이 페이지는 현재 비활성 상태이며 기록 참조용으로 보존되어 있다. 그 페이지는 더 이상 관련성이 없거나 그 목적에 대한 합의가 불분명해졌다.토론을 되살리려면 마을 펌프와 같은 포럼을 통해 보다 폭넓은 의견을 구하십시오.

지름길 WP:WML

위키 마크업 언어(WKML)는 닉 이렐란이 시작한 단체로, 위키에 XML 기반 포맷을 만들어 이들이 제시하는 정보가 매시업 등 제3자 프로그램에서 사용될 수 있도록 하려고 한다.

이 형식은 위키피디스가 RSS 피드와 유사하게 결합될 수 있는 방식으로 생성되어야 한다.

형식 및 유용한 특성 정의 요청

XML 경험이 있는 모든 편집자는 위키피디아가 만든 콘텐츠(예: Infoboxes에 국한되지 않고 제목이 포맷되어야 함)에 대해 의견을 개진하는 것을 환영한다.

어떤 기사의 광범위하게 정의된 구조는 무엇인가?

기사의 모든 공통부분은 프로그래머가 쉽게 작업할 수 있도록 각별한 주의를 기울여야 한다.예를 들어, 역사 부분은 아마 많이 쓰일 것이다.

• 제목
• 섹션
• 분류
• 정보 상자(?)

해당 기사의 광범위하게 정의된 속성은 무엇인가?

WKML에 기사의 속성이 포함되어야 하는 것은 무엇인가?

• 만든 날짜
• 업데이트

토론 페이지 형식 정의 요청

XML 경험이 있는 모든 편집자는 토론 페이지가 어떻게 포맷되어야 한다고 생각하는지에 대해 의견을 개진할 수 있다.

기본 원칙: 좁게 또는 광범위하게 정의되어 있는가?

모든 xml 형식은 매우 좁게 정의되는 형식과 매우 광범위하게 정의되는 형식이라는 두 가지 극단 사이에서 충돌하는 균형을 나타낸다.각 접근방식은 일련의 장점과 도전을 수반하며, 어떤 접근방식의 특성이 형식이 사용될 방법에 가장 적합한지 결정하는 것이 형식 설계자의 일이다.

일반적으로 말해서, 광범위하게 정의된 형식은 더 유용하며, 특히 채택될 가능성이 더 높다.RSS가 놀라운 성공을 거둔 이유들 중 하나는 그것이 매우 간단하고 쉽게 확장된다는 것이다.광범위하게 정의된 형식의 단점은 일반적으로 소비자가 문서의 특정 적용을 원할 때 개발자 부분에 대한 작업을 더 많이 요구한다는 것이다.다음 두 가지 형식을 고려하십시오.

좁은 정의

<위키기사> <상호>>조지 워싱턴은...</내용> </의사> </위키기사>

넓은 정의

<위키기사형="생물학" 제목="조지 워싱턴"> <내용> 조지 워싱턴은...</내용> </위키기사>

분명히, 두 번째 기사는 어떤 것에 관한 것일 수 있다.이는 위키피디아의 극히 느슨한 구조와 부합한다는 점에서는 장점이지만, 특정 포맷에 대한 개발을 더욱 어렵게 만든다는 점에서 단점이 있다.궁극적으로 좁은 형식을 정의하려면 최소한 템플릿에 부합하는 기사가 필요하며, 이는 WKML을 통해 기사 범위가 노출될 수 있는 범위를 크게 제한한다. 궁극적으로, 위키백과 기사에 적용할 수 있는 형식이 아무리 최소로 또는 기괴하게 정의된다 하더라도 가장 적절한 접근법일 것이다.infobox 또는 템플릿 특정 정보를 사용할 수 있는 경우 사용해야 하지만 필요하지 않다.

형식 사용 방법

XML은 사용되거나 변환되어야 한다.XML 문서는 테이블에 있는 레코드를 업데이트하는 업데이트그램 형태로 데이터베이스에 의해 사용되거나 RSS 리더의 경우 읽기 쉬운 형식으로 변환될 수 있다.

XML의 순수한 소비는 형식에 대한 직접 코딩을 포함하며, 일반적으로 매우 좁게 정의된다.위키피디아 콘텐츠가 이런 식으로 많이 사용될 것 같지 않아 보여서, 이것은 WKML의 최종 사용으로 변혁을 남겨둔다.

한 가지 접근방식은 RSS를 단순하게 활용하는 것이다.이 접근방식의 문제는 RSS가 아마도 너무 광범위하고, 아마도 위키백과의 백과사전적 성격에 맞지 않는다는 것이다.궁극적으로, 매시업(예를 들어 새로운 페이지의 RSS 피드 또는 페이지 변경)에 RSS가 필요한 경우, WKML이 일부 최소 요구사항을 만족하는 한, RSS로 변환될 수 있다.

혼합 접근법

실제로, 특수성 대 단순성의 문제를 해결하는 한 가지 방법은 예를 들어 템플릿 선과 같이 일반적인 기사 형식으로 롤다운된 별도의 형식이 될 것이다.이 접근방식은 그것이 즉시 실행될 필요가 없다는 더 큰 이점을 가지고 있다; 기본적인 WKML 포맷은 광범위한 사용을 위해 만들어지고 배치될 수 있다. 그리고 나중에 더 구체적인 포맷이 만들어질 때 롤다운 포맷으로 기능할 수 있다.궁극적으로, 글의 넓은 형식이든 좁은 형식이든 간에 요청의 속성이 될 수 있으며 롤다운 형식은 역호환성을 위한 기본값으로 간주된다.

질문 열기

1. 기사 내용과 메타데이터 문서가 분리되어 있는가, 아니면 단일 문서로 통일되어 있는가?
   • 내용과 이력은 분명히 같은 문서에 포함되어 있다.문서의 이전 수정사항을 나타내는 문서는 별도의 신디케이션/서비스 명령에 의해 검색된 별도의 문서들이다.
2. 어떤 기사의 광범위하게 정의된 구조는 무엇인가?(제목, 섹션, ?)
   • 광범위하게 정의된 구조는 다음과 같다.
     1. 루트, 루트 문서 요소 및 카테고리 정보와 같은 일부 문서 메타 데이터 포함.
     2. 칭호를 붙이다
     3. 내용 섹션
     4. 역사
3. 해당 기사의 광범위하게 정의된 속성은 무엇인가?(제목, 작성 날짜, 추가 날짜 질문이 질문 #1로 다시 전달됨)
4. How will infoboxes be handled?
   • 이 시점에서, 우리가 모든 infobox 내용을 다시 기억해야 한다는 것은 꽤 분명하다.
5. How much and how will HTML be scrubbed from the content?
   • A general principle which might be helpful is that markup that affects presentation (such as font-strength (bold) or italicization) will be scrubbed without re-notation, while markup that affects actions, such as links, will be renotated in a format that we have to determine. One exception to this will be images, which may need to be renotated, or may simple pass through as is.

Proposed date format

Wikipedia Markup Language documents use the date format specified in the ISO standard document ISO 8601:1988(E). An important distinction:

Document node values or document attributes which are dates are subject to this standard, dates used in the content are not.

