DNA and Jean-Baptiste Carpeaux: Difference between pages

From Wikipedia, the free encyclopedia
(Difference between pages)
Content deleted Content added
VisualWikitext
Karrmann (talk | contribs)
8,512 edits
 
image added
 
Line 1: Line 1:
[[Image:Jean-Baptiste Carpeaux's marble sculpture 'Ugolino and his Sons', Metropolitan Museum of Art.jpg|thumb|right|400px|Jean-Baptiste Carpeaux's marble sculpture 'Ugolino and his Sons', Metropolitan Museum of Art]]
{{otheruses}}
[[Image:DNA Overview.png|thumb|220px|The structure of part of a DNA double helix]]
[[Image:Jean-Baptiste_Carpeaux_La_Danse.jpg|thumb|right|400px|La Danse (The Dance), Opera Garnier in Paris]]
{{Commonscat}}
'''Deoxyribonucleic acid''', or '''DNA''' is a [[nucleic acid]] molecule that contains the [[genetics|genetic]] instructions used in the [[developmental biology|development]] and functioning of all [[life|living organisms]]. The main role of DNA is the long-term storage of information and it is often compared to a set of blueprints, since DNA contains the instructions needed to construct other components of [[cell (biology)|cell]]s, such as [[protein]]s and [[RNA]] [[molecule]]s. The DNA segments that carry this genetic information are called [[gene]]s, but other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information.


'''Jean-Baptiste Carpeaux''' ([[May 11]], [[1827]], [[Valenciennes]] –[[October 12]], [[1875]], [[Courbevoie]]) was a French sculptor and painter. His early studies were under [[François Rude]]. Carpeaux won the [[Prix de Rome]] in [[1854]], and moving to [[Rome]] to find inspiration, he there studied the works of [[Michelangelo Buonarroti|Michelangelo]], [[Donatello]] and [[Andrea del Verrocchio|Verrocchio]]. Staying in Rome from [[1854]] to [[1861]], he obtained a taste for movement and spontaneity, which he joined with the great principles of [[baroque art]]. In [[1861]] he made a bust of [[Mathilde Bonaparte|Princess Mathilde]], and this later brought him several commissions from [[Napoleon III]]. He worked at the pavilion of [[Flora (goddess)|Flora]], and the [[Opéra Garnier]]. His group La Danse (the Dance, [[1869]]), situated on the right side of the façade, was criticised as an offence to common decency.
Chemically, DNA is a long [[polymer]] of simple units called [[nucleotide]]s, with a backbone made of sugars and phosphate atoms joined by [[ester]] bonds. Attached to each sugar is one of four types of molecules called [[nucleobase|bases]]. It is the sequence of these four bases along the backbone that encodes information. This information is read using the [[genetic code]], which specifies the sequence of the [[amino acid]]s within proteins. The code is read by copying stretches of DNA into the related nucleic acid [[RNA]], in a process called [[transcription (genetics)|transcription]]. Most of these RNA molecules are used to synthesize proteins, but others are used directly in structures such as [[ribosome]]s and [[spliceosome]]s.


He never managed to finish his last work, the famous Fountain of the Four Parts of the Earth, on the Place Camille Jullian. He did finish the terrestrial globe, supported by the four figures of [[Asia]], [[Europe]], [[North America|America]] and [[Africa]], and it was [[Emmanuel Frémiet]] who completed the work by adding the eight leaping horses, the tortoises and the dolphins of the basin.
Within cells, DNA is organized into structures called [[chromosome]]s and the set of chromosomes within a cell make up a [[genome]]. These chromosomes are duplicated before cells [[cell division|divide]], in a process called [[DNA replication]]. [[Eukaryote|Eukaryotic organisms]] such as [[animal]]s, [[plant]]s, and [[fungi]] store their DNA inside the [[cell nucleus]], while in [[prokaryote]]s such as [[bacteria]] it is found in the cell's [[cytoplasm]]. Within the chromosomes, [[chromatin]] proteins such as [[histone]]s compact and organize DNA, which helps control its interactions with other proteins and thereby control which [[genes]] are transcribed.


== Sculptures by Carpeaux ==
==Physical and chemical properties==
[[Image:DNA_chemical_structure.svg|right|thumb|350px|The chemical structure of DNA.]]


* Ugolin et ses fils - [[Ugolino della Gherardesca|Ugolino]] and his Sons (1861, in the permanent collection of the [[Metropolitan Museum of Art]])[[http://www.insecula.com/oeuvre/photo_ME0000009025.html]] with versions in other museums including the [[Musée d'Orsay]]
DNA is a long [[polymer]] made from repeating units called [[nucleotide]]s.<ref name=Alberts>{{cite book | last = Alberts| first = Bruce| coauthors = Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, and Peter Walters | title = Molecular Biology of the Cell; Fourth Edition | publisher = Garland Science| date = 2002 | location = New York and London | url = http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=mboc4.TOC&depth=2 | id = ISBN 0-8153-3218-1}}</ref><ref name=Butler>Butler, John M. (2001) ''Forensic DNA Typing'' "Elsevier". pp. 14 – 15. ISBN 978-0-12-147951-0.</ref> The DNA chain is 22 to 24&nbsp;[[Ångström]]s wide (2.2 to 2.4&nbsp;[[nanometre]]s), and one nucleotide unit is 3.3&nbsp;Ångstroms (0.33&nbsp;nanometres) long.<ref>{{cite journal | author = Mandelkern M, Elias J, Eden D, Crothers D | title = The dimensions of DNA in solution | journal = J Mol Biol | volume = 152 | issue = 1 | pages = 153 – 61 | year = 1981 | id = PMID 7338906}}</ref> Although each individual repeating unit is very small, DNA polymers can be enormous molecules containing millions of nucleotides. For instance, the largest human [[chromosome]], chromosome number 1, is 220 million [[base pair]]s long.<ref>{{cite journal | author = Gregory S, ''et al.'' | title = The DNA sequence and biological annotation of human chromosome 1 | journal = Nature | volume = 441 | issue = 7091 | pages = 315 – 21 | year = 2006 | id = PMID 16710414}}</ref>
* The Dance (commissioned for the [[Palais Garnier|Opera Garnier]])
* Jeune pêcheur à la coquille - [[Naples|Neapolitan]] Fisherboy - in the [[Louvre]], [[Paris]] [[http://www.insecula.com/oeuvre/photo_ME0000034255.html]]
* Girl with Shell
* [[Antoine Watteau]] monument, [[Valenciennes]]


==Neapolitan Fisherboy==
In living organisms, DNA does not usually exist as a single molecule, but instead as a tightly-associated pair of molecules.<ref name=Watson>{{cite journal | author = Watson J, Crick F | title = Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid | url=http://profiles.nlm.nih.gov/SC/B/B/Y/W/_/scbbyw.pdf | journal = Nature | volume = 171 | issue = 4356 | pages = 737 – 8 | year = 1953 | id = PMID 13054692}}</ref><ref name=berg>Berg J., Tymoczko J. and Stryer L. (2002) ''Biochemistry.'' W. H. Freeman and Company ISBN 0-7167-4955-6</ref> These two long strands entwine like vines, in the shape of a [[helix|double helix]]. The nucleotide repeats contain both the segment of the backbone of the molecule, which holds the chain together, and a base, which interacts with the other DNA strand in the helix. In general, a base 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]]. If multiple nucleotides are linked together, as in DNA, this polymer is referred to as a [[polynucleotide]].<ref name=IUPAC>[http://www.chem.qmul.ac.uk/iupac/misc/naabb.html Abbreviations and Symbols for Nucleic Acids, Polynucleotides and their Constituents] IUPAC-IUB Commission on Biochemical Nomenclature (CBN) Accessed 03 Jan 2006</ref>


Carpeaux submitted a plaster version of ''Pêcheur napolitain à la coquille'', the Neapolitan Fisherboy, to the [[French Academy]] while a student in [[Rome]]. He carved the marble version several years later, showing it in the Salon exhibition of 1863. It was purchased for [[Napoleon III]]'s empress, [[Eugénie de Montijo|Eugènie]]. The statue of the young smiling boy was very popular, and Carpeaux created a number of reproductions and variations in marble and bronze. There is a copy, for instance, in the Samuel H. Kress Collection in the [[National Gallery of Art]] in [[Washington D.C.]]
The backbone of the DNA strand is made from alternating [[phosphate]] and [[carbohydrate|sugar]] residues.<ref name=Ghosh>{{cite journal | author = Ghosh A, Bansal M | title = A glossary of DNA structures from A to Z | journal = Acta Crystallogr D Biol Crystallogr | volume = 59 | issue = Pt 4 | pages = 620 – 6 | year = 2003 | id = PMID 12657780}}</ref> 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 bond]]s between the third and fifth carbon [[atom]]s of adjacent sugar rings. These asymmetric [[covalent bond|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. This arrangement of DNA strands is called antiparallel. The asymmetric ends of a strand of DNA bases are referred to as the [[directionality (molecular biology)|5′]] (''five prime'') and [[directionality (molecular biology)|3′]] (''three prime'') ends. One of the major differences between DNA and RNA is the sugar, with 2-deoxyribose being replaced by the alternative pentose sugar [[ribose]] in RNA.<ref name=berg/>


Some years later, he carved the Girl with a Shell, a very similar study.
The DNA double helix is stabilized by [[hydrogen bond]]s between the bases attached to the two strands. The four bases found in DNA are [[adenine]] (abbreviated A), [[cytosine]] (C), [[guanine]] (G) and [[thymine]] (T). These four bases are shown below and are attached to the sugar/phosphate to form the complete nucleotide, as shown for adenosine monophosphate.


