baseparing

Base pairing refers to the specific hydrogen-bonded interactions between nucleobases on opposite strands of nucleic acids that enable the formation of the DNA double helix and the folded structures of RNA. In DNA, canonical pairs are adenine with thymine and guanine with cytosine; A–T pairs form two hydrogen bonds and G–C pairs form three. In RNA, thymine is replaced by uracil, so adenine pairs with uracil. Base pairing follows Chargaff's rules: in a double-stranded DNA molecule, the amount of adenine equals thymine, and guanine equals cytosine.

Base pairing is reinforced by the antiparallel orientation of the two strands and by base stacking interactions between adjacent pairs. The pairing is sequence-specific and underpins the fidelity of DNA replication and transcription. During replication, complementary base pairing guides the synthesis of new strands; during transcription, it directs the synthesis of RNA from a DNA template. Variations exist in noncanonical structures and during RNA folding; wobble base pairing at the third codon position and certain non-Watson-Crick pairs can occur, contributing to structure and function.

Historically, the concept was established through the work of Watson and Crick, with crucial data from Chargaff and Rosalind Franklin. Today, base pairing is foundational in molecular biology and is exploited in technologies such as PCR, DNA sequencing, and RNA structure prediction and design.