For example:

Standard applies

<wikiarticle linkback="Neuralizer" revisiondate="2007-01-01T16:28:49Z">

Standard does not apply

Brett Bretterson was born at 8:14 PM on Saturday, June 21st, 1954.

Differently grained attributes may require different formats specified within the standard, e.g., some dates may not require time. As per the standard, all times are UTC.

Examples

Highly developed article in XML format

(In Progress)

<wikiarticle title="DNA">  <template type="sprotect2" />  <template type="otheruses" />  <section id="0">   <link type="internal">Image:DNA Overview.png thumb 220px The structure of part of a DNA double helix</link>   'Deoxyribonucleic acid' ('DNA') is a <link type="internal">nucleic acid</link> that contains the <link type="internal">genetics genetic</link> instructions for the <link type="internal">developmental biology development</link> and function of <link type="internal">life living organisms</link>. All living things contain DNA <link type="internal">genome</link>s. A possible exception are a group of <link type="internal">virus</link>es that have <link type="internal">retrovirus RNA genomes</link>, but viruses are not normally considered as living organisms. The main role of DNA in the <link type="internal">cell (biology) cell</link> is the long-term storage of information. It is often compared to a <link type="internal">blueprint</link>, since it contains the instructions to construct other components of the cell, such as <link type="internal">protein</link>s and <link type="internal">RNA</link> <link type="internal">molecule</link>s. The DNA segments that carry genetic information are called <link type="internal">gene</link>s, but other DNA sequences have structural purposes, or are involved in regulating the expression of genetic information.   In <link type="internal">eukaryote</link>s such as <link type="internal">animal</link>s and <link type="internal">plant</link>s, DNA is stored inside the <link type="internal">cell nucleus</link>, while in <link type="internal">prokaryote</link>s such as <link type="internal">bacteria</link>, the DNA is in the cell's <link type="internal">cytoplasm</link>. Unlike <link type="internal">enzyme</link>s, DNA does not act directly on other molecules; rather, various enzymes act on DNA and copy its information into either more DNA, in <link type="internal">DNA replication</link>, or <link type="internal">transcription (genetics) transcribe</link> and <link type="internal">translation (biology) translate</link> it into protein. In <link type="internal">chromosome</link>s, <link type="internal">chromatin</link> proteins such as <link type="internal">histone</link>s compact and organize DNA, which helps control its interactions with other proteins in the nucleus.   DNA is a long <link type="internal">polymer</link> of simple units called <link type="internal">nucleotide</link>s, which are held together by a backbone made of <link type="internal">carbohydrate sugars</link> and <link type="internal">phosphate</link> groups. This backbone carries four types of molecules called <link type="internal">nucleobase bases</link>, and it is the sequence of these four bases that encodes information. The major function of DNA is to encode the sequence of <link type="internal">amino acid residue</link>s in proteins, using the <link type="internal">genetic code</link>. To read the genetic code, cells make a copy of a stretch of DNA in the nucleic acid RNA. These RNA copies can then be used to direct <link type="internal">protein biosynthesis</link>, but they can also be used directly as parts of <link type="internal">ribosome</link>s or <link type="internal">spliceosome</link>s.  </section>  <section id="1" title="Physical and chemical properties">   <link type="image">    <filename>DNA_chemical_structure.png</filename>    <thumb>280px</thumb>    <description>The two strands of DNA are held together by hydrogen bonds between bases. The sugars in the backbone are shown in light blue.</description>   </link>   DNA is a long <link type="internal">polymer</link> made from repeating units called <link type="internal">nucleotide</link>s.<ref name=Alberts>   <cite type="book">    <last>Alberts</last>    <first>Bruce</first>    <coauthors>Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, and Peter Walters</coauthors>    <title>Molecular Biology of the Cell; Fourth Edition</title>    <publisher>Garland Science</publisher>    <date>2002</date>    <location>New York and London</location>    <url>http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=mboc4.TOC&depth=2</url>    <id>ISBN 0-8153-3218-1</id>   </cite>   <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 <link type="internal"><actual>Ångström</actual><display>angstroms</display></link> wide, and one nucleotide unit is 3.3 angstroms long.   <cite type="journal">    <author>Mandelkern M, Elias J, Eden D, Crothers D</author>    <title>The dimensions of DNA in solution</title>    <journal>J Mol Biol</journal>    <volume>152</volume>    <issue>1</issue>    <pages>153-61</pages>    <year>1981</year>    <id>PMID 7338906</id>   </cite>   Although these repeating units are very small, DNA polymers can be enormous molecules containing millions of nucleotides. For instance, the largest human <link type="internal">chromosome</link> is 220 million <link type="internal">base pair</link>s long.<ref><template type="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>   In living organisms, DNA does not usually exist as a single molecule, but instead as a tightly-associated pair of molecules.<ref name=Watson><template type="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 <link type="internal">helix double helix</link>. The nucleotide repeats contain both 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 <link type="internal">nucleoside</link> and a base linked to a sugar and one or more phosphate groups is called a <link type="internal">nucleotide</link>. If multiple nucleotides are linked together, as in DNA, this polymer is referred to as a <link type="internal">polynucleotide</link>.   <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>   The backbone of the DNA strand is made from alternating <link type="internal">phosphate</link> and <link type="internal">carbohydrate sugar</link> residues.<ref name=Ghosh><template type="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 the <link type="internal">pentose</link> (five <link type="internal">carbon</link>) sugar 2-deoxyribose. The sugars are joined together by phosphate groups that form <link type="internal">phosphodiester bond</link>s between the third and fifth carbon <link type="internal">atom</link>s in the sugar rings. These asymmetric <link type="internal">covalent bond bonds</link> 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 <link type="internal">5' end 5'</link> (five prime) and <link type="internal">3' end 3'</link> (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 <link type="internal">ribose</link> in RNA.<ref name=berg/>   The DNA double helix is held together by <link type="internal">hydrogen bond</link>s between the bases attached to the two strands. The four bases found in DNA are <link type="internal">adenine</link> (abbreviated A), <link type="internal">cytosine</link> (C), <link type="internal">guanine</link> (G) and <link type="internal">thymine</link> (T). These four bases are shown below and are attached to the sugar/phosphate to form the complete nucleotide, as shown for adenosine monophosphate.   <infotable caption="Structures of the four bases found in DNA and the nucleotide adenosine monophosphate">    <element><link type="image"><filename>Adenine chemical structure.png</filename><width>80px</width></link></element>    <element><link type="image"><filename>Guanine chemical structure.png</filename><width>118px</width></link></element>    <element><link type="image"><filename>Thymine chemical structure.png</filename><width>97px</width></link></element>    <element><link type="image"><filename>Cytosine chemical structure.png</filename><width>75px</width></link></element>    <element><link type="image"><filename>AMP chemical structure.png</filename><width>130px</width></link></element>    <element>-</element>    <element><link type="internal">Adenine</link></element>    <element><link type="internal">Guanine</link></element>    <element><link type="internal">Thymine</link></element>    <element><link type="internal">Cytosine</link></element>    <element><link type="internal">Adenosine monophosphate</link></element>   </infotable>    These bases are classified into two types; adenine and guanine are fused five- and six-membered <link type="internal">heterocyclic compound</link>s called <link type="internal">purine</link>s, while cytosine and thymine are six-membered rings called <link type="internal">pyrimidine</link>s.<ref name=IUPAC/> A fifth pyrimidine base, called <link type="internal">uracil</link> (U), replaces thymine in RNA and differs from thymine by lacking a <link type="internal">methyl group</link> 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 <link type="internal">phage bacterial virus</link> called PBS1 that contains uracil in its DNA.