferson Park, Chicago at the entrance to the Jefferson Park Transit Center along Milwaukee Avenue in 2005.

Reputation

Jefferson has often been seen as a major American icon of liberty, democracy and republicanism. Many have hailed him as one of the most articulate spokesmen of the American Revolution, and as a renaissance man who promoted science and scholarship. He is seen by many as having championed a political philosophy that has retained its power over the centuries. Abraham Lincoln cited Jefferson when articulating his own philosophy of liberty and equality in the battle against slavery. Lincoln used the natural rights precepts of the Declaration of Independence as his guide to a better Union. He once said that Jefferson was "the most distinguished politician in our history."

During the New Deal era of the 1930s, Democrats honored Jefferson and Andrew Jackson as their party's founding fathers and continued inspiration. He was portrayed as the spokesman for democracy and the common man and archfoe of Hamilton, portrayed as the front man for bankers and aristocrats. President Franklin D. Roosevelt took the lead in building his monument in Washington.

Historian Gordon Wood has noted how the views of Jefferson and the other founders have changed as the values of the modern age have changed. He argues that during the progressive era of the late 19th and early 20th century, when scholars saw revolutionary America as a struggle between "haves" and "have nots", Jefferson's reputation reached new heights as his presidency was seen as the final defeat of the moneyed classes. Wood argues that this predominated until the 1940s, when the progressive era view fell from favor, and thus Jefferson's reputation declined from its prior heights. As modern historians see slavery as a greater evil than the mercantilism that Jefferson's adversaries championed (a view without consensus until recently), Wood argues, Jefferson's legacy in recent decades has come under further scrutiny and criticism.

After the Civil Rights Revolution came a reappraisal focused on race. Some historians expressed dismay at his harsh treatment of Native Americans, while others have been more forgiving. There is also dismay about his opposition to a biracial society, and his views on blacks and their supposed racial inferiority. The likelihood of his relationship with Sally Hemings, a slave who was three-quarters white, and his "shadow family" by her suggests he kept his privacy and was a complex man of apparent contradictions. Jefferson's legacy as a champion of Enlightenment ideals has been challenged by modern historians who find his ownership of hundreds of slaves at Monticello to be in contradiction to his views on freedom and the equality of men. Historian Peter Onuf stated that "Jefferson's failure to address the problem of slavery generally and the situation of his own human chattel...is in itself the most damning possible commentary on his iconic standing as 'apostle of freedom'." The historian Clarence E. Walker said that Jefferson could rationalize being a slave owner and defender of freedom since he believed blacks were inferior and needed supervision.

Writings

''A Summary View of the Rights of British America'' (1774)

''Declaration of the Causes and Necessity of Taking Up Arms'' (1775)

''Memorandums taken on a journey from Paris into the southern parts of France and Northern Italy, in the year 1787''

''Notes on the State of Virginia'' (1781)

''Manual of Parliamentary Practice for the Use of the Senate of the United States'' (1801)

''Autobiography'' (1821)

''Jefferson Bible, or The Life and Morals of Jesus of Nazareth''

See also

Jeffersonian democracy

Maria Cosway

Monticello Association

Uriah P. Levy

Jefferson Levy

France in the American Revolutionary War

Founding Fathers of the United States

US Presidents on US postage stamps

List of Presidents of the United States

Notes

Bibliography

Biographical

Appleby, Joyce. ''Thomas Jefferson'' (2003), short interpretive essay by leading scholar.

Bernstein, R. B. ''Thomas Jefferson''. (2003) Well-regarded short biography.

Brodie, Fawn McKay. ''Thomas Jefferson: An Intimate History'', W.W. Norton, 1974,the "first extensive investigation of the Sally Hemings story".

Burstein, Andrew. ''Jefferson's Secrets: Death and Desire at Monticello'', New York: Basic Books, 2005

Gordon-Reed, Annette. ''Thomas Jefferson and Sally Hemings: An American controversy'',Charlottesville, Virginia: University of Virginia Press, 1997 (reprint 1998 to include discussion of DNA analysis)

Cunningham, Noble E. ''In Pursuit of Reason'' (1988) well-reviewed short biography.