Carpeaux sought real life subjects in the streets and broke with the classical tradition. The Neapolitan Fisherboy's body is carved in intimate detail and shows an intricately balanced pose. Carpeaux claimed that he based the Neapolitan Fisherboy on a boy he had seen during a trip to [[Naples]].
These bases are classified into two types; adenine and guanine are fused five- and six-membered [[heterocyclic compound]]s called [[purine]]s, while cytosine and thymine are six-membered rings called [[pyrimidine]]s.<ref name=IUPAC/> A fifth pyrimidine base, called [[uracil]] (U), usually takes the place of thymine in RNA and differs from thymine by lacking a [[methyl group]] on its ring. Uracil is normally only found in DNA as a breakdown product of cytosine, but a very rare exception to this rule is a [[phage|bacterial virus]] called PBS1 that contains uracil in its DNA.<ref name="nature1963-takahashi">{{cite journal | author=Takahashi I, Marmur J. | title=Replacement of thymidylic acid by deoxyuridylic acid in the deoxyribonucleic acid of a transducing phage for Bacillus subtilis | journal=Nature | year=1963 | pages=794 – 5 | volume=197 | id=PMID 13980287}}</ref> In contrast, following synthesis of certain RNA molecules, a significant number of the uracils are converted to thymines by the enzymatic addition of the missing methyl group. This occurs mostly on structural and enzymatic RNAs like [[transfer RNA]]s and [[ribosomal RNA]].<ref>{{cite journal |author=Agris P |title=Decoding the genome: a modified view |
url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=14715921 |journal=Nucleic Acids Res |volume=32 |issue=1 |pages=223 – 38 |year=2004 |pmid=14715921}}</ref>

[[Image:DNA orbit animated small.gif|frame|right|Animation of the structure of a section of DNA. The bases lie horizontally between the two spiraling strands. [[:Image:DNA orbit animated.gif|Large version]]<ref>Created from [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1D65 PDB 1D65]</ref>]]

The double helix is a right-handed spiral. As the DNA strands wind around each other, they leave gaps between each set of phosphate backbones, revealing the sides of the bases inside (see animation). There are two of these grooves twisting around the surface of the double helix: one groove, the major groove, is 22&nbsp;Å wide and the other, the minor groove, is 12&nbsp;Å wide.<ref>{{cite journal | author = Wing R, Drew H, Takano T, Broka C, Tanaka S, Itakura K, Dickerson R | title = Crystal structure analysis of a complete turn of B-DNA | journal = Nature | volume = 287 | issue = 5784 | pages = 755 – 8 | year = 1980 | id = PMID 7432492}}</ref> 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 factor]]s that can bind to specific sequences in double-stranded DNA usually make contacts to the sides of the bases exposed in the major groove.<ref>{{cite journal | author = Pabo C, Sauer R | title = Protein-DNA recognition | journal = Annu Rev Biochem | volume = 53 | issue = | pages = 293 – 321 | year = | id = PMID 6236744}}</ref>

===Base pairing===
{{further|[[Base pair]]}}


<div class="thumb tleft" style="background-color: #f9f9f9; border: 1px solid #CCCCCC; margin:0.5em;">
{|border="0" width=230px border="0" cellpadding="2" cellspacing="0" style="font-size: 85%; border: 1px solid #CCCCCC; margin: 0.3em;"
|[[Image:GC DNA base pair.svg|280px]]
|}
{|border="0" width=230px border="0" cellpadding="2" cellspacing="0" style="font-size: 85%; border: 1px solid #CCCCCC; margin: 0.3em;"
|[[Image:AT DNA base pair.svg|280px]]
|}
<div style="border: none; width:280px;"><div class="thumbcaption">At top, a '''GC''' base pair with three [[hydrogen bond]]s. At the bottom, '''AT''' base pair with two hydrogen bonds. Hydrogen bonds are shown as dashed lines.</div></div></div>

Each type of base on one strand forms a bond with just one type of base on the other strand. This is called complementary [[base pair]]ing. Here, purines form [[hydrogen bond]]s 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. In a double helix, the two strands are also held together via [[force]]s generated by the [[hydrophobic effect]] and [[pi stacking]], which are not influenced by the sequence of the DNA.<ref>{{cite journal | author = Ponnuswamy P, Gromiha M | title = On the conformational stability of oligonucleotide duplexes and tRNA molecules | journal = J Theor Biol | volume = 169 | issue = 4 | pages = 419 – 32 | year = 1994 | id = PMID 7526075}}</ref> As hydrogen bonds are not [[covalent bond|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]].<ref>{{cite journal | author = Clausen-Schaumann H, Rief M, Tolksdorf C, Gaub H | title = Mechanical stability of single DNA molecules | url=http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1300792&blobtype=pdf | journal = Biophys J | volume = 78 | issue = 4 | pages = 1997 – 2007 | year = 2000 | id = PMID 10733978}}</ref> 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.<ref name=Alberts/>

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). The GC base pair is therefore stronger than the AT base pair. 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.<ref>{{cite journal | author = Chalikian T, Völker J, Plum G, Breslauer K | title = A more unified picture for the thermodynamics of nucleic acid duplex melting: a characterization by calorimetric and volumetric techniques | url=http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=22151&blobtype=pdf | journal = Proc Natl Acad Sci U S A | volume = 96 | issue = 14 | pages = 7853 – 8 | year = 1999 | id = PMID 10393911}}</ref> Parts of the DNA double helix that need to separate easily, such as the TATAAT [[Pribnow box]] in bacterial [[promoter]]s, tend to have sequences with a high AT content, making the strands easier to pull apart.<ref>{{cite journal | author = deHaseth P, Helmann J | title = Open complex formation by Escherichia coli RNA polymerase: the mechanism of polymerase-induced strand separation of double helical DNA | journal = Mol Microbiol | volume = 16 | issue = 5 | pages = 817 – 24 | year = 1995 | id = PMID 7476180}}</ref> 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<sub>m</sub>'' 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 have no single common shape, but some conformations are more stable than others.<ref>{{cite journal | author = Isaksson J, Acharya S, Barman J, Cheruku P, Chattopadhyaya J | title = Single-stranded adenine-rich DNA and RNA retain structural characteristics of their respective double-stranded conformations and show directional differences in stacking pattern | journal = Biochemistry | volume = 43 | issue = 51 | pages = 15996 – 6010 | year = 2004 | id = PMID 15609994}}</ref>

===Sense and antisense===
{{further|[[Sense (molecular biology)]]}}

A DNA sequence is called "sense" if its sequence is the same as that of a [[messenger RNA]] (mRNA) copy that is translated into protein. The sequence on the opposite strand is complementary to the sense sequence and is therefore called the "antisense" sequence. Since [[RNA polymerase]]s work by making a complementary copy of their templates, it is this antisense strand that is the template for producing the sense mRNA. 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.<ref>{{cite journal | author = Hüttenhofer A, Schattner P, Polacek N | title = Non-coding RNAs: hope or hype? | journal = Trends Genet | volume = 21 | issue = 5 | pages = 289 – 97 | year = 2005 | id = PMID 15851066}}</ref> One proposal is that antisense RNAs are involved in regulating [[gene expression]] through RNA-RNA base pairing.<ref>{{cite journal | author = Munroe S | title = Diversity of antisense regulation in eukaryotes: multiple mechanisms, emerging patterns | journal = J Cell Biochem | volume = 93 | issue = 4 | pages = 664 – 71 | year = 2004 | id = PMID 15389973}}</ref>

A few DNA sequences in prokaryotes and eukaryotes, and more in [[plasmid]]s and [[virus]]es, blur the distinction made above between sense and antisense strands by having overlapping genes.<ref>{{cite journal | author = Makalowska I, Lin C, Makalowski W | title = Overlapping genes in vertebrate genomes | journal = Comput Biol Chem | volume = 29 | issue = 1 | pages = 1 – 12 | year = 2005 | id = PMID 15680581}}</ref> In these cases, some DNA sequences do double duty, encoding one protein when read 5′ to 3′ along one strand, and a second protein when read in the opposite direction (still 5′ to 3′) along the other strand. In [[bacteria]], this overlap may be involved in the regulation of gene transcription,<ref>{{cite journal | author = Johnson Z, Chisholm S | title = Properties of overlapping genes are conserved across microbial genomes | journal = Genome Res | volume = 14 | issue = 11 | pages = 2268 – 72 | year = 2004 | id = PMID 15520290}}</ref> while in viruses, overlapping genes increase the amount of information that can be encoded within the small viral genome.<ref>{{cite journal | author = Lamb R, Horvath C | title = Diversity of coding strategies in influenza viruses | journal = Trends Genet | volume = 7 | issue = 8 | pages = 261 – 6 | year = 1991 | id = PMID 1771674}}</ref> Another way of reducing genome size is seen in some viruses that contain linear or circular single-stranded DNA as their genetic material.<ref>{{cite journal | author = Davies J, Stanley J | title = Geminivirus genes and vectors | journal = Trends Genet | volume = 5 | issue = 3 | pages = 77 – 81 | year = 1989 | id = PMID 2660364}}</ref><ref>{{cite journal | author = Berns K | title = Parvovirus replication | journal = Microbiol Rev | volume = 54 | issue = 3 | pages = 316 – 29 | year = 1990 | id = PMID 2215424}}</ref>

===Supercoiling===
{{Further|[[DNA supercoil]]}}
DNA can be twisted like a rope in a process called [[DNA supercoil]]ing. 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.<ref>{{cite journal | author = Benham C, Mielke S | title = DNA mechanics | journal = Annu Rev Biomed Eng | volume = 7 | issue = | pages = 21 – 53 | year = | id = PMID 16004565}}</ref> 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 [[topoisomerase]]s.<ref name=Champoux>{{cite journal | author = Champoux J | title = DNA topoisomerases: structure, function, and mechanism | journal = Annu Rev Biochem | volume = 70 | issue = | pages = 369 – 413 | year = | id = PMID 11395412}}</ref> These enzymes are also needed to relieve the twisting stresses introduced into DNA strands during processes such as [[transcription (genetics)|transcription]] and [[DNA replication]].<ref name=Wang>{{cite journal | author = Wang J | title = Cellular roles of DNA topoisomerases: a molecular perspective | journal = Nat Rev Mol Cell Biol | volume = 3 | issue = 6 | pages = 430 – 40 | year = 2002 | id = PMID 12042765}}</ref>

[[Image:A-DNA, B-DNA and Z-DNA.png|thumb|right|290px|From left to right, the structures of A, B and Z DNA]]

===Alternative double-helical structures===
{{Further|[[Mechanical properties of DNA]]}}

