Detection of a guanine X adenine base pair in a decadeoxyribonucleotide by proton magnetic resonance spectroscopy.

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Abstract
A decadeoxyribonucleotide, d(C-C-A-A-G-A-T-T-G-G) (I), forms a duplex in solution. The base pairing pattern in this duplex was studied by proton NMR spectroscopy. Five NH.cntdot..cntdot..cntdot.N hydrogen-bonded proton resonances were observed, and they were assigned by nuclear Overhauser enhancement experiments as well as by comparison to 5 previously assigned NH.cntdot..cntdot..cntdot.N H-bonded proton resonances in a self-complementary duplex of similar sequence, d(C-C-A-A-G-C-T-T-G-G) (II). The results suggest that the central -G-A- residues of I form G.cntdot.A base pairs in the helical state. The fact that the H2 proton of A at the 6th position from the 5'' end of I showed nuclear Overhauser enhancement when the NH.cntdot..cntdot..cntdot.N hydrogen-bonded proton resonance of G.cntdot.A was irradiated suggests that the bases of the G.cntdot.A base pair are oriented in an anti-anti conformation. Comparison of the linewidths at the half height of the NH.cntdot..cntdot..cntdot.N H-bonded proton resonances of I at 1.degree. C suggest that the G.cntdot.A base pairs are less stable than adjacent A.cntdot.T base pairs.