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Base pair
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==Hydrogen bonding and stability== <div class="thumb tright" style="background:#f9f9f9; border:1px solid #ccc; margin:0.5em;"> {| border="0" cellpadding="2" cellspacing="0" style="width:230px; font-size:85%; border:1px solid #ccc; margin:0.3em;" |- |[[File:Base pair GC.svg|282px]] |} {| border="0" cellpadding="2" cellspacing="0" style="width:230px; font-size:85%; border:1px solid #ccc; margin:0.3em;" |- |[[File:Base pair AT.svg|282px]] |} <div style="border: none; width:282px;"><div class="thumbcaption">Top, a '''G.C''' base pair with three [[hydrogen bond]]s. Bottom, an '''A.T''' base pair with two hydrogen bonds. Non-covalent hydrogen bonds between the bases are shown as dashed lines. The wiggly lines stand for the connection to the pentose sugar and point in the direction of the minor groove. </div></div></div> [[Hydrogen bond]]ing is the chemical interaction that underlies the base-pairing rules described above. Appropriate geometrical correspondence of hydrogen bond donors and acceptors allows only the "right" pairs to form stably. DNA with high [[GC-content]] is more stable than DNA with low GC-content. Crucially, however, [[stacking (chemistry)|stacking interactions]] are primarily responsible for stabilising the double-helical structure; Watson-Crick base pairing's contribution to global structural stability is minimal, but its role in the specificity underlying complementarity is, by contrast, of maximal importance as this underlies the template-dependent processes of the [[Central dogma of molecular biology|central dogma]] (e.g. [[DNA replication]]).<ref name="Yakovchuk2006">{{cite journal | vauthors = Yakovchuk P, Protozanova E, Frank-Kamenetskii MD | title = Base-stacking and base-pairing contributions into thermal stability of the DNA double helix | journal = Nucleic Acids Research | volume = 34 | issue = 2 | pages = 564–574 | date = 2006-01-30 | pmid = 16449200 | pmc = 1360284 | doi = 10.1093/nar/gkj454 }}</ref> The bigger [[nucleobase]]s, adenine and guanine, are members of a class of double-ringed chemical structures called [[purine]]s; the smaller nucleobases, cytosine and thymine (and uracil), are members of a class of single-ringed chemical structures called [[pyrimidine]]s. Purines are complementary only with pyrimidines: pyrimidine–pyrimidine pairings are energetically unfavorable because the molecules are too far apart for hydrogen bonding to be established; purine–purine pairings are energetically unfavorable because the molecules are too close, leading to overlap repulsion. Purine–pyrimidine base-pairing of AT or GC or UA (in RNA) results in proper duplex structure. The only other purine–pyrimidine pairings would be AC and GT and UG (in RNA); these pairings are mismatches because the patterns of hydrogen donors and acceptors do not correspond. The GU pairing, with two hydrogen bonds, does occur fairly often in [[RNA]] (see [[wobble base pair]]). Paired DNA and RNA molecules are comparatively stable at room temperature, but the two nucleotide strands will separate above a [[Dna melting|melting point]] that is determined by the length of the molecules, the extent of mispairing (if any), and the GC content. Higher GC content results in higher melting temperatures; it is, therefore, unsurprising that the genomes of [[extremophile]] organisms such as ''[[Thermus thermophilus]]'' are particularly GC-rich. On the converse, regions of a genome that need to separate frequently — for example, the promoter regions for often-[[transcription (genetics)|transcribed]] genes — are comparatively GC-poor (for example, see [[TATA box]]). GC content and melting temperature must also be taken into account when designing [[primer (molecular biology)|primers]] for [[Polymerase chain reaction|PCR]] reactions.{{citation needed|date=August 2022}} ===Examples=== The following DNA sequences illustrate pair double-stranded patterns. By convention, the top strand is written from the [[5′-end]] to the [[3′-end]]; thus, the bottom strand (complementary strand) is written 3′ to 5′. :A base-paired DNA sequence: ::{{code|ATCGATTGAGCTCTAGCG}} ::{{code|TAGCTAACTCGAGATCGC}} :The corresponding RNA sequence, in which [[uracil]] is substituted for thymine in the RNA strand: ::{{code|AUCGAUUGAGCUCUAGCG}} ::{{code|UAGCUAACUCGAGAUCGC}}
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