<ref name="nature1963-takahashi"><template type="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>   <link type="Image">:    <filename>DNA orbit animated small.gif</filename>    <description>Structure of a section of DNA. The bases lie horizontally between the two spiralling strands</description>    <ref>     Created from <link type="external>     <url>http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1D65</url>     <title>PDB 1D65</title>    </ref>   </link>    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 is 22 angstroms wide and the other is 12 angstroms wide.   <cite type="journal">    <author>Wing R, Drew H, Takano T, Broka C, Tanaka S, Itakura K, Dickerson R</author>    <title> Crystal structure analysis of a complete turn of B-DNA</title>    <journal>Nature</journal>    <volume>287</volume>    <issue>5784</issue>    <pages>755-8</pages>    <year>1980</year>    <id >PMID 7432492</id>   </cite>    The larger groove is called the major groove, while the smaller, narrower groove is called the minor groove. 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 <link type="internal">transcription factor</link>s that can bind to specific sequences in double-stranded DNA usually read the sequence by making contacts to the sides of the bases exposed in the major groove.   <cite type="journal">    <author>Pabo C, Sauer R</author>    <title>Protein-DNA recognition</title>    <journal>Annu Rev Biochem</journal>    <volume>53</volume>    <issue />    <pages>293-321</pages>    <year />    <id>PMID 6236744</id>   </cite>    <infotable caption="At top, a 'GC' base pair with three <link type="internal">hydrogen bond</link>s. At the bottom, 'AT' base pair with two hydrogen bonds. Hydrogen bonds are shown as dashed lines.">    <item><link type="image"><filename>GC_Watson_Crick_basepair.png</filename><width>230px</width></link>    <item><link type="image"><filename>AT_Watson_Crick_basepair.png,/filename><width>230px</width></link>   </infotable>   <section id="2" title="Base pairing">    <further>Base pair</further>    Each type of base on one strand forms a bond with just one type of base on the other strand. This is called complementary <link type="internal">base pair</link>ing. Here, purines form <link type="internal">hydrogen bond</link>s to pyrimidines, with A bonding only to T, and C bonding only to G. This arrangement of two nucleotides joined together across the double helix is called a base pair. In a double helix, the two strands are also held together by <link type="internal">force</link>s generated by the <link type="internal">hydrophobic effect</link> and <link type="internal">pi stacking</link>, but these forces are not affected by the sequence of the DNA.<ref><template type="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 <link type="internal">covalent bond covalent</link>, 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 <link type="internal">temperature</link>.<ref><template type="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 strongly interacting strands, while short helices with high AT content have weakly interacting strands.<ref><template type="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 <link type="internal">Pribnow box</link> in bacterial <link type="internal">promoter</link>s, tend to have sequences with a high AT content, making the strands easier to pull apart.<ref><template type="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 <link type="internal">melting temperature</link> (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 shape, but some conformations are more stable than others.<ref><template type="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> The base pairing, or lack of it, can create various topologies at the <link type="internal">DNA end</link>. These can be exploited in <link type="internal">biotechnology</link>.   </section>   <section id="3" title="Sense and antisense">    <further>Sense (molecular biology)</further>     DNA is copied into RNA by <link type="internal">RNA polymerase</link> enzymes that only work in the 5' to 3' direction.<ref name=Joyce><template type="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> A DNA sequence is called "sense" if its sequence is copied by these enzymes and then translated into protein. The sequence on the opposite strand is complementary to the sense sequence and is therefore called the "antisense" sequence. Both sense and antisense sequences can exist on different parts of the same strand of DNA. In both prokaryotes and eukaryotes, antisense sequences are transcribed, but the functions of these RNAs are not entirely clear.<ref><template type="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 <link type="internal">gene expression</link> through RNA-RNA base pairing.<ref><template type="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 <link type="internal">plasmid</link>s and <link type="internal">virus</link>es, blur the distinction made above between sense and antisense strands by having overlapping genes.<ref><template type="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 <link type="internal">bacteria</link>, this overlap may be involved in the regulation of gene transcription,<ref><template type="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><template type="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><template type="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><template type="cite journal   author = Berns K   title = Parvovirus replication   journal = Microbiol Rev   volume = 54   issue = 3   pages = 316-29   year = 1990   id = PMID 2215424" /></ref>    </section>   <section id="4" title="Supercoiling">    <further>DNA supercoil</further>    DNA can be twisted like a rope in a process called <link type="internal">DNA supercoil</link>ing. Normally, with DNA in its "relaxed" state, a strand 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><template type="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 <link type="internal">topoisomerase</link>s.<ref name=Champoux><template type="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 <link type="internal">transcription (genetics) transcription</link> and <link type="internal">DNA replication</link>.<ref name=Wang><template type="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>    <link type="internal">Image:A-DNA, B-DNA and Z-DNA.png thumb right 290px From left to right, the structures of A, B and Z DNA</link>   </section>   <section id="5" title="Alternative double-helical structures">    <further>Mechanical properties of DNA</further>    DNA exists in several possible conformations. The conformations so far identified are: <link type="internal">A-DNA</link>, B-DNA, C-DNA, D-DNA,<ref name=Hayashi2005><template type="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><template type="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><template type="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><template type="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> and <link type="internal">Z-DNA</link>.<ref name=Ghosh/><ref><template type="cite journal   author = Palecek E   title = Local supercoil-stabilized DNA structures   journal = Crit Rev Biochem Mol Biol   volume = 26   issue = 2   pages = 151-226   year = 1991   id = PMID 1914495" /></ref> However, only A-DNA, B-DNA, and Z-DNA are believed to be found in nature. 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 <link type="internal">metal</link> <link type="internal">ion</link>s and <link type="internal">polyamine</link>s.<ref><template type="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. 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.<ref><template type="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> Segments of DNA where the bases have been <link type="internal">methylation methylated</link> may undergo a larger change in conformation and adopt the <link type="internal">Z-DNA Z form</link>. Here, the strands turn about the helical axis in a left-handed spiral, the opposite of the more common B form.<ref><template type="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>    <link type="internal">Image:Telomere quadruplex.jpg thumb left 300px Structure of a DNA quadruplex formed by <link type="internal">telomere</link> repeats.<ref>Created from [http://ndbserver.rutgers.edu/atlas/xray/structures/U/ud0017/ud0017.html NDB UD0017]</ref></link>   </section>   <section id="6" title="Quadruplex structures">    At the ends of the linear <link type="internal">chromosome</link>s are specialized regions of DNA called <link type="internal">telomere</link>s. The main function of these regions is to allow the cell to replicate chromosome ends using the enzyme <link type="internal">telomerase</link>, as normal <link type="internal">DNA polymerase</link>s working on the <link type="internal">lagging strand</link> cannot copy the extreme 3' ends of their DNA templates.<ref name=Greider><template type="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> 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 <link type="internal">exonuclease</link>s and stop the <link type="internal">DNA repair</link> systems in the cell from treating them as damage to be corrected.<ref name=Nugent><template type="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><template type="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#B34   journal = Genes Dev   volume = 11   issue = 21   pages = 2801-9   year = 1997   id = PMID 9353250" /></ref>    These guanine-rich sequences may stabilise chromosome ends by forming very unusual quadruplex structures. Here, four guanine bases form a flat plate, through hydrogen bonding, and these flat four-base units then stack on top of each other, to form a stable quadruplex.