Crawford, Alan Pell, ''Twilight at Monticello'', Random House, New York, (2008)

Ellis, Joseph. ''American Sphinx: The Character of Thomas Jefferson'' (1996).Prize-winning essays; assumes prior reading of his biography. Gordon-Reed, Annette. ''Thomas Jefferson and Sally Hemings: An American controversy'',Charlottesville, Virginia: University of Virginia Press, 1997 (reprint 1998 to include discussion of DNA analysis) , short biography. Malone, Dumas. ''Jefferson and His Time'', 6 vols. (1948–82). Multi-volume biography of TJ by leading expert; A short version is online.

Padover, Saul K. ''Jefferson: A Great American's Life and Ideas''

A standard scholarly biography. Peterson, Merrill D. (ed.) ''Thomas Jefferson: A Reference Biography'' (1986),24 essays by leading scholars on aspects of Jefferson's career. Abook detailing Thomas Jefferson's love of music. 2 volumes.

Scharff, Virginia. ''The Women Jefferson Loved'' (2010)

Politics and ideas

Ackerman, Bruce. ''The Failure of the Founding Fathers: Jefferson, Marshall, and the Rise of Presidential Democracy.'' (2005)

Adams, Henry. ''History of the United States of America during the Administrations of Thomas Jefferson'' (1889; Library of America edition 1986) famous 4-volume history

* Wills, Garry, ''Henry Adams and the Making of America'' (2005), detailed analysis of Adams' ''History''

Banning, Lance. ''The Jeffersonian Persuasion: Evolution of a Party Ideology'' (1978)

Channing; Edward. ''The Jeffersonian System: 1801–1811'' (1906), "American Nation" survey of political history

Dunn, Susan. ''Jefferson's Second Revolution: The Election Crisis of 1800 and the Triumph of Republicanism'' (2004)

Elkins, Stanley and Eric McKitrick. ''The Age of Federalism'' (1995) in-depth coverage of politics of 1790s

Fatovic, Clement. "Constitutionalism and Presidential Prerogative: Jeffersonian and Hamiltonian Perspectives." '': American Journal of Political Science,'' 2004 48(3): 429–444. Issn: 0092-5853 Fulltext: in Swetswise, Ingenta, Jstor, and Ebsco

Finkelman, Paul. ''Slavery and the Founders: Race and Liberty in the Age of Jefferson'' (2001), esp ch 6–7

Hatzenbuehler, Ronald L. ''"I Tremble for My Country": Thomas Jefferson and the Virginia Gentry,'' (University Press of Florida; 206 pages; 2007). Argues that the TJ's critique of his fellow gentry in Virginia masked his own reluctance to change

Horn, James P. P. Jan Ellen Lewis, and Peter S. Onuf, eds. ''The Revolution of 1800: Democracy, Race, and the New Republic'' (2002) 17 essays by scholars

Jayne, Allen. ''Jefferson's Declaration of Independence: Origins, Philosophy and Theology'' (2000); traces TJ's sources and emphasizes his incorporation of Deist theology into the Declaration.

Roger G. Kennedy. ''Mr. Jefferson's Lost Cause: Land, Farmers, Slavery, and the Louisiana Purchase'' (2003).

