The two strands of ordinary DNA pair selectively: adenine (A) pairs with thymine (T), while guanine (G) pairs with cytosine (C).

This complementarity comes from a combination of molecular geometry and chemical interaction patterns.

Hydrogen-bond donors and acceptors

The Watson–Crick edge of each base presents hydrogen-bond donors and acceptors in a particular arrangement.

A–T can form two characteristic hydrogen bonds, while G–C can form three. Other pairings generally place donors opposite donors, acceptors opposite acceptors, or produce less compatible geometry.

Size complementarity

Pairing one purine with one pyrimidine keeps the width of the double helix approximately uniform. Purine–purine pairs are too wide for the standard geometry, while pyrimidine–pyrimidine pairs are too narrow.

Pairing is not only bond counting

It is tempting to conclude that G–C is 'stronger' simply because it has three hydrogen bonds rather than two. DNA duplex stability also depends strongly on base stacking, sequence context, solvent, ions and temperature.

Hydrogen bonds are particularly important for specificity: they help distinguish which opposing geometries are chemically compatible.

Complementarity carries information

Because one strand determines the compatible base at each position on the other,

A ↔ T
G ↔ C

sequence information can be copied by using an existing strand as a template.