A(+)-C MISMATCHED BASE-PAIRING IN DNA

The structural aspects of an antiparallel DNA duplex with A(+)-C misma tched base-pair by molecular dynamics calculations are discussed. The A(+)-C mismatched base-pair which has been characterized by NMR with t wo hydrogen bonds namely, A(+)(6NH(2))-C(3N) and A(+)(1NH)-C(2O), fits into B-form duplex with little distortion in the pyrimidine strand. a in the A(+)-C mispair is efficiently stacked to the flanking purine b ases. Such efficient purine-purine stacking provides extra stabilizati on to this mismatched base-pair. On the other hand, C in the mispair i s displaced from the helix axis while adjacent T (i.e, T7) is slightly off because of the enhanced base-pair twist. This supports the experi mental observation of unusual chemical shifts for the H5 and H6 proton s belonging to the C of the A(+)-C mismatched base-pair.