base pairing

Meaning: Base pairing is the specific hydrogen bonding between a purine and a pyrimidine on opposite nucleic acid strands. Adenine pairs with thymine in DNA (adenine with uracil in RNA), and guanine pairs with cytosine. Pairing a purine with a pyrimidine keeps the width of the double helix constant. The two strands run antiparallel (5′→3′ opposite 3′→5′). Base pairs are held by hydrogen bonds, and stacking of the bases adds further stability. The sequence of one strand therefore determines the sequence of its complement. This is the basis of replication, transcription, translation (codon–anticodon pairing) and PCR primer binding.

Equation: Chargaff's rules for double-stranded DNA: [A] = [T] and [G] = [C], so [purines] = [pyrimidines].

On the MCAT: Expect a question giving one strand and asking for the complementary strand, remembering the antiparallel orientation. Another common setup compares melting temperature (Tm) or denaturation of DNA samples with different G–C content: higher G–C content means a higher Tm. Passages may give base percentages (if A is 20%, then T is 20%, and G plus C is 60%). Also expect questions on tRNA anticodon pairing, hairpins in RNA, and primer annealing in PCR.

Common confusion: Students say the covalent phosphodiester bonds break when DNA melts. They do not. Only the hydrogen bonds between bases break, and the backbone stays intact. Also, Chargaff's rules apply to double-stranded DNA, not to single-stranded RNA or DNA.