Basepairs

Base pairs are the pairs of nucleobases on opposite strands of nucleic acids that form the rungs of the DNA or RNA double helix. In DNA, the standard Watson-Crick base pairs are adenine paired with thymine (A–T) and guanine paired with cytosine (G–C). In RNA, thymine is replaced by uracil (A–U). Base pairing is mediated by hydrogen bonds: A–T forms two hydrogen bonds, G–C forms three, contributing to the overall stability and specificity of the molecules. Base pairing is complementary, and the two strands run in opposite directions (antiparallel), enabling uniform helical structure. The sequence of one strand determines the sequence of its complement.

Base pairs are usually counted per pair rather than per nucleotide; a length of 1,000 base pairs corresponds to 2,000 nucleotides in double-stranded DNA. The concept of GC content (the proportion of guanine and cytosine) affects duplex stability and melting temperature, because G–C pairs are more thermodynamically stable than A–T pairs.

Chargaff's rules describe the base content of DNA: in a given double-stranded molecule, the amount of adenine equals thymine, and guanine equals cytosine. These rules underpin the mechanism of DNA replication: each strand serves as a template; DNA polymerase adds complementary nucleotides, preserving base pairing, with proofreading and repair pathways correcting mispairs.

Noncanonical base pairing occurs in RNA and in certain DNA contexts, including wobble pairing and damaged bases. Base pairing underlies higher-order DNA and RNA structures, gene expression, and genome stability.