DNA exists in several possible [[Conformational isomerism|conformations]]. The conformations so far identified are: [[A-DNA]], B-DNA, C-DNA, D-DNA,<ref name=Hayashi2005>{{cite journal | author = Hayashi G, Hagihara M, Nakatani K | title = Application of L-DNA as a molecular tag | journal = Nucleic Acids Symp Ser (Oxf) | volume = 49 | pages = 261 – 262 | year = 2005 | id = PMID 17150733}}</ref> E-DNA,<ref name=Vargason2000>{{cite journal | author = Vargason JM, Eichman BF, Ho PS | title = The extended and eccentric E-DNA structure induced by cytosine methylation or bromination | journal = Nature Structural Biology | volume = 7 | pages = 758 – 761 | year = 2000 | id = PMID 10966645}}</ref> H-DNA,<ref name=Wang2006>{{cite journal | author = Wang G, Vasquez KM | title = Non-B DNA structure-induced genetic instability | journal = Mutat Res | volume = 598 | issue = 1 – 2 | pages = 103 – 119 | year = 2006 | id = PMID 16516932}}</ref> L-DNA,<ref name=Hayashi2005>{{cite journal | author = Hayashi G, Hagihara M, Nakatani K | title = Application of L-DNA as a molecular tag | journal = Nucleic Acids Symp Ser (Oxf) | volume = 49 | pages = 261 – 262 | year = 2005 | id = PMID 17150733}}</ref> P-DNA,<ref name="Allemand1998">{{cite journal |author=Allemand, et al |title=Stretched and overwound DNA forms a Pauling-like structure with exposed bases |journal=PNAS |volume=24 |pages=14152-14157 |year=1998 |id=PMID 9826669}}</ref> and [[Z-DNA]].<ref name=Ghosh/><ref>{{cite journal | author = Palecek E | title = Local supercoil-stabilized DNA structures | journal = Critical Reviews in Biochemistry and Molecular Biology | volume = 26 | issue = 2 | pages = 151 – 226 | year = 1991 | id = PMID 1914495}}</ref> However, only A-DNA, B-DNA, and Z-DNA have been observed in naturally occurring biological systems. Which conformation DNA adopts depends on the sequence of the DNA, the amount and direction of supercoiling, chemical modifications of the bases and also solution conditions, such as the concentration of [[metal]] [[ion]]s and [[polyamine]]s.<ref>{{cite journal | author = Basu H, Feuerstein B, Zarling D, Shafer R, Marton L | title = Recognition of Z-RNA and Z-DNA determinants by polyamines in solution: experimental and theoretical studies | journal = J Biomol Struct Dyn | volume = 6 | issue = 2 | pages = 299 – 309 | year = 1988 | id = PMID 2482766}}</ref> Of these three conformations, the "B" form described above is most common under the conditions found in cells.<ref>{{cite journal |author=Leslie AG, Arnott S, Chandrasekaran R, Ratliff RL |title=Polymorphism of DNA double helices |journal=J. Mol. Biol. |volume=143 |issue=1 |pages=49–72 |year=1980 |pmid=7441761}}</ref> The two alternative double-helical forms of DNA differ in their geometry and dimensions.

The A form is a wider right-handed spiral, with a shallow and wide minor groove and a narrower and deeper major groove. The A form occurs under non-physiological conditions in 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.<ref>{{cite journal | author = Wahl M, Sundaralingam M | title = Crystal structures of A-DNA duplexes | journal = Biopolymers | volume = 44 | issue = 1 | pages = 45 – 63 | year = 1997 | id = PMID 9097733}}</ref><ref>{{cite journal |author=Lu XJ, Shakked Z, Olson WK |title=A-form conformational motifs in ligand-bound DNA structures |journal=J. Mol. Biol. |volume=300 |issue=4 |pages=819-40 |year=2000 |pmid=10891271}}</ref> Segments of DNA where the bases have been chemically-modified by [[methylation]] may undergo a larger change in conformation and adopt the [[Z-DNA|Z form]]. Here, the strands turn about the helical axis in a left-handed spiral, the opposite of the more common B form.<ref>{{cite journal | author = Rothenburg S, Koch-Nolte F, Haag F | title = DNA methylation and Z-DNA formation as mediators of quantitative differences in the expression of alleles | journal = Immunol Rev | volume = 184 | issue = | pages = 286 – 98 | year = | id = PMID 12086319}}</ref> These unusual structures can be recognised by specific Z-DNA binding proteins and may be involved in the regulation of transcription.<ref>{{cite journal |author=Oh D, Kim Y, Rich A |title=Z-DNA-binding proteins can act as potent effectors of gene expression in vivo |url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12486233 |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=99 |issue=26 |pages=16666-71 |year=2002 |pmid=12486233}}</ref>

[[Image:Telomere quadruplex.jpg|thumb|left|300px|Structure of a DNA quadruplex formed by [[telomere]] repeats.<ref>Created from [http://ndbserver.rutgers.edu/atlas/xray/structures/U/ud0017/ud0017.html NDB UD0017]</ref>]]

===Quadruplex structures===
At the ends of the linear [[chromosome]]s are specialized regions of DNA called [[telomere]]s. 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.<ref name=Greider>{{cite journal | author = Greider C, Blackburn E | title = Identification of a specific telomere terminal transferase activity in Tetrahymena extracts | journal = Cell | volume = 43 | issue = 2 Pt 1 | pages = 405 – 13 | year = 1985 | id = PMID 3907856}}</ref> As a result, if a chromosome lacked telomeres it would become shorter each time it was replicated. These specialized chromosome caps also help protect the DNA ends from [[exonuclease]]s and stop the [[DNA repair]] systems in the cell from treating them as damage to be corrected.<ref name=Nugent>{{cite journal | author = Nugent C, Lundblad V | title = The telomerase reverse transcriptase: components and regulation | url=http://www.genesdev.org/cgi/content/full/12/8/1073 | journal = Genes Dev | volume = 12 | issue = 8 | pages = 1073 – 85 | year = 1998 | id = PMID 9553037}}</ref> In human cells, telomeres are usually lengths of single-stranded DNA containing several thousand repeats of a simple TTAGGG sequence.<ref>{{cite journal | author = Wright W, Tesmer V, Huffman K, Levene S, Shay J | title = Normal human chromosomes have long G-rich telomeric overhangs at one end | url=http://www.genesdev.org/cgi/content/full/11/21/2801 | journal = Genes Dev | volume = 11 | issue = 21 | pages = 2801 – 9 | year = 1997 | id = PMID 9353250}}</ref>

These guanine-rich sequences may stabilize chromosome ends by forming very unusual 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 ''quadruplex'' structure.<ref name=Burge>{{cite journal | author = Burge S, Parkinson G, Hazel P, Todd A, Neidle S | title = Quadruplex DNA: sequence, topology and structure | url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17012276 | journal = Nucleic Acids Res | volume = 34 | issue = 19 | pages = 5402 – 15 | year = 2006 | id = PMID 17012276}}</ref> 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. The structure shown to the left is a top view of the quadruplex formed by a DNA sequence found in human telomere repeats. The single DNA strand forms a loop, with the sets of four bases stacking in a central quadruplex three plates deep. In the space at the centre of the stacked bases are three chelated [[potassium]] ions.<ref>{{cite journal | author = Parkinson G, Lee M, Neidle S | title = Crystal structure of parallel quadruplexes from human telomeric DNA | journal = Nature | volume = 417 | issue = 6891 | pages = 876 – 80 | year = 2002 | id = PMID 12050675}}</ref> 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.<ref>{{cite journal | author = Griffith J, Comeau L, Rosenfield S, Stansel R, Bianchi A, Moss H, de Lange T | title = Mammalian telomeres end in a large duplex loop | journal = Cell | volume = 97 | issue = 4 | pages = 503 – 14 | year = 1999 | id = PMID 10338214}}</ref> 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.<ref name=Burge/>

==Chemical modifications==
<div class="thumb tright" style="background-color: #f9f9f9; border: 1px solid #CCCCCC; margin:0.5em;">
{|border="0" width=300px border="0" cellpadding="2" cellspacing="0" style="font-size: 85%; border: 1px solid #CCCCCC; margin: 0.3em;"
|[[Image:Cytosine chemical structure.png|75px]]
|[[Image:5-methylcytosine.png|95px]]
|[[Image:Thymine chemical structure.png|97px]]
|-
|align=center|[[cytosine]]
|align=center|[[5-Methylcytosine|5-methylcytosine]]
|align=center|[[thymine]]
|}
<div style="border: none; width:300px;font-size: 85%;"><div class="thumbcaption">Structure of cytosine with and without the 5-methyl group. After deamination the 5-methylcytosine has the same structure as thymine</div></div></div>
===Base modifications===
{{further|[[DNA methylation]]}}
The expression of genes is influenced by the [[chromatin]] structure of a chromosome and regions of [[heterochromatin]] (low or no gene expression) correlate with the [[methylation]] of [[cytosine]]. For example, cytosine methylation, to produce [[5-Methylcytosine|5-methylcytosine]], is important for [[X-inactivation|X-chromosome inactivation]].<ref>{{cite journal | author = Klose R, Bird A | title = Genomic DNA methylation: the mark and its mediators | journal = Trends Biochem Sci | volume = 31 | issue = 2 | pages = 89 – 97 | year = 2006 | id = PMID 16403636}}</ref> The average level of methylation varies between organisms, with ''[[Caenorhabditis elegans]]'' lacking cytosine methylation, while [[vertebrate]]s show higher levels, with up to 1% of their DNA containing 5-methylcytosine.<ref>{{cite journal | author = Bird A | title = DNA methylation patterns and epigenetic memory | journal = Genes Dev | volume = 16 | issue = 1 | pages = 6 – 21 | year = 2002 | id = PMID 11782440}}</ref> Despite the biological role of 5-methylcytosine it is susceptible to spontaneous [[deamination]] to leave the thymine base, and methylated cytosines are therefore [[mutation]] hotspots.<ref>{{cite journal | author = Walsh C, Xu G | title = Cytosine methylation and DNA repair | journal = Curr Top Microbiol Immunol | volume = 301 | issue = | pages = 283 – 315 | year = | id = PMID 16570853}}</ref> Other base modifications include adenine methylation in bacteria and the [[glycosylation]] of uracil to produce the "J-base" in [[kinetoplastid]]s.<ref>{{cite journal | author = Ratel D, Ravanat J, Berger F, Wion D | title = N6-methyladenine: the other methylated base of DNA | journal = Bioessays | volume = 28 | issue = 3 | pages = 309 – 15 | year = 2006 | id = PMID 16479578}}</ref><ref>{{cite journal | author = Gommers-Ampt J, Van Leeuwen F, de Beer A, Vliegenthart J, Dizdaroglu M, Kowalak J, Crain P, Borst P | title = beta-D-glucosyl-hydroxymethyluracil: a novel modified base present in the DNA of the parasitic protozoan T. brucei | journal = Cell | volume = 75 | issue = 6 | pages = 1129 – 36 | year = 1993 | id = PMID 8261512}}</ref>