Knudson, Jerry W. ''Jefferson and the Press: Crucible of Liberty.'' (2006)

Lewis, Jan Ellen, and Onuf, Peter S., eds. ''Sally Hemings and Thomas Jefferson: History, Memory, Civic Culture''. (1999)

McDonald, Forrest. ''The Presidency of Thomas Jefferson'' (1987) intellectual history approach to Jefferson's Presidency

Matthews, Richard K. "The Radical Political Philosophy of Thomas Jefferson: An Essay in Retrieval," ''Midwest Studies in Philosophy,'' XXVIII (2004)

Mayer, David N. ''The Constitutional Thought of Thomas Jefferson'' (2000)

Onuf, Peter S., "Every Generation Is An 'Independant Nation': Colonization, Miscegenation and the Fate of Jefferson's Children", ''William and Mary Quarterly'', Vol. LVII, No.1, January 2000, JSTOR

Onuf, Peter S. ''Jefferson's Empire: The Languages of American Nationhood''. (2000). Online review

Onuf, Peter. "Thomas Jefferson, Federalist" (1993) online journal essay

Rahe, Paul A. "Thomas Jefferson's Machiavellian Political Science". ''Review of Politics'' 1995 57(3): 449–481. ISSN 0034–6705 Fulltext online at Jstor and Ebsco.

Sears, Louis Martin. ''Jefferson and the Embargo'' (1927), state by state impact

Sloan, Herbert J. ''Principle and Interest: Thomas Jefferson and the Problem of Debt'' (1995). Shows the burden of debt in Jefferson's personal finances and political thought.

Smelser, Marshall. ''The Democratic Republic: 1801–1815'' (1968). "New American Nation" survey of political and diplomatic history

Staloff, Darren. ''Hamilton, Adams, Jefferson: The Politics of Enlightenment and the American Founding.'' (2005)

Tucker, Robert W. and David C. Hendrickson. ''Empire of Liberty: The Statecraft of Thomas Jefferson'' (1992); called "probably the most important study of the theory & means of Jefferson's foreign policy. by Cogliano, ''Thomas Jefferson: reputation and legacy'' (2008) p. 237

Urofsky, Melvin I. "Thomas Jefferson and John Marshall: What Kind of Constitution Shall We Have?" ''Journal of Supreme Court History'' 2006 31(2): 109–125. Issn: 1059-4329 Fulltext: in Swetswise, Ingenta and Ebsco

Valsania, Maurizio. "'Our Original Barbarism': Man Vs. Nature in Thomas Jefferson's Moral Experience." ''Journal of the History of Ideas'' 2004 65(4): 627–645. Issn: 0022-5037 Fulltext: in Project Muse and Swetswise

Wagoner, Jennings L., Jr. ''Jefferson and Education.'' (2004).

Religion

Gaustad, Edwin S. ''Sworn on the Altar of God: A Religious Biography of Thomas Jefferson'' (2001) Wm. B. Eerdmans Publishing, ISBN 0-8028-0156-0

Sanford, Charles B. ''The Religious Life of Thomas Jefferson'' (1987) University of Virginia Press, ISBN 0-8139-1131-1

Sheridan, Eugene R. ''Jefferson and Religion'', preface by Martin Marty, (2001) University of North Carolina Press, ISBN 1-882886-08-9

Edited by Jackson, Henry E., President, College for Social Engineers, Washington, D. C. ''The Thomas Jefferson Bible'' (1923) Copyright Boni and Liveright, Inc. Printed in the United States of America. Arranged by Thomas Jefferson. Translated by R. F. Weymouth. Located in the National Museum, Washington, D. C.

Legacy and historiography

Cogliano, Francis D. ''Thomas Jefferson: Reputation and Legacy'' (Edinburgh University Press, 2006) online edition

Gordon-Reed, Annette. ''Thomas Jefferson and Sally Hemings: An American controversy'', Charlottesville, Virginia: University of Virginia Press, 1997 (reprint 1998 to include discussion of DNA analysis)

Onuf, Peter. "The Scholars' Jefferson," ''William and Mary Quarterly'' 3d Series, L:4 (October 1993), 671–699. Historiographical review or scholarship about TJ; in JSTOR

Onuf, Peter S., ed. ''Jeffersonian Legacies''. (1993)

Onuf, Peter S., ed. (with Jan Ellen Lewis). ''Sally Hemings and Thomas Jefferson: History, Memory, and Civic Culture'', University Press of Virginia, 1999, Google preview.