<ref name=Burge><template type="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 often stabilized by <link type="internal">chelation</link> of a metal ion in the centre of each four-base unit. The structure shown to the left is of a quadruplex formed by a DNA sequence containing four consecutive 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 <link type="internal">potassium</link> ions.<ref><template type="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 and the central set of four bases can come from either one folded strand, or several different parallel strands.    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 circle stabilized by telomere-binding proteins.<ref><template type="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> 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/>   </section>  </section>  <section id="7" title="Chemical modifications">   <section id="8" title="Regulatory base modifications">   <further>DNA methylation</further>   The expression of genes is influenced by modifications of the bases in DNA. In humans, the most common base modification is <link type="internal">cytosine</link> <link type="internal">methylation</link> to produce <link type="internal">5-Methylcytosine 5-methylcytosine</link>. This modification reduces gene expression and is important in <link type="internal">X-inactivation X-chromosome inactivation</link>.<ref><template type="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 level of methylation varies between organisms, with <link type="internal">Caenorhabditis elegans</link> lacking cytosine methylation, while <link type="internal">vertebrate</link>s show high levels, with up to 1% of their DNA being 5-methylcytosine.<ref><template type="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> Unfortunately, the spontaneous <link type="internal">deamination</link> of 5-methylcytosine produces thymine, and methylated cytosines are therefore <link type="internal">mutation</link> hotspots.<ref><template type="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 <link type="internal">glycosylation</link> of uracil to produce the "J-base" in <link type="internal">kinetoplastid</link>s <cite type="journal">  <author>Ratel D, Ravanat J, Berger F, Wion D</author>   <title>N6-methyladenine: the other methylated base of DNA</title>    <journal>Bioessays</journal>   <volume>28</volume>   <issue>3</issue>   <pages>309-15</pages>   <year>2006</year>   <id>PMID 16479578</id>  </cite> <cite type="journal">   <author>Gommers-Ampt J, Van Leeuwen F, de Beer A, Vliegenthart J, Dizdaroglu M, Kowalak J, Crain P, Borst P</author>  <title>beta-D-glucosyl-hydroxymethyluracil: a novel modified base present in the DNA of the parasitic protozoan T. brucei </title>  <journal>Cell</journal>  <volume>75</volume>  <issue>6</issue>  <pages>1129-36</pages>  <year>1993</year>  <id>PMID 8261512</id> </cite>    </section>   <section id="9" title="DNA damage">    <template type="further <link type="internal">Mutation</link>" />   <link type="Image"><filename>Benzopyrene DNA adduct 1JDG.png</filename><thumb /><width>250px</width><text>Benzopyrene</text></link>, the major mutagen in <link type="internal">tobacco smoking tobacco smoke</link>, in an adduct to DNA.<ref>Created from [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1JDG PDB 1JDG]</ref></link>  DNA can be damaged by many different sorts of <link type="internal">mutagen</link>s. These include <link type="internal">oxidizing agent</link>s, <link type="internal">alkylating agent</link>s and also high-energy <link type="internal">electromagnetic radiation</link> such as <link type="internal">ultraviolet</link> light and <link type="internal">x-ray</link>s. The type of DNA damage produced depends on the type of mutagen. For example, UV light mostly damages DNA by producing <link type="internal">thymine dimer</link>s, which are cross-links between adjacent pyrimidine bases in a DNA strand.<ref><template type="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 <link type="internal">free radical</link>s or <link type="internal">hydrogen peroxide</link> produce multiple forms of damage, including base modifications, particularly of guanosine, as well as double-strand breaks.<ref><template type="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><template type="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><template type="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 they can produce <link type="internal">point mutation</link>s, insertions and deletions from the DNA sequence, as well as <link type="internal">chromosomal translocation</link>s.<ref><template type="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 <link type="internal">intercalation (chemistry) intercalate</link> into the space between two adjacent base pairs. These molecules are mostly polycyclic, <link type="internal">aromaticity aromatic</link>, and planar molecules, and include <link type="internal">ethidium</link>, <link type="internal">proflavin</link>, <link type="internal">daunomycin</link>, <link type="internal">doxorubicin</link> and <link type="internal">thalidomide</link>. DNA intercalators are used in <link type="internal">chemotherapy</link> to inhibit DNA replication in rapidly-growing <link type="internal">cancer</link> cells.<ref><template type="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> 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 modifications inhibit <link type="internal">transcription (genetics) transcription</link> and <link type="internal">DNA replication replication</link> processes, causing both toxicity and mutations. As a result, DNA intercalators are often <link type="internal">carcinogen</link>s, with <link type="internal">benzopyrene benzopyrene diol epoxide</link>, <link type="internal">acridine</link>s, <link type="internal">aflatoxin</link> and <link type="internal">ethidium bromide</link> being well-known examples.<ref><template type="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><template type="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>   ==Overview of biological functions==  DNA contains the genetic information that allows living things to function, grow and reproduce. This information is held in the <link type="internal">DNA sequence sequence</link> of pieces of DNA called <link type="internal">gene</link>s. Genetic information in genes is transmitted through complementary base pairing. For example, when a cell uses the information in a gene, the DNA sequence is copied into a complementary RNA sequence in a process called transcription. Usually, this RNA copy is then used to make a matching protein sequence in a process called translation. 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 that happen in these processes between DNA and other molecules.  <link type="internal">Image:RNA pol.jpg thumb left 300px <link type="internal">T7 RNA polymerase</link> producing a mRNA (green) from a DNA template (red and blue). The protein is shown as a purple ribbon.<ref>Created from [http://www.rcsb.org/pdb/explore/explore.do?structureId=1MSW PDB 1MSW]</ref></link>  ===Transcription and translation===  <template type="further <link type="internal">Genetic code</link>, <link type="internal">Transcription (genetics)</link>, <link type="internal">Protein biosynthesis</link>" />  A gene is a sequence of DNA that contains genetic information and can influence the <link type="internal">phenotype</link> of an organism. Within a gene, the sequence of bases along a DNA strand defines a <link type="internal">messenger RNA</link> sequence which then defines a protein sequence. The relationship between the nucleotide sequences of genes and the <link type="internal">amino acid amino-acid</link> sequences of proteins is determined by the rules of <link type="internal">translation (genetics) translation</link>, known collectively as the <link type="internal">genetic code</link>. 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 <link type="internal">RNA polymerase</link>. This RNA copy is then decoded by a <link type="internal">ribosome</link> that reads the RNA sequence by base-pairing the messenger RNA to <link type="internal">transfer RNA</link>, 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 <link type="internal">list of standard amino acids standard amino acids</link>. Most amino acids, therefore, have 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.   <link type="internal">Image:Dnareplication.png frame DNA replication. The double helix (blue) is unwound by a <link type="internal">helicase</link>. Next, <link type="internal">DNA polymerase III</link> (green) produces the <link type="internal">leading strand</link> copy (red). A DNA polymerase I molecule (green) binds to the <link type="internal">lagging strand</link>. This enzyme makes discontinuous segments (called <link type="internal">Okazaki fragment</link>s) before <link type="internal">DNA ligase</link> (violet) joins them together.</link>   ===Replication===  <template type="further <link type="internal">DNA replication</link>" />   <link type="internal">Cell division</link> 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 <link type="internal">DNA replication</link>. Here, the two strands are separated and then each strand's complementary DNA sequence is recreated by an enzyme called <link type="internal">DNA polymerase</link>. 