Editing DNA (section)

=== Base pairing ===
{{further|Base pair}}
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<div style="border: none; width:282px;"><div class="thumbcaption">Top, a '''{{mono|GC}}''' base pair with three [[hydrogen bond]]s. Bottom, an '''{{mono|AT}}''' base pair with two hydrogen bonds. Non-covalent hydrogen bonds between the pairs are shown as dashed lines.</div></div></div>

In a DNA double helix, each type of nucleobase on one strand bonds with just one type of nucleobase on the other strand. This is called [[Complementarity (molecular biology)|complementary]] [[base pair]]ing. Purines form [[hydrogen bond]]s to pyrimidines, with adenine bonding only to thymine in two hydrogen bonds, and cytosine bonding only to guanine in three hydrogen bonds. This arrangement of two nucleotides binding together across the double helix (from six-carbon ring to six-carbon ring) is called a Watson-Crick base pair. DNA with high [[GC-content]] is more stable than DNA with low {{mono|GC}}-content. A [[Hoogsteen base pair]] (hydrogen bonding the 6-carbon ring to the 5-carbon ring) is a rare variation of base-pairing.<ref name="pmid23818176">{{cite journal |vauthors=Nikolova EN, Zhou H, Gottardo FL, Alvey HS, Kimsey IJ, Al-Hashimi HM |title=A historical account of Hoogsteen base-pairs in duplex DNA |journal=Biopolymers |volume=99 |issue=12 |pages=955–68 |year=2013 |pmid=23818176 |pmc=3844552 |doi=10.1002/bip.22334 }}</ref> As hydrogen bonds are not [[covalent bond|covalent]], they can be broken and rejoined relatively easily. The two strands of DNA in a double helix can thus be pulled apart like a zipper, either by a mechanical force or high [[temperature]].<ref>{{cite journal | vauthors = Clausen-Schaumann H, Rief M, Tolksdorf C, Gaub HE | title = Mechanical stability of single DNA molecules | journal = Biophysical Journal | volume = 78 | issue = 4 | pages = 1997–2007 | date = April 2000 | pmid = 10733978 | pmc = 1300792 | doi = 10.1016/S0006-3495(00)76747-6 | bibcode = 2000BpJ....78.1997C }}</ref> As a result of this base pair complementarity, all the information in the double-stranded sequence of a DNA helix is duplicated on each strand, which is vital in DNA replication. This reversible and specific interaction between complementary base pairs is critical for all the functions of DNA in organisms.<ref name=Alberts />

{{Anchor|ssDNA}}

==== ssDNA vs. dsDNA ====
Most DNA molecules are actually two polymer strands, bound together in a helical fashion by noncovalent bonds; this double-stranded (dsDNA) structure is maintained largely by the intrastrand base stacking interactions, which are strongest for {{mono|G,C}} stacks. The two strands can come apart—a process known as melting—to form two single-stranded DNA (ssDNA) molecules. Melting occurs at high temperatures, low salt and high [[pH]] (low pH also melts DNA, but since DNA is unstable due to acid depurination, low pH is rarely used).

The stability of the dsDNA form depends not only on the {{mono|GC}}-content (% {{mono|G,C}} basepairs) but also on sequence (since stacking is sequence specific) and also length (longer molecules are more stable). The stability can be measured in various ways; a common way is the [[DNA melting|melting temperature]] (also called ''T<sub>m</sub>'' value), which is the temperature at which 50% of the double-strand molecules are converted to single-strand molecules; melting temperature is dependent on ionic strength and the concentration of DNA. As a result, it is both the percentage of {{mono|GC}} base pairs and the overall length of a DNA double helix that determines the strength of the association between the two strands of DNA. Long DNA helices with a high {{mono|GC}}-content have more strongly interacting strands, while short helices with high {{mono|AT}} content have more weakly interacting strands.<ref>{{cite journal | vauthors = Chalikian TV, Völker J, Plum GE, Breslauer KJ | title = A more unified picture for the thermodynamics of nucleic acid duplex melting: a characterization by calorimetric and volumetric techniques | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 96 | issue = 14 | pages = 7853–58 | date = July 1999 | pmid = 10393911 | pmc = 22151 | doi = 10.1073/pnas.96.14.7853 | bibcode = 1999PNAS...96.7853C | doi-access = free }}</ref> In biology, parts of the DNA double helix that need to separate easily, such as the {{mono|TATAAT}} [[Pribnow box]] in some [[promoter (biology)|promoters]], tend to have a high {{mono|AT}} content, making the strands easier to pull apart.<ref>{{cite journal | vauthors = deHaseth PL, Helmann JD | title = Open complex formation by Escherichia coli RNA polymerase: the mechanism of polymerase-induced strand separation of double helical DNA | journal = Molecular Microbiology | volume = 16 | issue = 5 | pages = 817–24 | date = June 1995 | pmid = 7476180 | doi = 10.1111/j.1365-2958.1995.tb02309.x | s2cid = 24479358 }}</ref>

In the laboratory, the strength of this interaction can be measured by finding the melting temperature ''T<sub>m</sub>'' necessary to break half of the hydrogen bonds. When all the base pairs in a DNA double helix melt, the strands separate and exist in solution as two entirely independent molecules. These single-stranded DNA molecules have no single common shape, but some conformations are more stable than others.<ref>{{cite journal | vauthors = 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 | date = December 2004 | pmid = 15609994 | doi = 10.1021/bi048221v | url = http://www.boc.uu.se/boc14www/thesis/johan2005/Paper%20V/Paper%20V.pdf | url-status=live | archive-url = https://web.archive.org/web/20070610205112/http://www.boc.uu.se/boc14www/thesis/johan2005/Paper%20V/Paper%20V.pdf | archive-date = 10 June 2007 | df = dmy-all }}</ref>