Perry, Barbara A. "Jefferson's Legacy to the Supreme Court: Freedom of Religion", ''Journal of Supreme Court History'' 2006 31(2): 181–198. Issn: 1059-4329 Fulltext in Swetswise, Ingenta and Ebsco

Peterson, Merrill D. ''The Jefferson Image in the American Mind'' (1960), how Americans interpreted and remembered Jefferson

Taylor, Jeff. ''Where Did the Party Go?: William Jennings Bryan, Hubert Humphrey, and the Jeffersonian Legacy'' (2006), on Jefferson's role in Democratic history and ideology.

Wiltse, Charles Maurice. ''The Jeffersonian Tradition in American Democracy'' (1935), analysis of Jefferson's political philosophy

"Thomas Jefferson", PBS interviews with 24 historians

Primary sources

''Thomas Jefferson: Writings: Autobiography / Notes on the State of Virginia / Public and Private Papers / Addresses / Letters'' (1984, ISBN 978-0-940450-16-5) Library of America edition. There are numerous one-volume collections; this is perhaps the best place to start.

''Thomas Jefferson, Political Writings'' ed by Joyce Appleby and Terence Ball. Cambridge University Press. 1999 online

Lipscomb, Andrew A. and Albert Ellery Bergh, eds. ''The Writings Of Thomas Jefferson'' 19 vol. (1907) not as complete nor as accurate as Boyd edition, but covers TJ from birth to death. It is out of copyright, and so is online free.

Edwin Morris Betts (editor), ''Thomas Jefferson's Farm Book'', (Thomas Jefferson Memorial: December 1, 1953) ISBN 1-882886-10-0. Letters, notes, and drawings—a journal of plantation management recording his contributions to scientific agriculture, including an experimental farm implementing innovations such as horizontal plowing and crop-rotation, and Jefferson's own moldboard plow. It is a window to slave life, with data on food rations, daily work tasks, and slaves' clothing. The book portrays the industries pursued by enslaved and free workmen, including in the blacksmith's shop and spinning and weaving house.

Boyd, Julian P. et al., eds. ''The Papers of Thomas Jefferson.'' The definitive multivolume edition; available at major academic libraries. 36 volumes covers TJ to March 1802.

''The Jefferson Cyclopedia'' (1900) large collection of TJ quotations arranged by 9000 topics; searchable; copyright has expired and it is online free.

The Thomas Jefferson Papers, 1606–1827, 27,000 original manuscript documents at the Library of Congress online collection

Jefferson, Thomas. ''Notes on the State of Virginia'' (1787), London: Stockdale. This was Jefferson's only book

* Shuffelton, Frank, ed., (1998) Penguin Classics paperback: ISBN 0-14-043667-7

* Waldstreicher, David, ed., (2002) Palgrave Macmillan hardcover: ISBN 0-312-29428-X

* online edition

Cappon, Lester J., ed. ''The Adams-Jefferson Letters'' (1959)

A MANUAL OF PARLIAMENTARY PRACTICE:, for the Use of the Senate of the United States. BY THOMAS JEFFERSON.

Howell, Wilbur Samuel, ed. ''Jefferson's Parliamentary Writings'' (1988). Jefferson's Manual of Parliamentary Practice, written when he was vice-President, with other relevant papers

Melton, Buckner F.: ''The Quotable Founding Fathers'', Potomac Books, Washington D.C. (2004).

Smith, James Morton, ed. ''The Republic of Letters: The Correspondence between Thomas Jefferson and James Madison, 1776–1826'', 3 vols. (1995)

External links

The Works of Thomas Jefferson (1904 - 12 Vols.), Paul Leicester Ford (Editor)- The Online Library of Liberty

The Papers of Thomas Jefferson – Digital Edition

* University of Virginia Jefferson Papers

* B. L. Rayner's 1829 ''Life of Thomas Jefferson'', an on-line etext

* "The Hobby of My Old Age": Jefferson's University of Virginia

* Quotations from Jefferson

* University of Virginia biography

Biography on White House website

A collection of photographs of Thomas Jefferson's architecture

Library of Congress

* Library of Congress: Jefferson exhibition

* Library of Congress: Jefferson timeline

* Thomas Jefferson: A Resource Guide from the Library of Congress

Massachusetts Historical Society

* Thomas Jefferson Papers: An Electronic Archive This digital collection of Thomas Jefferson manuscripts held by the Massachusetts Historical Society includes the page images and transcriptions of Jefferson's Farm Book and Garden Book, also page images of Jefferson's library catalogs and architectural drawings.