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><template type="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.   ==Genes and genomes==  <template type="further <link type="internal">Cell nucleus</link>, <link type="internal">Gene</link>, <link type="internal">Non-coding DNA</link>" />  DNA is located in the <link type="internal">cell nucleus</link> of eukaryotes, as well as small amounts in <link type="internal">mitochondrion mitochondria</link> and <link type="internal">chloroplast</link>s. In prokaryotes, the DNA is held within an irregularly shaped body in the cytoplasm called the <link type="internal">nucleoid</link>.<ref><template type="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 DNA is usually in linear <link type="internal">chromosome</link>s in eukaryotes, and circular chromosomes in prokaryotes. In the <link type="internal">human genome</link>, there is approximately 3 billion base pairs of DNA arranged into 46 chromosomes.<ref><template type="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 genetic information in a genome is held within genes. A gene is a unit of <link type="internal">heredity</link> and is a region of DNA that influences a particular characteristic in an organism. Genes contain an <link type="internal">open reading frame</link> that can be transcribed, as well as <link type="internal">regulatory sequence</link>s such as <link type="internal">promoter</link>s and <link type="internal">enhancer (genetics) enhancers</link>, which control the expression of the open reading frame.   In many <link type="internal">species</link>, only a small fraction of the total sequence of the <link type="internal">genome</link> encodes protein. For example, only about 1.5% of the human genome consists of protein-coding <link type="internal">exon</link>s, with over 50% of human DNA consisting of non-coding <link type="internal">repeated sequence (DNA) repetitive sequences</link>.<ref><template type="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 <link type="internal">noncoding DNA non-coding DNA</link> in eukaryotic genomes and the extraordinary differences in <link type="internal">genome size</link>, or <link type="internal">C-value</link>, among species represent a long-standing puzzle known as the "<link type="internal">C-value enigma</link>".<ref><template type="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>   Some non-coding DNA sequences play structural roles in chromosomes. <link type="internal">Telomere</link>s and <link type="internal">centromere</link>s typically contain few genes, but are important for the function and stability of chromosomes.<ref name=Nugent/><ref><template type="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 <link type="internal">pseudogene</link>s, which are copies of genes that have been disabled by mutation.<ref><template type="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 <link type="internal">fossil</link>s, although they can occasionally serve as raw genetic material for the creation of new genes through the process of <link type="internal">gene duplication</link> and <link type="internal">divergent evolution divergence</link>.<ref><template type="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>   ==Interactions with proteins==  All the functions of DNA depend on interactions with proteins. These protein interactions can either be non-specific, or the protein can only bind to a particular 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;"   <link type="internal">Image:Nucleosome 2.jpg 260px</link>   -   <link type="internal">Image:Nucleosome_(opposites_attracts).JPG 260px</link>   }  <div style="border: none; width:260px;"><div class="thumbcaption">Interaction of DNA with <link type="internal">histone</link>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 between DNA and structural proteins. These proteins organize the DNA into a compact structure called <link type="internal">chromatin</link>. In eukaryotes this structure involves DNA binding to a complex of small basic proteins called <link type="internal">histone</link>s, while in prokaryotes multiple types of proteins are involved.<ref><template type="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> The histones form a disk-shaped complex called a <link type="internal">nucleosome</link>, 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 <link type="internal">ionic bond</link>s to the acidic sugar-phosphate backbone of the DNA, and are therefore largely independent of the base sequence.<ref><template type="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 <link type="internal">methylation</link>, <link type="internal">phosphorylation</link> and <link type="internal">acetylation</link>.<ref><template type="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 <link type="internal">transcription factor</link>s and changing the rate of transcription.<ref><template type="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><template type="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><template type="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><template type="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 <link type="internal">stem loop</link>s or being degraded by <link type="internal">nuclease</link>s.   <link type="internal">Image:Lambda repressor 1LMB.png thumb right 185px The lambda repressor <link type="internal">helix-turn-helix</link> transcription factor bound to its DNA target<ref>Created from [http://www.rcsb.org/pdb/explore/explore.do?structureId=1LMB PDB 1LMB]</ref></link>  In contrast, other proteins have evolved to specifically bind particular DNA sequences. The most intensively studied of these are the various classes of <link type="internal">transcription factor</link>s. These proteins control gene 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 <link type="internal">promoter</link>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><template type="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 <link type="internal">enzyme</link>s that modify the histones at the promoter; this will change the accessibility of the DNA template to the polymerase.<ref><template type="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><template type="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 <link type="internal">signal transduction</link> 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><template type="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>   <link type="internal">Image:EcoRV 1RVA.png thumb left 250px The <link type="internal">restriction enzyme</link> <link type="internal">EcoRV</link> (green) in a complex with its substrate DNA<ref>Created from [http://www.rcsb.org/pdb/explore/explore.do?structureId=1RVA PDB 1RVA]</ref></link>   ===DNA-modifying enzymes===  ====Nucleases and ligases====  Nucleases are <link type="internal">enzyme</link>s that cut DNA strands by catalyzing the <link type="internal">hydrolysis</link> of the <link type="internal">phosphodiester bond</link>s. Nucleases that hydrolyse nucleotides from the ends of DNA strands are called <link type="internal">exonuclease</link>s, while <link type="internal">endonuclease</link>s cut within strands. The most frequently-used nucleases in <link type="internal">molecular biology</link> are the <link type="internal">restriction enzyme restriction endonucleases</link>, 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 <link type="internal">bacteria</link> against <link type="internal">phage</link> infection by digesting the phage DNA when it enters the bacterial cell, acting as part of the <link type="internal">restriction modification system</link>.<ref><template type="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 <link type="internal">clone (genetics) molecular cloning</link> and <link type="internal">DNA fingerprinting</link>.   Enzymes called <link type="internal">DNA ligase</link>s can rejoin cut or broken DNA strands, using the energy from either <link type="internal">adenosine triphosphate</link> or <link type="internal">nicotinamide adenine dinucleotide</link>.<ref name=Doherty><template type="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 <link type="internal">lagging strand</link> DNA replication, as they join together the short segments of DNA produced at the <link type="internal">replication fork</link> into a complete copy of the DNA template. They are also used in <link type="internal">DNA repair</link> and <link type="internal">genetic recombination</link>.<ref name=Doherty/>   ====Topoisomerases and helicases====  <link type="internal">Topoisomerase</link>s are enzymes with both nuclease and ligase activity. These proteins change the amount of <link type="internal">DNA supercoil supercoiling</link> 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><template type="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/>   Helicases are proteins that are a type of <link type="internal">molecular motor</link>. They use the chemical energy in <link type="internal">adenosine triphosphate</link> to break the hydrogen bonds between bases and unwind a DNA double helix into single strands.<ref><template type="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 <link type="internal">nucleoside triphosphate</link>s. They function by adding nucleotides onto the 3' <link type="internal">hydroxyl hydroxyl group</link> of the previous nucleotide in the DNA strand. As a consequence, all polymerases work in a 5' to 3' direction.