===DNA damage===
{{further|[[Mutation]]}}

[[Image:Benzopyrene DNA adduct 1JDG.png|thumb|right|250px|[[Benzopyrene]], the major mutagen in [[tobacco smoking|tobacco smoke]], in an adduct to DNA.<ref>Created from [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1JDG PDB 1JDG]</ref>]]
DNA can be damaged by many different sorts of [[mutagen]]s. These include [[oxidizing agent]]s, [[alkylating agent]]s and also high-energy [[electromagnetic radiation]] such as [[ultraviolet]] light and [[x-ray]]s. The type of DNA damage produced depends on the type of mutagen. For example, UV light mostly damages DNA by producing [[thymine dimer]]s, which are cross-links between adjacent pyrimidine bases in a DNA strand.<ref>{{cite journal | author = Douki T, Reynaud-Angelin A, Cadet J, Sage E | title = Bipyrimidine photoproducts rather than oxidative lesions are the main type of DNA damage involved in the genotoxic effect of solar UVA radiation | journal = Biochemistry | volume = 42 | issue = 30 | pages = 9221 – 6 | year = 2003 | id = PMID 12885257}},</ref> On the other hand, oxidants such as [[free radical]]s or [[hydrogen peroxide]] produce multiple forms of damage, including base modifications, particularly of guanosine, as well as double-strand breaks.<ref>{{cite journal | author = Cadet J, Delatour T, Douki T, Gasparutto D, Pouget J, Ravanat J, Sauvaigo S | title = Hydroxyl radicals and DNA base damage | journal = Mutat Res | volume = 424 | issue = 1 – 2 | pages = 9 – 21 | year = 1999 | id = PMID 10064846}}</ref> It has been estimated that in each human cell, about 500 bases suffer oxidative damage per day.<ref>{{cite journal | author = Shigenaga M, Gimeno C, Ames B | title = Urinary 8-hydroxy-2′-deoxyguanosine as a biological marker of ''in vivo'' oxidative DNA damage | url=http://www.pnas.org/cgi/reprint/86/24/9697 | journal = Proc Natl Acad Sci U S A | volume = 86 | issue = 24 | pages = 9697 – 701 | year = 1989 | id = PMID 2602371}}</ref><ref>{{cite journal | author = Cathcart R, Schwiers E, Saul R, Ames B | title = Thymine glycol and thymidine glycol in human and rat urine: a possible assay for oxidative DNA damage | url=http://www.pnas.org/cgi/reprint/81/18/5633.pdf | journal = Proc Natl Acad Sci U S A | volume = 81 | issue = 18 | pages = 5633 – 7 | year = 1984 | id = PMID 6592579}}</ref> Of these oxidative lesions, the most dangerous are double-strand breaks, as these lesions are difficult to repair and can produce [[point mutation]]s, [[Insertion (genetics)|insertions]] and [[Genetic deletion|deletions]] from the DNA sequence, as well as [[chromosomal translocation]]s.<ref>{{cite journal | author = Valerie K, Povirk L | title = Regulation and mechanisms of mammalian double-strand break repair | journal = Oncogene | volume = 22 | issue = 37 | pages = 5792 – 812 | year = 2003 | id = PMID 12947387}}</ref>

Many mutagens [[intercalation (chemistry)|intercalate]] into the space between two adjacent base pairs. Intercalators are mostly [[aromaticity|aromatic]] and planar molecules, and include [[ethidium]], [[daunomycin]], [[doxorubicin]] and [[thalidomide]]. In order for an intercalator to fit between base pairs, the bases must separate, distorting the DNA strands by unwinding of the double helix. These structural changes inhibit both transcription and DNA replication, causing toxicity and mutations. As a result, DNA intercalators are often [[carcinogen]]s, with [[benzopyrene|benzopyrene diol epoxide]], [[acridine]]s, [[aflatoxin]] and [[ethidium bromide]] being well-known examples.<ref>{{cite journal | author = Ferguson L, Denny W | title = The genetic toxicology of acridines | journal = Mutat Res | volume = 258 | issue = 2 | pages = 123 – 60 | year = 1991 | id = PMID 1881402}}</ref><ref>{{cite journal | author = Jeffrey A | title = DNA modification by chemical carcinogens | journal = Pharmacol Ther | volume = 28 | issue = 2 | pages = 237 – 72 | year = 1985 | id = PMID 3936066}}</ref><ref>{{cite journal |author=Stephens T, Bunde C, Fillmore B |title=Mechanism of action in thalidomide teratogenesis |journal=Biochem Pharmacol |volume=59 |issue=12 |pages=1489 – 99 |year=2000 |id=PMID 10799645}}</ref> Nevertheless, due to their properties of inhibiting DNA transcription and replication, they are also used in [[chemotherapy]] to inhibit rapidly-growing [[cancer]] cells.<ref>{{cite journal | author = Braña M, Cacho M, Gradillas A, de Pascual-Teresa B, Ramos A | title = Intercalators as anticancer drugs | journal = Curr Pharm Des | volume = 7 | issue = 17 | pages = 1745 – 80 | year = 2001 | id = PMID 11562309}}</ref>

==Overview of biological functions==
DNA usually occurs as linear [[chromosome]]s 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.<ref>{{cite journal | author = Venter J, ''et al.'' | title = The sequence of the human genome | journal = Science | volume = 291 | issue = 5507 | pages = 1304 – 51 | year = 2001 | id = PMID 11181995}}</ref> The information carried by DNA is held in the [[DNA sequence|sequence]] of pieces of DNA called [[gene]]s. 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 (biology)|translation]] which depends on the same interaction between RNA nucleotides. Alternatively, 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.
===Genome structure===
{{further|[[Cell nucleus]], [[Chromatin]], [[Chromosome]], [[Gene]], [[Non-coding DNA]]}}
Genomic DNA is located in the [[cell nucleus]] of eukaryotes, as well as small amounts in [[mitochondrion|mitochondria]] and [[chloroplast]]s. In prokaryotes, the DNA is held within an irregularly shaped body in the cytoplasm called the [[nucleoid]].<ref>{{cite journal | author = Thanbichler M, Wang S, Shapiro L | title = The bacterial nucleoid: a highly organized and dynamic structure | journal = J Cell Biochem | volume = 96 | issue = 3 | pages = 506 – 21 | year = 2005 | id = PMID 15988757}}</ref> The genetic information in a genome is held within genes. 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 sequence]]s such as [[promoter]]s and [[enhancer (genetics)|enhancers]], which control the expression 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 [[exon]]s, with over 50% of human DNA consisting of non-coding [[repeated sequence (DNA)|repetitive sequences]].<ref>{{cite journal | author = Wolfsberg T, McEntyre J, Schuler G | title = Guide to the draft human genome | journal = Nature | volume = 409 | issue = 6822 | pages = 824 – 6 | year = 2001 | id = PMID 11236998}}</ref> The reasons for the presence of so much [[noncoding DNA|non-coding 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]]."<ref>{{cite journal | author = Gregory T | title = The C-value enigma in plants and animals: a review of parallels and an appeal for partnership | url=http://aob.oxfordjournals.org/cgi/content/full/95/1/133 | journal = Ann Bot (Lond) | volume = 95 | issue = 1 | pages = 133 – 46 | year = 2005 | id = PMID 15596463}}</ref>
[[Image:RNA pol.jpg|thumb|left|300px|[[T7 RNA polymerase]] producing a mRNA (green) from a DNA template (red and blue). The enzyme is shown as a purple ribbon.<ref>Created from [http://www.rcsb.org/pdb/explore/explore.do?structureId=1MSW PDB 1MSW]</ref>]]
Some non-coding DNA sequences play structural roles in chromosomes. [[Telomere]]s and [[centromere]]s typically contain few genes, but are important for the function and stability of chromosomes.<ref name=Nugent/><ref>{{cite journal | author = Pidoux A, Allshire R | title = The role of heterochromatin in centromere function | url=http://www.journals.royalsoc.ac.uk/media/804t6y8vmh5utlb6ua5y/contributions/p/x/7/a/px7ahm740dq5ueuk.pdf | journal = Philos Trans R Soc Lond B Biol Sci | volume = 360 | issue = 1455 | pages = 569 – 79 | year = 2005 | id = PMID 15905142}}</ref> An abundant form of non-coding DNA in humans are [[pseudogene]]s, which are copies of genes that have been disabled by mutation.<ref>{{cite journal | author = Harrison P, Hegyi H, Balasubramanian S, Luscombe N, Bertone P, Echols N, Johnson T, Gerstein M | title = Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22 | url=http://www.genome.org/cgi/content/full/12/2/272 | journal = Genome Res | volume = 12 | issue = 2 | pages = 272 – 80 | year = 2002 | id = PMID 11827946}}</ref> These sequences are usually just molecular [[fossil]]s, although they can occasionally serve as raw genetic material for the creation of new genes through the process of [[gene duplication]] and [[divergent evolution|divergence]].<ref>{{cite journal | author = Harrison P, Gerstein M | title = Studying genomes through the aeons: protein families, pseudogenes and proteome evolution | journal = J Mol Biol | volume = 318 | issue = 5 | pages = 1155 – 74 | year = 2002 | id = PMID 12083509}}</ref>

===Transcription and translation===
{{further|[[Genetic code]], [[Transcription (genetics)]], [[Protein biosynthesis]]}}
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 a protein sequence. The relationship between the nucleotide sequences of genes and the [[amino acid|amino-acid]] sequences of proteins is determined by the rules of [[translation (genetics)|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 (<math>4^3</math> combinations). These encode the twenty [[list of standard amino acids|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.

[[Image:DNA replication.svg|thumb|450px|right|DNA replication. The double helix is unwound by a [[helicase]] and [[topoisomerase]]. Next, one [[DNA polymerase]] produces the [[leading strand]] copy. Another DNA polymerase binds to the [[lagging strand]]. This enzyme makes discontinuous segments (called [[Okazaki fragment]]s) before [[DNA ligase]] joins them together.]]

===Replication===
{{further|[[DNA 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.<ref>{{cite journal | author = Albà M | title = Replicative DNA polymerases | url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=11178285 | journal = Genome Biol | volume = 2 | issue = 1 | pages = REVIEWS3002 | year = 2001 | id = PMID 11178285}}</ref> 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===
<div class="thumb tleft" style="background-color: #f9f9f9; border: 1px solid #CCCCCC; margin:0.5em;">
{|border="0" width=260px border="0" cellpadding="0" cellspacing="0" style="font-size: 85%; border: 1px solid #CCCCCC; margin: 0.3em;"
|[[Image:Nucleosome 2.jpg|260px]]
|-
|[[Image:Nucleosome_(opposites_attracts).JPG|260px]]
|}
<div style="border: none; width:260px;"><div class="thumbcaption">Interaction of DNA with [[histone]]s (shown in white, top). These proteins' basic amino acids (below left, blue) bind to the acidic phosphate groups on DNA (below right, red).</div></div></div>