National Park Service

* ''Thomas Jefferson's Plan for the University of Virginia: Lessons from the Lawn,'' a National Park Service Teaching with Historic Places (TwHP) lesson plan

* Jefferson Memorial, Washington DC

Monticello – Home of Thomas Jefferson

Poplar Forest-Thomas Jefferson's second home

"Frontline: Jefferson's blood: Chronology: The Sally Hemings story (1977), PBS

The Papers of Thomas Jefferson at the Avalon Project

Notes on the State of Virginia from American Studies at the University of Virginia.

Online catalog of Thomas Jefferson's personal library, based on the catalog of books he sold to the Library of Congress in 1815

The Thomas Jefferson Encyclopedia, for information on TJ's life and times, written and referenced by historians at Monticello

A Guide to the Executive Papers of Governor Thomas Jefferson, 1779-1781 at The Library of Virginia

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Coordinates	15°48′00″N47°54′00″N
name	H. Frank Lawrence
sport	Football, basketball
overall record	19–3–2 (football)63–43 (basketball)
coach years	Football1924–1926Basketball1923–1929
coach teams	Northwest Missouri StateNorthwest Missouri State
cfbhof year	}}

H. Frank Lawrence was the seventh head of the football coach for the Northwest Missouri State University Bearcats located in Maryville, Missouri and he held that position for three seasons, from 1924 until 1926. His career coaching record at Northwest Missouri State was 19 wins, 3 losses, and 2 ties. This ranks him ninth at Northwest Missouri State in total wins and first at Northwest Missouri State in winning percentage.

References

Category:Year of birth missing Category:Year of death missing Category:Northwest Missouri State Bearcats football coaches Category:Northwest Missouri State Bearcats men's basketball coaches

Coordinates	15°48′00″N47°54′00″N
name	Payal Rohatgi
birth date	November 9
birth place	Hyderabad, Andhra Pradesh, India
yearsactive	2002–present
occupation	Actress, Model
spouse	None
homepage	http://www.mypayalrohatgi.com }}

Payal Rohatgi (born in Hyderabad) is an Indian actress and model who appears in Bollywood films.

Early life

Rohatgi was born in Banjara Hills, Hyderabad, India. She is the daughter of Veena Rohatgi and Shashank Rohatgi. She has a brother named Gaurav Rohatgi. She was brought up in a middle class family and grew up in Ahmedabad in Gujarat. She completed her schooling from Udgam School and did her engineering from L.D. College of Engineering, Ahmedabad. She is a computer engineer by profession.

Career

Modeling

Rohatgi started her career by modeling for popular brands like Amul, Nirma, and Nescafe. She gained attention after appearing in a television ad for Cadbury's Temptations Chocolates. Around this time she also appeared in music videos by rock band, ''Silk Route'' and Indipop artist, Kay Kay.

In 2002, she participated in the Femina Miss India contest. The same year, she won the Miss Tourism World in Medellin, South America. After starting her career in Bollywood, Rohatgi has cut back on the number of advertisements she works in. However, she appeared along with cricketer Virender Sehwag in an ad film for Dabur's ''Lal Dantmanjan''. The film was directed by Pradeep Sarkar. She was also seen in an ad film for Eveready battery in 2006 with Amitabh Bachchan, which was directed by Pradeep Sarkar.