<ref name=Joyce/> In the <link type="internal">active site</link> 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 depending of the type of template they use.   In <link type="internal">DNA replication</link>, a DNA-dependent <link type="internal">DNA polymerase</link> make a DNA copy of a DNA sequence. Accuracy is vital in this process, so many of these polymerases have a <link type="internal">Proofreading#Proofreading in biology proofreading</link> 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' <link type="internal">exonuclease</link> activity is activated and the incorrect base removed.<ref><template type="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 <link type="internal">replisome</link> that contains multiple accessory subunits, such as the <link type="internal">DNA clamp</link> or <link type="internal">helicase</link>s.<ref><template type="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 a RNA strand into DNA. They include <link type="internal">reverse transcriptase</link>, which is a <link type="internal">virus viral</link> enzyme involved in the infection of cells by <link type="internal">retrovirus</link>es, and <link type="internal">telomerase</link>, which is required for the replication of <link type="internal">telomere</link>s.<ref><template type="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 <link type="internal">RNA polymerase</link> 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 <link type="internal">promoter</link> and separates the DNA strands. It then copies the gene sequence into a <link type="internal">messenger RNA</link> transcript until it reaches a region of DNA called the <link type="internal">terminator (genetics) terminator</link>, 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><template type="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;"   <link type="internal">Image:Holliday Junction cropped.png 250px</link>   -   <link type="internal">Image:Holliday junction coloured.png 250px</link>   }  <div style="border: none; width:250px;"><div class="thumbcaption">Structure of the <link type="internal">Holliday junction</link> intermediate in <link type="internal">genetic recombination</link>. 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>  <template type="further <link type="internal">Genetic recombination</link>" />  <link type="internal">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).</link>   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><template type="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 when they <link type="internal">genetic recombination recombine</link>. Recombination is when two DNA helices break, swap a section and then rejoin. In eukaryotes this process usually occurs during <link type="internal">meiosis</link>, when the two sister <link type="internal">chromatid</link>s are paired together in the center of the cell. Recombination allows chromosomes to exchange genetic information and produces new combinations of genes, which increases the efficiency of <link type="internal">selection</link> and can be important in the rapid evolution of new proteins.<ref><template type="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><template type="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 recombination is <link type="internal">chromosomal crossover homologous recombination</link>, where the two chromosomes involved share very similar sequences. Non-homologous recombination can be damaging to cells, as it can produce <link type="internal">chromosomal translocation</link>s and genetic abnormalities. The recombination reaction is catalyzed by enzymes known as recombinases, such as <link type="internal">Cre recombinase</link>.<ref><template type="cite journal   author = Ghosh K, Van Duyne G   title = Cre-loxP biochemistry   journal = Methods   volume = 28   issue = 3   pages = 374-83   year = 2002   id = PMID 12431441" /></ref> In the first step, the recombinase creates a nick in one strand of a DNA double helix, allowing the nicked strand to pull apart from its <link type="internal">complementarity (molecular biology) complementary</link> strand and <link type="internal">annealing (biology) anneal</link> to one strand of the double helix on the opposite chromatid. A second nick allows the strand in the second chromatid to pull apart and anneal to the remaining strand in the first helix, forming a structure known as a cross-strand exchange or a <link type="internal">Holliday junction</link>. The Holliday junction is a tetrahedral junction structure which 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><template type="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>   ==Uses in technology==  ===Forensics ===  <template type="further <link type="internal">Genetic fingerprinting</link>" />   <link type="internal">Forensic science Forensic scientists</link> can use DNA in <link type="internal">blood</link>, <link type="internal">semen</link>, <link type="internal">skin</link>, <link type="internal">saliva</link> or <link type="internal">hair</link> at a crime scene to identify a perpetrator. This process is called <link type="internal">genetic fingerprinting</link>, or more accurately, DNA profiling. In DNA profiling, the lengths of variable sections of repetitive DNA, such as <link type="internal">short tandem repeat</link>s and <link type="internal">minisatellite</link>s, are compared between people. This method is usually an extremely reliable technique for identifying a criminal.<ref><template type="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><template type="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 <link type="internal">Alec Jeffreys</link>,<ref><template type="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 <link type="internal">Enderby murders</link> 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><template type="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===  <template type="further <link type="internal">Bioinformatics</link>" />  <link type="internal">Bioinformatics</link> involves the manipulation, searching, and <link type="internal">data mining</link> of DNA sequence data. The development of techniques to store and search DNA sequences have led to widely-applied advances in <link type="internal">computer science</link>, especially <link type="internal">string searching algorithm</link>s, <link type="internal">machine learning</link> and <link type="internal">database theory</link>.<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, was 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 <link type="internal">1997</link>. ISBN 978-0-521-58519-4.</ref> In other applications such as <link type="internal">text editor</link>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 <link type="internal">sequence alignment</link> aims to identify <link type="internal">homology (biology) homologous</link> sequences and locate the specific <link type="internal">mutation</link>s that make them distinct. These techniques, especially <link type="internal">multiple sequence alignment</link>, are used in studying <link type="internal">phylogenetics phylogenetic</link> relationships and protein function.<ref><template type="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 <link type="internal">Human Genome Project</link>, 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 <link type="internal">gene finding</link> algorithms, which allow researchers to predict the presence of particular <link type="internal">gene product</link>s in an organism even before they have been isolated experimentally.<ref name="Mount"><template type="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 ===  <template type="further <link type="internal">DNA computing</link>" />  DNA was first used in computing to solve a small version of the directed <link type="internal">Hamiltonian path problem</link>, an <link type="internal">NP-complete</link> problem.<ref><template type="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> <link type="internal">DNA computing</link> is advantageous over electronic computers in power use, space use, and efficiency, due to its ability to compute in a highly parallel fashion (see <link type="internal">parallel computing</link>). A number of other problems, including simulation of various <link type="internal">abstract machine</link>s, the <link type="internal">boolean satisfiability problem</link>, and the bounded version of the <link type="internal">travelling salesman problem</link>, have since been analysed using DNA computing.<ref><template type="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 <link type="internal">cryptography</link>, where in particular it allows unbreakable <link type="internal">one-time pad</link>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===  <template type="further <link type="internal">Phylogenetics</link> and <link type="internal">Genetic genealogy</link>" />  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 <link type="internal">phylogeny</link>.