Page "Base pair" Paragraph 5

The larger nucleobases, adenine and guanine, are members of a class of double-ringed chemical structures called purines ; the smaller nucleobases, cytosine and thymine ( and uracil ), are members of a class of single-ringed chemical structures called pyrimidines.

Purines are complementary only with pyrimidines: pyrimidine-pyrimidine pairings are energetically unfavorable because the molecules are too far apart for hydrogen bonding to be established ; purine-purine pairings are energetically unfavorable because the molecules are too close, leading to overlap repulsion.

Purine-pyrimidine base pairing of AT or GC results in proper duplex structure.

The only other purine-pyrimidine pairings would be AC and GT and UA ( in RNA ); these pairings are mismatches because the pattern of hydrogen donors and acceptors do not correspond.

The GU pairing, with two hydrogen bonds, does occur fairly often in RNA ( see wobble base pair ).