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 [[histone]]s, while in prokaryotes multiple types of proteins are involved.<ref>{{cite journal | author = Sandman K, Pereira S, Reeve J | title = Diversity of prokaryotic chromosomal proteins and the origin of the nucleosome | journal = Cell Mol Life Sci | volume = 54 | issue = 12 | pages = 1350 – 64 | year = 1998 | id = PMID 9893710}}</ref><ref>{{cite journal |author=Dame RT |title=The role of nucleoid-associated proteins in the organization and compaction of bacterial chromatin |journal=Mol. Microbiol. |volume=56 |issue=4 |pages=858-70 |year=2005 |pmid=15853876}}</ref> 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 bond]]s to the acidic sugar-phosphate backbone of the DNA, and are therefore largely independent of the base sequence.<ref>{{cite journal | author = Luger K, Mäder A, Richmond R, Sargent D, Richmond T | title = Crystal structure of the nucleosome core particle at 2.8 A resolution | journal = Nature | volume = 389 | issue = 6648 | pages = 251 – 60 | year = 1997 | id = PMID 9305837}}</ref> Chemical modifications of these basic amino acid residues include [[methylation]], [[phosphorylation]] and [[acetylation]].<ref>{{cite journal | author = Jenuwein T, Allis C | title = Translating the histone code | journal = Science | volume = 293 | issue = 5532 | pages = 1074 – 80 | year = 2001 | id = PMID 11498575}}</ref> These chemical changes alter the strength of the interaction between the DNA and the histones, making the DNA more or less accessible to [[transcription factor]]s and changing the rate of transcription.<ref>{{cite journal | author = Ito T | title = Nucleosome assembly and remodelling | journal = Curr Top Microbiol Immunol | volume = 274 | issue = | pages = 1 – 22 | year = | id = PMID 12596902}}</ref> Other non-specific DNA-binding proteins found in chromatin include the high-mobility group proteins, which bind preferentially to bent or distorted DNA.<ref>{{cite journal | author = Thomas J | title = HMG1 and 2: architectural DNA-binding proteins | journal = Biochem Soc Trans | volume = 29 | issue = Pt 4 | pages = 395 – 401 | year = 2001 | id = PMID 11497996}}</ref> These proteins are important in bending arrays of nucleosomes and arranging them into more complex chromatin structures.<ref>{{cite journal | author = Grosschedl R, Giese K, Pagel J | title = HMG domain proteins: architectural elements in the assembly of nucleoprotein structures | journal = Trends Genet | volume = 10 | issue = 3 | pages = 94–100 | year = 1994 | id = PMID 8178371}}</ref>

A distinct group of DNA-binding proteins are the single-stranded-DNA-binding proteins that specifically bind single-stranded DNA. In humans, replication protein A is the best-characterised member of this family and is essential for most processes where the double helix is separated, including DNA replication, recombination and DNA repair.<ref>{{cite journal | author = Iftode C, Daniely Y, Borowiec J | title = Replication protein A (RPA): the eukaryotic SSB | journal = Crit Rev Biochem Mol Biol | volume = 34 | issue = 3 | pages = 141 – 80 | year = 1999 | id = PMID 10473346}}</ref> These binding proteins seem to stabilize single-stranded DNA and protect it from forming [[stem loop]]s or being degraded by [[nuclease]]s.

[[Image:Lambda repressor 1LMB.png|thumb|right|185px|The lambda repressor [[helix-turn-helix]] transcription factor bound to its DNA target<ref>Created from [http://www.rcsb.org/pdb/explore/explore.do?structureId=1LMB PDB 1LMB]</ref>]]
In contrast, other proteins have evolved to specifically bind particular DNA sequences. The most intensively studied of these are the various classes of [[transcription factor]]s, which are proteins that regulate transcription. Each one of these proteins bind to one particular set of DNA sequences and thereby activates or inhibits the transcription of genes with these sequences close to their [[promoter]]s. 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.<ref>{{cite journal | author = Myers L, Kornberg R | title = Mediator of transcriptional regulation | journal = Annu Rev Biochem | volume = 69 | issue = | pages = 729 – 49 | year = | id = PMID 10966474}}</ref> Alternatively, transcription factors can bind [[enzyme]]s that modify the histones at the promoter; this will change the accessibility of the DNA template to the polymerase.<ref>{{cite journal | author = Spiegelman B, Heinrich R | title = Biological control through regulated transcriptional coactivators | journal = Cell | volume = 119 | issue = 2 | pages = 157-67 | year = 2004 | id = PMID 15479634}}</ref>

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.<ref>{{cite journal | author = Li Z, Van Calcar S, Qu C, Cavenee W, Zhang M, Ren B | title = A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells | url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12808131 | journal = Proc Natl Acad Sci U S A | volume = 100 | issue = 14 | pages = 8164 – 9 | year = 2003 | id = PMID 12808131}}</ref> Consequently, these proteins are often the targets of the [[signal transduction]] processes that mediate 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.<ref>{{cite journal | author = Pabo C, Sauer R | title = Protein-DNA recognition | journal = Annu Rev Biochem | volume = 53 | issue = | pages = 293 – 321 | year = | id = PMID 6236744}}</ref>

[[Image:EcoRV 1RVA.png|thumb|left|250px|The [[restriction enzyme]] [[EcoRV]] (green) in a complex with its substrate DNA<ref>Created from [http://www.rcsb.org/pdb/explore/explore.do?structureId=1RVA PDB 1RVA]</ref>]]

===DNA-modifying enzymes===
====Nucleases and ligases====
Nucleases are [[enzyme]]s that cut DNA strands by catalyzing the [[hydrolysis]] of the [[phosphodiester bond]]s. Nucleases that hydrolyse nucleotides from the ends of DNA strands are called [[exonuclease]]s, while [[endonuclease]]s cut within strands. The most frequently-used nucleases in [[molecular biology]] are the [[restriction enzyme|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]].<ref>{{cite journal | author = Bickle T, Krüger D | title = Biology of DNA restriction | url=http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=372918&blobtype=pdf | journal = Microbiol Rev | volume = 57 | issue = 2 | pages = 434 – 50 | year = 1993 | id = PMID 8336674}}</ref> In technology, these sequence-specific nucleases are used in [[clone (genetics)|molecular cloning]] and [[DNA fingerprinting]].

Enzymes called [[DNA ligase]]s can rejoin cut or broken DNA strands, using the energy from either [[adenosine triphosphate]] or [[nicotinamide adenine dinucleotide]].<ref name=Doherty>{{cite journal | author = Doherty A, Suh S | title = Structural and mechanistic conservation in DNA ligases. | url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=11058099 | journal = Nucleic Acids Res | volume = 28 | issue = 21 | pages = 4051 – 8 | year = 2000 | id = PMID 11058099}}</ref> 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]].<ref name=Doherty/>

====Topoisomerases and helicases====
[[Topoisomerase]]s are enzymes with both nuclease and ligase activity. These proteins change the amount of [[DNA supercoil|supercoiling]] in DNA. Some of these enzyme 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.<ref name=Champoux/> 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.<ref>{{cite journal | author = Schoeffler A, Berger J | title = Recent advances in understanding structure-function relationships in the type II topoisomerase mechanism | journal = Biochem Soc Trans | volume = 33 | issue = Pt 6 | pages = 1465 – 70 | year = 2005 | id = PMID 16246147}}</ref> Topoisomerases are required for many processes involving DNA, such as DNA replication and transcription.<ref name=Wang/>

[[Helicase]]s are proteins that are a type of [[molecular motor]]. They use the chemical energy in [[nucleoside triphosphate]]s, predominantly [[Adenosine triphosphate|ATP]], to break hydrogen bonds between bases and unwind the DNA double helix into single strands.<ref>{{cite journal | author = Tuteja N, Tuteja R | title = Unraveling DNA helicases. Motif, structure, mechanism and function | url=http://www.blackwell-synergy.com/links/doi/10.1111%2Fj.1432-1033.2004.04094.x | journal = Eur J Biochem | volume = 271 | issue = 10 | pages = 1849–63 | year = 2004 | id = PMID 15128295}}</ref> These enzymes are essential for most processes where enzymes need to access the DNA bases.

====Polymerases====
Polymerases are enzymes that synthesise polynucleotide chains from [[nucleoside triphosphate]]s. They function by adding nucleotides onto the 3′ [[hydroxyl|hydroxyl group]] of the previous nucleotide in the DNA strand. As a consequence, all polymerases work in a 5′ to 3′ direction.<ref name=Joyce>{{cite journal | author = Joyce C, Steitz T | title = Polymerase structures and function: variations on a theme? | url=http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=177480&blobtype=pdf | journal = J Bacteriol | volume = 177 | issue = 22 | pages = 6321 – 9 | year = 1995 | id = PMID 7592405}}</ref> In the [[active site]] of these enzymes, the nucleoside triphosphate substrate base-pairs to a single-stranded polynucleotide template: this allows polymerases to accurately synthesise the complementary strand of this template. Polymerases are classified according to the type of template that they use.

In [[DNA replication]], a DNA-dependent [[DNA polymerase]] makes a DNA copy of a DNA sequence. Accuracy is vital in this process, so many of these polymerases have a [[Proofreading#Proofreading in biology|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.<ref>{{cite journal | author = Hubscher U, Maga G, Spadari S | title = Eukaryotic DNA polymerases | journal = Annu Rev Biochem | volume = 71 | issue = | pages = 133 – 63 | year = | id = PMID 12045093}}</ref> In most organisms DNA polymerases function in a large complex called the [[replisome]] that contains multiple accessory subunits, such as the [[DNA clamp]] or [[helicase]]s.<ref>{{cite journal | author = Johnson A, O'Donnell M | title = Cellular DNA replicases: components and dynamics at the replication fork | journal = Annu Rev Biochem | volume = 74 | issue = | pages = 283 – 315 | year = | id = PMID 15952889}}</ref>

RNA-dependent DNA polymerases are a specialised class of polymerases that copy the sequence of an RNA strand into DNA. They include [[reverse transcriptase]], which is a [[virus|viral]] enzyme involved in the infection of cells by [[retrovirus]]es, and [[telomerase]], which is required for the replication of [[telomere]]s.<ref>{{cite journal | author = Tarrago-Litvak L, Andréola M, Nevinsky G, Sarih-Cottin L, Litvak S | title = The reverse transcriptase of HIV-1: from enzymology to therapeutic intervention | url=http://www.fasebj.org/cgi/reprint/8/8/497 | journal = FASEB J | volume = 8 | issue = 8 | pages = 497–503 | year = 1994 | id = PMID 7514143}}</ref><ref name=Greider/> Telomerase is an unusual polymerase because it contains its own RNA template as part of its structure.<ref name=Nugent/>

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 (genetics)|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.<ref>{{cite journal | author = Martinez E | title = Multi-protein complexes in eukaryotic gene transcription | journal = Plant Mol Biol | volume = 50 | issue = 6 | pages = 925 – 47 | year = 2002 | id = PMID 12516863}}</ref>

==Genetic recombination==
<div class="thumb tright" style="background-color: #f9f9f9; border: 1px solid #CCCCCC; margin:0.5em;">
{|border="0" width=250px border="0" cellpadding="0" cellspacing="0" style="font-size: 85%; border: 1px solid #CCCCCC; margin: 0.3em;"
|[[Image:Holliday Junction cropped.png|250px]]
|-
|[[Image:Holliday junction coloured.png|250px]]
|}
<div style="border: none; width:250px;"><div class="thumbcaption">Structure of the [[Holliday junction]] intermediate in [[genetic recombination]]. The four separate DNA strands are coloured red, blue, green and yellow.<ref>Created from [http://www.rcsb.org/pdb/explore/explore.do?structureId=1M6G PDB 1M6G]</ref></div></div></div>
{{further|[[Genetic recombination]]}}
[[Image:Chromosomal Recombination.svg|thumb|250px|left|Recombination involves the breakage and rejoining of two chromosomes (M and F) to produce two re-arranged chromosomes (C1 and C2).]]