<ref><template type="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 <link type="internal">phylogenetics</link> is a powerful tool in <link type="internal">evolutionary biology</link>. If DNA sequences within a species are compared, <link type="internal">population genetics population geneticists</link> can learn the history of particular populations. This can be used in studies ranging from <link type="internal">ecological genetics</link> to <link type="internal">anthropology</link>; for example, DNA evidence is being used to try to identify the <link type="internal">Ten Lost Tribes of Israel</link>.<ref>Lost Tribes of Israel, <link type="internal">NOVA (TV series) NOVA</link>, 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 <link type="internal">Sally Hemings</link> and <link type="internal">Thomas Jefferson</link>. 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==  <link type="internal">Image:Francis Crick.png thumb right <link type="internal">Francis Crick</link></link>  <link type="internal">Image:JamesWatson.jpg thumb <link type="internal">James D. Watson James Watson</link> in the <link type="internal">Cavendish Laboratory</link> at the <link type="internal">University of Cambridge</link></link>  <template type="further <link type="internal">History of molecular biology</link>" />  DNA was first isolated by <link type="internal">Friedrich Miescher</link> who, in 1869, discovered a microscopic substance in the <link type="internal">pus</link> of discarded surgical bandages. As it resided in the nuclei of cells, he called it "nuclein".<ref><template type="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 <link type="internal">Phoebus Levene</link>'s identification of the base, sugar and phosphate nucleotide unit.<ref><template type="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 <link type="internal">William Astbury</link> produced the first <link type="internal">X-ray diffraction</link> patterns that showed that DNA had a regular structure.<ref><template type="cite journal   author =Astbury W,   title = Nucleic acid   journal = Symp. SOC. Exp. Bbl   volume = 1   issue = 66   year = 1947" /></ref>   In 1943, <link type="internal">Oswald Theodore Avery</link> discovered that <link type="internal">trait (biology) traits</link> 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 <link type="internal">transforming principle</link>.<ref><template type="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 = 149   issue = 2   pages = 297-326   year = 1979   id = PMID 33226" /></ref> DNA's role in <link type="internal">heredity</link> was confirmed in 1953, when <link type="internal">Alfred Hershey</link> and <link type="internal">Martha Chase</link> in the <link type="internal">Hershey-Chase experiment</link> showed that DNA is the <link type="internal">genetic material</link> of the <link type="internal">T2 phage</link>.<ref><template type="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>   Using <link type="internal">X-ray diffraction</link> data from <link type="internal">Rosalind Franklin</link> and the information that the bases were paired, <link type="internal">James D. Watson</link> and <link type="internal">Francis Crick</link> produced the first accurate model of DNA structure in 1953 in their article <link type="internal">Molecular structure of Nucleic Acids The Molecular structure of Nucleic Acids</link>.<ref name=Watson/> Watson and Crick proposed the <link type="internal">central dogma of molecular biology</link> in 1957, describing how proteins are produced from <link type="internal">cell nucleus nucleic</link> DNA. In 1962 Watson, Crick, and <link type="internal">Maurice Wilkins</link> jointly received the <link type="internal">Nobel Prize</link> in <link type="internal">Nobel Prize in Physiology or Medicine Physiology or Medicine</link>.<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", 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 <link type="internal">Meselson-Stahl experiment</link>.<ref><template type="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 <link type="internal">Har Gobind Khorana</link>, <link type="internal">Robert W. Holley</link> and <link type="internal">Marshall Warren Nirenberg</link> to decipher the <link type="internal">genetic code</link>.<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 <link type="internal">molecular biology</link>.   ==References==  <div class="references-small" style="-moz-column-count:2; column-count:2;">  <references/>  </div>   ==Further reading==  <list>   <item> Clayton, Julie. (Ed.). 50 Years of DNA, Palgrave MacMillan Press, 2003. ISBN 978-1-40-391479-8</item>   <item> 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</item>   <item> <link type="internal">Robert Olby Olby, Robert</link>. 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.</item>   <item> <link type="internal">Matt Ridley Ridley, Matt</link>. Francis Crick: Discoverer of the Genetic Code (Eminent Lives) first published in June 2006 in the USA and then to be in the UK September 2006, by HarperCollins Publishers; 192 pp, ISBN 978-0-06-082333-7   <item> Rose, Steven. The Chemistry of Life, Penguin, ISBN 978-0-14-027273-4</item>.   <item> Watson, James D. and Francis H.C. Crick. [http://www.nature.com/nature/dna50/watsoncrick.pdf A structure for Deoxyribose Nucleic Acid] (PDF). <link type="internal">Nature (journal) Nature</link> 171, 737 – 738, <link type="internal">25 April</link> <link type="internal">1953</link>.</item>   <item> Watson, James D. DNA: The Secret of Life ISBN 978-0-375-41546-3.</item>   <item> Watson, James D. <link type="internal">The Double Helix The Double Helix: A Personal Account of the Discovery of the Structure of DNA (Norton Critical Editions)</link>. ISBN 978-0-393-95075-5</item>  </list>   ==External links==  <template type="Spoken Wikipedia dna.ogg 2007-02-12" />  <template type="commonscat DNA" />  *[http://www.dnaftb.org/dnaftb/ DNA from the beginning]  *[http://www.nature.com/nature/dna50/archive.html Double helix: 50 years of DNA], <link type="internal">Nature (journal) Nature</link>  *[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]  *[http://www.dnakin.com Using DNA in Genealogical Research]  *[http://www.dnai.org DNA Interactive] (requires <link type="internal">Adobe Flash</link>)  *[http://www.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb23_1.html DNA: RCSB PDB Molecule of the Month]  *[http://www.fidelitysystems.com/Unlinked_DNA.html DNA under electron microscope]  *<template type="dmoz Science/Biology/Biochemistry_and_Molecular_Biology/Biomolecules/Nucleic_Acids/DNA/ DNA" />  *[http://dnawiz.com/ DNA Articles] - articles and information collected from various sources  *<template type="McGrawHillAnimation genetics Dna%20Replication" />  *[http://biostudio.com/c_%20education%20mac.htm DNA coiling to form chromosomes]   <template type="Nucleic acids" />  <template type="featured article" />   <!--Categories-->  <category>DNA</category>  <category>Genetics</category>   <template type="Link FA de" />  <template type="link FA nl" />  <template type="Link FA nl" />   <!--Interwiki-->  <link type="interwiki">ar:??? ???? ???? ????? ????????</link>  <link type="interwiki">zh-min-nan:DNA</link>  <link type="interwiki">bs:Dezoksiribonukleinska kiselina</link>  <link type="interwiki">bg:???</link>  <link type="interwiki">ca:Àcid desoxiribonucleic</link>  <link type="interwiki">cs:DNA</link>  <link type="interwiki">cy:DNA</link>  <link type="interwiki">da:Dna</link>  <link type="interwiki">pdc:DNA</link>  <link type="interwiki">de:Desoxyribonukleinsäure</link>  <link type="interwiki">et:Desoksüribonukleiinhape</link>  <link type="interwiki">el:DNA</link>  <link type="interwiki">es:ADN</link>  <link type="interwiki">eo:DNA</link>  <link type="interwiki">eu:ADN</link>  <link type="interwiki">fr:Acide désoxyribonucléique</link>  <link type="interwiki">ga:ADN</link>  <link type="interwiki">gl:ADN</link>  <link type="interwiki">ko:DNA</link>  <link type="interwiki">hr:Deoksiribonukleinska kiselina</link>  <link type="interwiki">id:Asam deoksiribonukleat</link>  <link type="interwiki">it:DNA</link>  <link type="interwiki">he:DNA</link>  <link type="interwiki">ht:ADN</link>  <link type="interwiki">la:Acidum deoxyribonucleinicum</link>  <link type="interwiki">lv:Dezoksiribonukleinskabe</link>  <link type="interwiki">lt:Deoksiribonukleorugštis</link>  <link type="interwiki">hu:DNS (biológia)</link>  <link type="interwiki">mk:???</link>  <link type="interwiki">ms:DNA</link>  <link type="interwiki">nl:DNA</link>  <link type="interwiki">ja:????????</link>  <link type="interwiki">no:DNA</link>  <link type="interwiki">nn:Deoksyribonukleinsyre</link>  <link type="interwiki">pam:DNA</link>  <link type="interwiki">pl:Kwas deoksyrybonukleinowy</link>  <link type="interwiki">pt:DNA</link>  <link type="interwiki">ro:ADN</link>  <link type="interwiki">ru:?????????????????????? ???????</link>  <link type="interwiki">sq:ADN</link>  <link type="interwiki">simple:DNA</link>  <link type="interwiki">sk:Deoxyribonukleová kyselina</link>  <link type="interwiki">sl:Deoksiribonukleinska kislina</link>  <link type="interwiki">sr:???</link>  <link type="interwiki">sh:DNK</link>  <link type="interwiki">su:DNA</link>  <link type="interwiki">fi:DNA</link>  <link type="interwiki">sv:DNA</link>  <link type="interwiki">tl:DNA</link>  <link type="interwiki">ta:?????????? ???? ??? ??????</link>  <link type="interwiki">th:????????</link>  <link type="interwiki">vi:DNA</link>  <link type="interwiki">tr:DNA</link>  <link type="interwiki">uk:???</link>  <link type="interwiki">ur:?? ??? ??</link>  <link type="interwiki">yi:?? ?? ???</link>  <link type="interwiki">zh:??????</link> </wikiarticle> 