Film career

Rohatgi made her Bollywood debut in 2002 with Harry Baweja's, ''Yeh Kya Ho Raha Hai?'', a Hindi remake of the Hollywood teen flick ''American Pie''. In later years, she appeared in the films, ''Plan'' (2003), ''Police Force'' (2003) and ''Rakht'' (2004).

In 2006, she got her major breakthrough with the film, ''36 China Town'', also starring Shahid Kapoor, Kareena Kapoor, and Paresh Rawal. Later that year in July, she appeared in the critically acclaimed, ''Corporate'', in which she played the part of an item girl.

In 2007, her first release was Priyadarshan's ''Dhol'', produced by the Percept Picture Company. She played a positive second lead character, paired opposite Arbaaz Khan.

In 2008, she was seen in a cameo opposite Ranvir Shorey in PNC film ''Ugly Aur Pagli'' which was released in August. In mid-September, she appeared opposite Irrfan Khan in a TV18 film ''Dil Kabaddi''. She played the role of an aerobics instructor in the film.

In 2010, she signed a comedy film ''30 Takka'' also starring Boman Irani. She has been doing theater workshops with Quasar Thakur and has made debut on stage in Vandana Sajnani Khattar's English play ''Four Play'' on October 16, 2010 in Mumbai.

Television

In August 2008, Rohatgi appeared in season 2 of the reality television show, ''Bigg Boss'' on Colors TV as a contestant. She was involved in a lot of controversies relating to Rahul Mahajan, whom she dismissed as a seven-year old friend. The same year, she was seen in the adventurous game show, ''Khatron Ke Khiladi''.

In 2009, Rohatgi performed a comedy skit as a celebrity performer in Comedy Circus - Chinchpokli to China on Sony Television.

On 11 January 2010, she appeared in the Ndtv Imagine show ''Raaz Pichle Janam Ka''.

In February 2011, she will be seen as a contestant on Imagine TV's show ''Zor Ka Jhatka'' hosted by Shahrukh Khan.

in October 2011, she will be seen as a contestant in star plus's show "Survivor India" which is No. 1 reality show in 70 countries worldwide and will be having its first season run in India.

Personal life

In 2008, during the second season of the show, ''Bigg Boss'', Rohatgi was romantically linked with fellow inmate, Rahul Mahajan. The couple broke up later, with Rohatgi citing abuse and physical assault as the main reasons of their split. Reports have also surfaced of her dating South African cricketer, Herschelle Gibbs in 2010.

Social work

Rohatgi is actively associated with the cause of rehabilitation of drugs addicts and alcoholics and celebrated World Anti Drugs Day with them. She is also actively working for an NGO ''Jeevan Dhara'' in Mumbai.

Awards

On 2 May 2010, Rohatgi received her first award for excellence in the field of arts by International Creative Arts Society ICAS in Ahmadabad.

Filmography

''Plan (film) ''Police Force'' ''Rakht'' ''Chetna: The Excitement'' ''Tauba Tauba'' ''Mazaa Mazaa'' ''36 China Town'' ''Corporate (film) ''Heyy Babyy'' ''Dhol (2007 film) ''Dil Kabaddi''

Year !! Title !! Role !! Other notes
2002	''Yeh Kya Ho Raha Hai?''
2003	Plan'' ||	Tanya
2003	|		Special appearance in a song
2004	|	Tanya	Bipasha Basu's friend
2005	|	Chetna
2005	|
2005	|
2006	|	Gracy
2006	Corporate'' ||	(Dancer)	Special appearance in an item song
2007	|	Special Appearance
2007	Dhol'' ||	Sophie
2008	|	Kaya

Television

''Bigg Boss (Season 2)'' (2008) .... Herself ''Khatron Ke Khiladi'' (2008) .... Herself

''Raaz Pichle Janam Ka'' (2009) .... Herself

''CID'' (2010) .... Herself

''Survivor India''

References

External links

Official website

Category:Living people Category:Indian Hindus Category:Indian actors Category:Indian film actors Category:Hindi film actors Category:Indian female models Category:People from Hyderabad, India