A DNA helix does not usually interact with other segments of DNA, and in human cells the different chromosomes even occupy separate areas in the nucleus called "chromosome territories".<ref>{{cite journal | author = Cremer T, Cremer C | title = Chromosome territories, nuclear architecture and gene regulation in mammalian cells | journal = Nat Rev Genet | volume = 2 | issue = 4 | pages = 292–301 | year = 2001 | id = PMID 11283701}}</ref> 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 [[genetic recombination|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.<ref>{{cite journal | author = Pál C, Papp B, Lercher M | title = An integrated view of protein evolution | journal = Nat Rev Genet | volume = 7 | issue = 5 | pages = 337 – 48 | year = 2006 | id = PMID 16619049}}</ref> Genetic recombination can also be involved in DNA repair, particularly in the cell's response to double-strand breaks.<ref>{{cite journal | author = O'Driscoll M, Jeggo P | title = The role of double-strand break repair - insights from human genetics | journal = Nat Rev Genet | volume = 7 | issue = 1 | pages = 45 – 54 | year = 2006 | id = PMID 16369571}}</ref>

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 translocation]]s and genetic abnormalities. The recombination reaction is catalyzed by enzymes known as ''recombinases'', such as [[RAD51]].<ref>{{cite journal |author=Vispé S, Defais M |title=Mammalian Rad51 protein: a RecA homologue with pleiotropic functions |journal=Biochimie |volume=79 |issue=9-10 |pages=587-92 |year=1997 |pmid=9466696}}</ref> The first step in recombination is a double-stranded break either caused by an [[endonuclease]] or damage to the DNA.<ref>{{cite journal |author=Neale MJ, Keeney S |title=Clarifying the mechanics of DNA strand exchange in meiotic recombination |journal=Nature |volume=442 |issue=7099 |pages=153-8 |year=2006 |pmid=16838012}}</ref> 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.<ref>{{cite journal | author = Dickman M, Ingleston S, Sedelnikova S, Rafferty J, Lloyd R, Grasby J, Hornby D | title = The RuvABC resolvasome | journal = Eur J Biochem | volume = 269 | issue = 22 | pages = 5492 – 501 | year = 2002 | id = PMID 12423347}}</ref>

==Evolution of DNA-based metabolism==
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 [[Timeline of evolution|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.<ref name=Joyce>{{cite journal |author=Joyce G |title=The antiquity of RNA-based evolution |journal=Nature |volume=418 |issue=6894 |pages=214 – 21 |year=2002 |id=PMID 12110897}}</ref><ref>{{cite journal |author=Orgel L |title=Prebiotic chemistry and the origin of the RNA world | url=http://www.crbmb.com/cgi/reprint/39/2/99.pdf |journal=Crit Rev Biochem Mol Biol |volume=39 |issue=2 |pages=99 – 123 |year= |id=PMID 15217990}}</ref> 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 [[ribozyme]]s.<ref>{{cite journal |author=Davenport R |title=Ribozymes. Making copies in the RNA world |journal=Science |volume=292 |issue=5520 |pages=1278 |year=2001 |pmid=11360970}}</ref> This ancient [[RNA world hypothesis|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 unique 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.<ref>{{cite journal |author=Szathmáry E |title=What is the optimum size for the genetic alphabet? |url=http://www.pnas.org/cgi/reprint/89/7/2614.pdf |journal=Proc Natl Acad Sci U S A |volume=89 |issue=7 |pages=2614 – 8 |year=1992 |pmid=1372984}}</ref>

Unfortunately, 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.<ref>{{cite journal |author=Lindahl T |title=Instability and decay of the primary structure of DNA |journal=Nature |volume=362 |issue=6422 |pages=709 – 15 |year=1993 |id=PMID 8469282}}</ref> Although 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,<ref>{{cite journal |author=Vreeland R, Rosenzweig W, Powers D |title=Isolation of a 250 million-year-old halotolerant bacterium from a primary salt crystal |journal=Nature |volume=407 |issue=6806 |pages=897 – 900 |year=2000 |id=PMID 11057666}}</ref> these claims are controversial and have been disputed.<ref>{{cite journal |author=Hebsgaard M, Phillips M, Willerslev E |title=Geologically ancient DNA: fact or artefact? |journal=Trends Microbiol |volume=13 |issue=5 |pages=212 – 20 |year=2005 |id=PMID 15866038}}</ref><ref>{{cite journal |author=Nickle D, Learn G, Rain M, Mullins J, Mittler J |title=Curiously modern DNA for a "250 million-year-old" bacterium |journal=J Mol Evol |volume=54 |issue=1 |pages=134 – 7 |year=2002 |id=PMID 11734907}}</ref>

==Uses in technology==
===Genetic engineering===
{{further|[[Molecular biology]] and [[genetic engineering]]}}

Modern [[biology]] and [[biochemistry]] make intensive use of recombinant DNA technology. [[Recombinant DNA]] is a man-made DNA sequence that has been assembled from other DNA sequences. They can be [[transformation (genetics)|transformed]] into organisms in the form of [[plasmids]] or in the appropriate format, by using a [[viral vector]].<ref>{{cite journal |author=Goff SP, Berg P |title=Construction of hybrid viruses containing SV40 and lambda phage DNA segments and their propagation in cultured monkey cells |journal=Cell |volume=9 |issue=4 PT 2 |pages=695–705 |year=1976 |pmid=189942}}</ref> The [[genetic engineering|genetically modified]] organisms produced can be used to produce products such as recombinant [[protein]]s, used in medical research,<ref>{{cite journal |author=Houdebine L |title=Transgenic animal models in biomedical research |journal=Methods Mol Biol |volume=360 |issue= |pages=163 – 202 |year= |pmid=17172731}}</ref> or be grown in [[agriculture]].<ref>{{cite journal |author=Daniell H, Dhingra A |title=Multigene engineering: dawn of an exciting new era in biotechnology |journal=Curr Opin Biotechnol |volume=13 |issue=2 |pages=136 – 41 |year=2002 |pmid=11950565}}</ref><ref>{{cite journal |author=Job D |title=Plant biotechnology in agriculture |journal=Biochimie |volume=84 |issue=11 |pages=1105 – 10 |year=2002 |pmid=12595138}}</ref>

===Forensics ===
{{further|[[Genetic fingerprinting]]}}

[[Forensic science|Forensic scientists]] can use DNA in [[blood]], [[semen]], [[skin]], [[saliva]] or [[hair]] at a crime scene to identify a perpetrator. This process is called [[genetic fingerprinting]], or more accurately, DNA profiling. In DNA profiling, the lengths of variable sections of repetitive DNA, such as [[short tandem repeat]]s and [[minisatellite]]s, are compared between people. This method is usually an extremely reliable technique for identifying a criminal.<ref>{{cite journal | author = Collins A, Morton N | title = Likelihood ratios for DNA identification | url=http://www.pnas.org/cgi/reprint/91/13/6007.pdf | journal = Proc Natl Acad Sci U S A | volume = 91 | issue = 13 | pages = 6007 – 11 | year = 1994 | id = PMID 8016106}}</ref> However, identification can be complicated if the scene is contaminated with DNA from several people.<ref>{{cite journal | author = Weir B, Triggs C, Starling L, Stowell L, Walsh K, Buckleton J | title = Interpreting DNA mixtures | journal = J Forensic Sci | volume = 42 | issue = 2 | pages = 213 – 22 | year = 1997 | id = PMID 9068179}}</ref> DNA profiling was developed in 1984 by British geneticist Sir [[Alec Jeffreys]],<ref>{{cite journal | author = Jeffreys A, Wilson V, Thein S | title = Individual-specific 'fingerprints' of human DNA. | journal = Nature | volume = 316 | issue = 6023 | pages = 76 – 9 | year = | id = PMID 2989708}}</ref> and first used in forensic science to convict Colin Pitchfork in the 1988 [[Enderby murders]] case.<ref>[http://www.forensic.gov.uk/forensic_t/inside/news/list_casefiles.php?case=1 Colin Pitchfork — first murder conviction on DNA evidence also clears the prime suspect] Forensic Science Service Accessed 23 Dec 2006</ref> 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.<ref>{{cite web |url=http://massfatality.dna.gov/Introduction/ |title=DNA Identification in Mass Fatality Incidents |date=September 2006 |publisher=National Institute of Justice}}</ref>

===Bioinformatics===
{{further|[[Bioinformatics]]}}
[[Bioinformatics]] involves the manipulation, searching, and [[data mining]] of 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 algorithm]]s, [[machine learning]] and [[database theory]].<ref>Baldi, Pierre. Brunak, Soren. ''Bioinformatics: The Machine Learning Approach'' MIT Press (2001) ISBN 978-0-262-02506-5</ref> 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.<ref>Gusfield, Dan. ''Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology''. Cambridge University Press, 15 January 1997. ISBN 978-0-521-58519-4.</ref> In other applications such as [[text editor]]s, even simple algorithms for this problem usually suffice, but DNA sequences cause these algorithms to exhibit near-worst-case behaviour due to their small number of distinct characters. The related problem of [[sequence alignment]] aims to identify [[homology (biology)|homologous]] sequences and locate the specific [[mutation]]s that make them distinct. These techniques, especially [[multiple sequence alignment]], are used in studying [[phylogenetics|phylogenetic]] relationships and protein function.<ref>{{cite journal | author = Sjölander K | title = Phylogenomic inference of protein molecular function: advances and challenges | url=http://bioinformatics.oxfordjournals.org/cgi/reprint/20/2/170 | journal = Bioinformatics | volume = 20 | issue = 2 | pages = 170-9 | year = 2004 | id = PMID 14734307}}</ref> Data sets representing entire genomes' worth of DNA sequences, such as those produced by the [[Human Genome Project]], are difficult to use without annotations, which label 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 product]]s in an organism even before they have been isolated experimentally.<ref name="Mount">{{cite book|author = Mount DM | title = Bioinformatics: Sequence and Genome Analysis | edition = 2 | publisher = Cold Spring Harbor Laboratory Press | location | Cold Spring Harbor, NY | date = 2004 | isbn = 0879697121}}</ref>