XML 형식의 스텁 문서

<위키기사 링크백="프랭클린 피어스 고등학교" 개정 날짜="2007-02-08T20:18:03Z"><제목>프랭클린 피어스 고등학교 <카테고리> <카테고리> </카테고리> <인포박스형="2차 school">, <, infoboxattribute>,<>name>, name<, /name>,<>가.프랭클린 피어스 고등 School<, /value>,<>/infoboxattribute>, <, infoboxattribute>,<>name>, established<, /name>,<>가 1952<, /value>,<>/infoboxattribute>, <, infoboxattribute>,<>name>, city<, /name>,<>가.Tacoma</value </infoboxattribute> <infoboxattribute> <name>state</name> <value>워싱턴[/값][/값] <인피오박산트립>[이름] 국가[값]]USA</value </infoboxattribute> <infoboxattribute> <name> 캠퍼스 </name> <value>교외[/value] </infoboxattribute> <infoboxattribute> <name>type </name> <value>공공 secondary<, /value>,<>/infoboxattribute>, <, infoboxattribute>,<>name>, principal<, /name>,<>가.에릭 Hogan<, /value>,<>/infoboxattribute>, <, infoboxattribute>,<>name>, grades<, /name>,<>가 9-12<, /value>,<>/infoboxattribute>, <, infoboxattribute>,<>name>, enrollment<, /name>,<>valu.E>, 1,220(2005년)<, /value>,<>/infoboxattribute>, <, infoboxattribute>,<>name>, district<, /name>,<>가.프랭클린 피어스 학교 District<, /value>,<>/infoboxattribute>, <, infoboxattribute>,<>name>, mascot<, /name>,<>value>, Cardinals<, /value>,<>/infoboxattribute>, <, infoboxattribute>,<>name>, colors<, /n.ame> <가치>그리고 yellow<, /value>,<>/infoboxattribute>, <, infoboxattribute>,<>name>, website<, /name>,<>가<>링크 type="외부">,http://www.fp.k12.wa.us/fphs/</link></value>,<>/infoboxattribute>,<>/infobox>,<>섹션 id="0">. 프랭클린 피어스 고등 Scho 빨간.<>에 올;링크 type="내부">워싱턴 타코마(Tacoma)는 제14대 미국 대통령의 이름을 딴 것으로 <링크형="내부형"이다.>프랭클린 피어스, 1853년 워싱턴 준주(州)가 형성될 때 대통령이었던 사람.</섹션 id="1" 제목="아카데미" > <링크 유형="내부">고급 배치(Advanced Placement) 강좌는 미적분 AB, 통계, 화학(Washington H.S.) 및 미국 역사에서 개설된다.제공되는 언어 수업은 프랑스어, 스페인어, 일본어, 미국 수화가 있다.</섹션> <섹션 id="2" 제목="액티비즈">FPHS의 클럽은 드라마 클럽, <링크 타입="내부">이다.FBLA[/link], <링크 유형="내부">FFA[/link], <링크 유형="내부">전국아너 소사이어티, 국제문화클럽, 스키클럽.</섹션> <섹션 id="3" 제목="육상">축구, 골프, 크로스컨트리, 배구, 축구, 바스켓볼, 레슬링, 테니스, 야구, 패스트피치 소프트볼, 트랙.<링크 유형="내부">카테고리:워싱턴의 고등학교 <링크 유형="내부">카테고리:사우스 푸젯 사운드 리그 (/link) <링크 유형="내부">카테고리:1952년 설립된 교육기관 <</링크 </섹션> <역사> <개정형="소형"> <버전> 106992867</버전> <날짜> 2007-02-09T20:45:00Z </날짜> <사용자>Quirkyperki</user> <설명 /> </revision type="섹션"> <버전> 106992539</version> 2007-02-09T20:43:00Z </날짜> <사용자>Quirkyperki</user> <설명>('{Infobox 중등학교 이름 = 프랭클린 피어스 고등학교 설립 페이지 = 1952년 도시 = 타코마 주 = 워싱턴 국가 = 미국 캠퍼스 = 교외 유형)..') </> </> </역사> </위키기사>

XML 형식의 절대 최소 문서

<위키기사 링크백="신경안정제" 개정 날짜="2007-01-01T16:28:49Z"> <제목>신경작용제 </제목> <섹션 id="0" 제목=" 신경작용제는 1991년 영화 <맨인 블랙>에서 묘사된 가상의 장치다.그것은 외계인과 마주친 사람들의 기억을 지우는 데 사용된다.</섹션> <역사 /> </위키기사>