A base pair is an association of two nucleobases through hydrogen bonds in a compatible arrangement. It commonly joins opposite strands of a nucleic acid double helix, but can also join two regions of one folded RNA strand. Canonical Watson–Crick DNA base pairs match adenine with thymine and guanine with cytosine; canonical RNA base pairs use adenine with uracil instead. The nucleobases belong to complete nucleotides, including their attached sugars and backbone phosphate. See NHGRI: base pair.
The abbreviation bp also measures the length of a paired region. Our ACGTAC/TGCATG duplex has six base pairs, containing twelve nucleotides altogether. Its upper strand contains two adenine, two cytosine, one guanine, and one thymine nucleobase; the lower contains one, one, two, and two respectively. Combined, the counts are three of each nucleobase. Equality of total adenine and thymine, or of total guanine and cytosine, need not hold within either individual strand.
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 Clark, Douglas and Choi, Biology 2e: DNA structure.
Six canonical Watson–Crick DNA base pairs: opposite backbone directions and two or three hydrogen bonds per pair
. Details. 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: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 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.
Watson-Crick base pairing is the canonical geometry of pairing between complementary nucleic-acid bases, including adenine–thymine and guanine–cytosine in ordinary DNA. It is a particular pairing geometry, not a synonym for every possible base pair.
nucleic acid complementarity is the relation between sequences that permits specified base pairs to form when aligned with appropriate strand orientation. In homologous recombination, structural organization helps test pairing rather than reading one fixed base sequence.