===DNA and computation ===
{{further|[[DNA computing]]}}
DNA was first used in computing to solve a small version of the directed [[Hamiltonian path problem]], an [[NP-complete]] problem.<ref>{{cite journal | author = Adleman L | title = Molecular computation of solutions to combinatorial problems | journal = Science | volume = 266 | issue = 5187 | pages = 1021 – 4 | year = 1994 | id = PMID 7973651}}</ref> [[DNA computing]] is advantageous over electronic computers in power use, space use, and efficiency, due to its ability to compute in a highly parallel fashion (see [[parallel computing]]). A number of other problems, including simulation of various [[abstract machine]]s, the [[boolean satisfiability problem]], and the bounded version of the [[travelling salesman problem]], have since been analysed using DNA computing.<ref>{{cite journal | author = Parker J | title = Computing with DNA. | url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12524509 | journal = EMBO Rep | volume = 4 | issue = 1 | pages = 7 – 10 | year = 2003 | id = PMID 12524509}}</ref> Due to its compactness, DNA also has a theoretical role in [[cryptography]], where in particular it allows unbreakable [[one-time pad]]s to be efficiently constructed and used.<ref>Ashish Gehani, Thomas LaBean and John Reif. [http://citeseer.ist.psu.edu/gehani99dnabased.html DNA-Based Cryptography].
Proceedings of the 5th DIMACS Workshop on DNA Based Computers, Cambridge, MA, USA, 14 – 15 June 1999.</ref>

===History and anthropology===
{{further|[[Phylogenetics]] and [[Genetic genealogy]]}}
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]].<ref>{{cite journal | author = Wray G | title = Dating branches on the tree of life using DNA | url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=11806830 | journal = Genome Biol | volume = 3 | issue = 1 | pages = REVIEWS0001 | year = 2002 | id = PMID 11806830}}</ref> This field of [[phylogenetics]] is a powerful tool in [[evolutionary biology]]. If DNA sequences within a species are compared, [[population genetics|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]].<ref>''Lost Tribes of Israel'', [[NOVA (TV series)|NOVA]], PBS airdate: 22 February 2000. Transcript available from [http://www.pbs.org/wgbh/nova/transcripts/2706israel.html PBS.org,] (last accessed on 4 March 2006)</ref><ref>Kleiman, Yaakov. [http://www.aish.com/societywork/sciencenature/the_cohanim_-_dna_connection.asp "The Cohanim/DNA Connection: The fascinating story of how DNA studies confirm an ancient biblical tradition".] ''aish.com'' (January 13, 2000). Accessed 4 March 2006.</ref>

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.<ref>Bhattacharya, Shaoni. [http://www.newscientist.com/article.ns?id=dn4908 "Killer convicted thanks to relative's DNA".] ''newscientist.com'' (20 April 2004). Accessed 22 Dec 06</ref>

==History==
[[Image:Francis Crick.png|thumb|125px|right|[[Francis Crick]]]]
[[Image:JamesDWatson.jpg|thumb|125px|right|[[James D. Watson|James Watson]]]]

{{further|[[History of molecular biology]]}}
DNA was first isolated by the [[Switzerland|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".<ref>{{cite journal | author = Dahm R | title = Friedrich Miescher and the discovery of DNA | journal = Dev Biol | volume = 278 | issue = 2 | pages = 274 – 88 | year = 2005 | id = PMID 15680349}}</ref> In 1929 this discovery was followed by [[Phoebus Levene]]'s identification of the base, sugar and phosphate nucleotide unit.<ref>{{cite journal | author = Levene P, | title = The structure of yeast nucleic acid | url=http://www.jbc.org/cgi/reprint/40/2/415 | journal = J Biol Chem | volume = 40 | issue = 2 | pages = 415 – 24 | year = 1919}}</ref> 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.<ref>{{cite journal | author =Astbury W, | title = Nucleic acid | journal = Symp. SOC. Exp. Bbl | volume = 1 | issue = 66 | year = 1947}}</ref>

In 1943, [[Oswald Theodore Avery]] discovered that [[trait (biology)|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. Avery identified DNA as this [[transforming principle]].<ref>{{cite journal | author = Avery O, MacLeod C, McCarty M | title = Studies on the chemical nature of the substance inducing transformation of pneumococcal types. Inductions of transformation by a desoxyribonucleic acid fraction isolated from pneumococcus type III | url=http://www.jem.org/cgi/reprint/149/2/297 | journal = J Exp Med | volume = 79 | issue = 2 | pages = 137 – 158 | year = 1944 }}</ref> DNA's role in [[heredity]] was confirmed in 1953, when [[Alfred Hershey]] and [[Martha Chase]] in the [[Hershey-Chase experiment]] showed that DNA is the [[genetic material]] of the [[T2 phage]].<ref>{{cite journal | author = Hershey A, Chase M | title = Independent functions of viral protein and nucleic acid in growth of bacteriophage | url=http://www.jgp.org/cgi/reprint/36/1/39.pdf | journal = J Gen Physiol | volume = 36 | issue = 1 | pages = 39 – 56 | year = 1952 | id = PMID 12981234}}</ref>

In 1953, based on [[Photo 51|X-ray diffraction images]]<ref name=FWPUB>Watson J.D. and Crick F.H.C. [http://www.nature.com/nature/dna50/watsoncrick.pdf "A Structure for Deoxyribose Nucleic Acid".] (PDF) ''Nature'' 171, 737 – 738 (1953). Accessed 13 Feb 2007.</ref> taken by [[Rosalind Franklin]] and the information that the bases were paired, [[James D. Watson]] and [[Francis Crick]] suggested<ref name=FWPUB/> what is now accepted as the first accurate model of [[Molecular structure of Nucleic Acids|DNA structure]] in the journal [[Nature (journal)|''Nature'']].<ref name=Watson/> Experimental evidence for Watson and Crick's model were published in a series of five articles in the same issue of ''Nature''.<ref name=NatureDNA50>Nature Archives [http://www.nature.com/nature/dna50/archive.html Double Helix of DNA: 50 Years]</ref> Of these, [[Rosalind Franklin|Franklin]] and [[Raymond Gosling]]'s paper<ref name=NatFranGos>Molecular Configuration in Sodium Thymonucleate. Franklin R. and Gosling R.G.Nature 171, 740 – 741 (1953)[http://www.nature.com/nature/dna50/franklingosling.pdf Nature Archives Full Text (PDF)]</ref> saw the publication of the X-ray diffraction image<ref>[http://osulibrary.oregonstate.edu/specialcollections/coll/pauling/dna/pictures/franklin-typeBphoto.html Original X-ray diffraction image]</ref>, which was key in Watson and Crick interpretation, as well as another article, co-authored by [[Maurice Wilkins]] and his colleagues.<ref name=NatWilk>Molecular Structure of Deoxypentose Nucleic Acids. Wilkins M.H.F., A.R. Stokes A.R. & Wilson, H.R. Nature 171, 738 – 740 (1953)[http://www.nature.com/nature/dna50/wilkins.pdf Nature Archives (PDF)]</ref> Franklin and Gosling's subsequent paper identified the distinctions between the A and B structures of the double helix in DNA.<ref name=NatFrankGos2>Evidence for 2-Chain Helix in Crystalline Structure of Sodium Deoxyribonucleate. Franklin R. and Gosling R.G. Nature 172, 156 – 157 (1953)[http://www.nature.com/nature/dna50/franklingosling2.pdf Nature Archives, full text (PDF)]</ref> In 1962 Watson, Crick, and [[Maurice Wilkins]] jointly received the [[Nobel Prize]] in [[Nobel Prize in Physiology or Medicine|Physiology or Medicine]] (Franklin didn't share the prize with them since she had died earlier).<ref>[http://nobelprize.org/nobel_prizes/medicine/laureates/1962/ The Nobel Prize in Physiology or Medicine 1962] Nobelprize .org Accessed 22 Dec 06</ref>

In an influential presentation in 1957, Crick laid out the [[central dogma of molecular biology|"Central Dogma" of molecular biology]], which foretold the relationship between DNA, RNA, and proteins, and articulated the "adaptor hypothesis".<ref>Crick, F.H.C. [http://genome.wellcome.ac.uk/assets/wtx030893.pdf On degenerate templates and the adaptor hypothesis (PDF).] genome.wellcome.ac.uk (Lecture, 1955). Accessed 22 Dec 2006</ref> Final confirmation of the replication mechanism that was implied by the double-helical structure followed in 1958 through the [[Meselson-Stahl experiment]].<ref>{{cite journal | author = Meselson M, Stahl F | title = The replication of DNA in ''Escherichia coli'' | journal = Proc Natl Acad Sci U S A | volume = 44 | issue = 7 | pages = 671 – 82 | year = 1958 | id = PMID 16590258}}</ref> 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]].<ref>[http://nobelprize.org/nobel_prizes/medicine/laureates/1968/ The Nobel Prize in Physiology or Medicine 1968] Nobelprize.org Accessed 22 Dec 06</ref> These findings represent the birth of [[molecular biology]].

==See also==
* [[Genetic disorder]]
* [[Plasmid]]
* [[DNA sequencing]]
* [[Southern blot]]
* [[DNA microarray]]
* [[Polymerase chain reaction]]
* [[Phosphoramidite]]

==References==
{{reflist|2}}

==Further reading==
* Clayton, Julie. (Ed.). ''50 Years of DNA'', Palgrave MacMillan Press, 2003. ISBN 978-1-40-391479-8
* Judson, Horace Freeland. ''The Eighth Day of Creation: Makers of the Revolution in Biology'', Cold Spring Harbor Laboratory Press, 1996. ISBN 978-0-87-969478-4
* [[Robert Olby|Olby, Robert]]. ''The Path to The Double Helix: Discovery of DNA'', first published in October 1974 by MacMillan, with foreword by Francis Crick; ISBN 978-0-48-668117-7; the definitive DNA textbook, revised in 1994, with a 9 page postscript.
* [[Matt Ridley|Ridley, Matt]]. ''Francis Crick: Discoverer of the Genetic Code (Eminent Lives)'' HarperCollins Publishers; 192 pp, ISBN 978-0-06-082333-7 2006
* Rose, Steven. ''The Chemistry of Life'', Penguin, ISBN 978-0-14-027273-4.
* Watson, James D. and Francis H.C. Crick. [http://www.nature.com/nature/dna50/watsoncrick.pdf A structure for Deoxyribose Nucleic Acid] (PDF). ''[[Nature (journal)|Nature]]'' 171, 737 – 738, [[25 April]] [[1953]].
* Watson, James D. ''DNA: The Secret of Life'' ISBN 978-0-375-41546-3.
* Watson, James D. ''[[The Double Helix|The Double Helix: A Personal Account of the Discovery of the Structure of DNA (Norton Critical Editions)]]''. ISBN 978-0-393-95075-5
* Watson, James D. "Avoid boring people and other lessons from a life in science" New York: Random House. ISBN 978-0-375-421844 (0-375-41284-0)366pp 2007
* Calladine, Chris R.; Drew, Horace R.; Luisi, Ben F. and Travers, Andrew A. ''Understanding DNA'', Elsevier Academic Press, 2003. ISBN 978-0-12155089-9

