= Base pairing
<Base pairing> is the recognition and association of compatible <nucleobases>. In canonical Watson–Crick geometry, an <adenine>–<thymine> <base pair> has two <hydrogen bonds>, while a <guanine>–<cytosine> <base pair> has three. These counts refer to those specific geometries and usual chemical forms; they are not a definition of every possible <base pair>. <RNA> can also contain other pairings, and canonical <adenine>–<uracil> pairing replaces <adenine>–<thymine> pairing. See https://openstax.org/books/biology-2e/pages/14-2-dna-structure-and-sequencing[Clark, Douglas and Choi, Biology 2e: DNA structure].
\Image[/dna-antiparallel-base-pairs.png]
{title=Six canonical Watson–Crick <DNA> <base pairs>: opposite backbone directions and two or three <hydrogen bonds> per pair}
For this illustrative duplex, the six <base pairs> are A–T, C–G, G–C, T–A, A–T, and C–G. Thus three contribute two <hydrogen bonds> each and three contribute three each:
$$
3\times2+3\times3=15.
$$
Each dotted connector in the diagram counts one <hydrogen bond>; coloured boxes denote whole <nucleobases>, not individual <chemical atoms>. The solid rails denote the <covalent bond> scaffold. Separating the two strands disrupts <base pairing> and <base stacking> without requiring the backbone to be cut.
The count of fifteen <hydrogen bonds> is not fifteen identical contributions to a duplex's <Gibbs free energy>. <Base stacking>, interactions with <water> and <ions>, <temperature>, and the order of neighbouring <base pairs> also matter. Knowing the fraction of <guanine>–<cytosine> <base pairs> alone does not fix a <nucleic acid double helix>'s shape or stability. See https://www.ncbi.nlm.nih.gov/books/NBK21134/[Brown, Genomes: pairing and stacking interactions]. What makes <base pairing> especially useful is its selectivity: an exposed <DNA> strand constrains the partner's <nucleic acid sequence>, giving <DNA replication> a chemical recognition rule.
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