==DVD==
* ''[http://www.windfallfilms.com/html/productions/DNA.htm DNA — The Story of the Pioneers who Changed the World,]'' Windfall Films Production for [http://www.channel4.com/science/microsites/D/dna_thestoryoflife/ Channel Four Television] & [http://www.pbs.org/wnet/dna/ PBS Thirteen-WNET] (2003), PAL [http://www.ncbe.reading.ac.uk/DNA50/documentaries.html], NTSC [http://www.shoppbs.org/searchHandler/index.jsp?searchId=20744726972&keywords=dna&view=all PBS Shop]
* ''[http://www.dnai.org/feature/dnai_dvd.html DNA interactive]'', [http://www.scienceinschool.org/2006/issue1/dnainteractive/], PAL [http://www.ncbe.reading.ac.uk/DNA50/interactivepal.html], NTSC [http://www.ncbe.reading.ac.uk/DNA50/interactiventsc.html]
* ''[http://www.carolina.com/biotech/DNA_secret.asp DNA: The Secret of Life]'' Carolina Biological
* ''[http://shop.wgbh.org/webapp/wcs/stores/servlet/ProductDisplay?productId=51808&storeId=11051&catalogId=10051&langId=-1 DNA — Secret of Photo 51]'' Rosalind Franklin — NOVA documentary (NTSC — Region 1)
* ''[http://shop.wgbh.org/webapp/wcs/stores/servlet/ProductDisplay?productId=18308&storeId=11051&catalogId=10051&langId=-1 Cracking the Code of Life]'' NOVA documentary (NTSC — All Regions)


==External links==
==External links==
{{portalpar|Molecular and Cellular Biology|Portal.svg}}
{{Spoken Wikipedia|dna.ogg|2007-02-12}}
{{commonscat|DNA}}
* [http://orpheus.ucsd.edu/speccoll/testing/html/mss0660a.html#abstract] Crick's personal papers at Mandeville Special Collections Library, Geisel Library, University of California, San Diego
* [http://www.dnai.org/ DNA Interactive] (requires [[Adobe Flash]])
* [http://www.dnaftb.org/dnaftb/ DNA from the beginning]
* [http://www.ncbe.reading.ac.uk/DNA50/ Double Helix 1953 – 2003] National Centre for Biotechnology Education
* [http://www.nature.com/nature/dna50/archive.html Double helix: 50 years of DNA], ''[[Nature (journal)|Nature]]''
* [http://mason.gmu.edu/~emoody/rfranklin.html Rosalind Franklin's contributions to the study of DNA]
* [http://www.genome.gov/10506367 U.S. National DNA Day] — watch videos and participate in real-time chat with top scientists
* [http://www.genome.gov/10506718 Genetic Education Modules for Teachers] — ''DNA from the Beginning'' Study Guide
* [http://www.bbc.co.uk/bbcfour/audiointerviews/profilepages/crickwatson1.shtml Listen to Francis Crick and James Watson talking on the BBC in 1962, 1972, and 1974]
* {{PDB Molecule of the Month|pdb23_1}}
* [http://www.fidelitysystems.com/Unlinked_DNA.html DNA under electron microscope]
* {{dmoz|Science/Biology/Biochemistry_and_Molecular_Biology/Biomolecules/Nucleic_Acids/DNA/|DNA}}
* [http://dnawiz.com/ DNA Articles] — articles and information collected from various sources
* {{McGrawHillAnimation|genetics|Dna%20Replication}}
* [http://biostudio.com/c_%20education%20mac.htm DNA coiling to form chromosomes]
* [http://pipe.scs.fsu.edu/displar.html DISPLAR: DNA binding site prediction on protein]
* [http://www.dnalc.org/ Dolan DNA Learning Center]
* [[Robert Olby|Olby, R.]] (2003) [http://chem-faculty.ucsd.edu/joseph/CHEM13/DNA1.pdf "Quiet debut for the double helix"] ''Nature'' '''421''' (January 23): 402 – 405.
*[http://www.blackwellpublishing.com/trun/artwork/Animations/cloningexp/cloningexp.html Basic animated guide to DNA cloning]
* [http://nobelprize.org/educational_games/medicine/dna_double_helix/ DNA the Double Helix Game] From the official Nobel Prize web site

{{Nucleic acids}}
{{featured article}}

<!--Categories-->
[[Category:DNA| ]]
[[Category:Genetics]]


*[http://cartelfr.louvre.fr/cartelfr/visite?srv=rs_display_res&critere=jean+baptiste+carpeaux&operator=AND&nbToDisplay=5&langue=fr A page on the official Louvre site giving access to some of Carpeaux's works (French language only)]
{{Link FA|de}}
*[http://www.insecula.com/contact/A005511_oeuvre_1.html A page from insecula.com listing more views of Carpeaux's works (also in French;] it may be necessary to close an advertising window to view this page)
{{Link FA|nl}}
*[http://www.studiolo.org/MMA-Ugolino/Ugolino.htm A page analysing Carpeaux's ''Ugolino'', with numerous illustrations]


[[Category:French sculptors|Carpeaux, Jean-Baptiste]]
<!--Interwiki-->
[[Category:1827 births|Carpeaux, Jean-Baptiste]]
[[Category:1875 deaths|Carpeaux, Jean-Baptiste]]


[[de:Jean-Baptiste Carpeaux]]
[[ar:حمض نووي ريبي منقوص الأكسجين]]
[[fr:Jean-Baptiste Carpeaux]]
[[az:Dezoksiribonuklein turşusu]]
[[nl:Jean-Baptiste Carpeaux]]
[[zh-min-nan:DNA]]
[[pl:Jean-Baptiste Carpeaux]]
[[bs:Dezoksiribonukleinska kiselina]]
[[pt:Jean-Baptiste Carpeaux]]
[[bg:ДНК]]
[[zh:让-巴蒂斯·卡尔波]]
[[ca:Àcid desoxiribonucleic]]
[[cs:DNA]]
[[cy:DNA]]
[[da:Dna]]
[[pdc:DNA]]
[[de:Desoxyribonukleinsäure]]
[[et:Desoksüribonukleiinhape]]
[[el:DNA]]
[[es:ADN]]
[[eo:DNA]]
[[eu:Azido desoxirribonukleiko]]
[[fa:دی‌ان‌ای]]
[[fo:DNA]]
[[fr:Acide désoxyribonucléique]]
[[ga:ADN]]
[[gl:ADN]]
[[ko:DNA]]
[[hr:Deoksiribonukleinska kiselina]]
[[id:Asam deoksiribonukleat]]
[[is:DKS]]
[[it:DNA]]
[[he:DNA]]
[[pam:DNA]]
[[ka:დეზოქსირიბონუკლეინის მჟავა]]
[[ht:ADN]]
[[la:Acidum deoxyribonucleinicum]]
[[lv:Dezoksiribonukleīnskābe]]
[[lt:Deoksiribonukleorūgštis]]
[[hu:DNS (biológia)]]
[[mk:ДНК]]
[[ms:DNA]]
[[nl:DNA]]
[[ja:デオキシリボ核酸]]
[[no:DNA]]
[[nn:Deoksyribonukleinsyre]]
[[nov:DNA]]
[[oc:Acid desoxiribonucleïc]]
[[pl:Kwas deoksyrybonukleinowy]]
[[pt:DNA]]
[[ro:ADN]]
[[ru:Дезоксирибонуклеиновая кислота]]
[[sq:ADN]]
[[simple:DNA]]
[[sk:Deoxyribonukleová kyselina]]
[[sl:Deoksiribonukleinska kislina]]
[[sr:ДНК]]
[[sh:DNK]]
[[su:DNA]]
[[fi:DNA]]
[[sv:DNA]]
[[tl:DNA]]
[[ta:ஆக்சிஜனற்ற ரைபோ கரு அமிலம்]]
[[th:ดีเอ็นเอ]]
[[vi:DNA]]
[[tr:DNA]]
[[uk:ДНК]]
[[ur:ڈی این اے]]
[[yi:די ען עי]]
[[zh:脱氧核糖核酸]]

Revision as of 01:07, 19 June 2007

Jean-Baptiste Carpeaux's marble sculpture 'Ugolino and his Sons', Metropolitan Museum of Art
La Danse (The Dance), Opera Garnier in Paris
Wikimedia Commons has media related to Jean-Baptiste Carpeaux.

Jean-Baptiste Carpeaux (May 11, 1827, Valenciennes –October 12, 1875, Courbevoie) was a French sculptor and painter. His early studies were under François Rude. Carpeaux won the Prix de Rome in 1854, and moving to Rome to find inspiration, he there studied the works of Michelangelo, Donatello and Verrocchio. Staying in Rome from 1854 to 1861, he obtained a taste for movement and spontaneity, which he joined with the great principles of baroque art. In 1861 he made a bust of Princess Mathilde, and this later brought him several commissions from Napoleon III. He worked at the pavilion of Flora, and the Opéra Garnier. His group La Danse (the Dance, 1869), situated on the right side of the façade, was criticised as an offence to common decency.

He never managed to finish his last work, the famous Fountain of the Four Parts of the Earth, on the Place Camille Jullian. He did finish the terrestrial globe, supported by the four figures of Asia, Europe, America and Africa, and it was Emmanuel Frémiet who completed the work by adding the eight leaping horses, the tortoises and the dolphins of the basin.

Sculptures by Carpeaux

Neapolitan Fisherboy

Carpeaux submitted a plaster version of Pêcheur napolitain à la coquille, the Neapolitan Fisherboy, to the French Academy while a student in Rome. He carved the marble version several years later, showing it in the Salon exhibition of 1863. It was purchased for Napoleon III's empress, Eugènie. The statue of the young smiling boy was very popular, and Carpeaux created a number of reproductions and variations in marble and bronze. There is a copy, for instance, in the Samuel H. Kress Collection in the National Gallery of Art in Washington D.C.

Some years later, he carved the Girl with a Shell, a very similar study.

Carpeaux sought real life subjects in the streets and broke with the classical tradition. The Neapolitan Fisherboy's body is carved in intimate detail and shows an intricately balanced pose. Carpeaux claimed that he based the Neapolitan Fisherboy on a boy he had seen during a trip to Naples.

External links

Retrieved from "https://en.wikipedia.org/w/index.php?title=DNA&oldid=139104583"