Preopening of the DNA base pairs

Abstract

Abstract The lower‐energy stable structures of the A⋅T base pair are revealed under a search of its potential energy surface in the vicinity of its Watson–Crick configuration performed at the PM3 computational level. Their properties and the mutual position of the nucleic acid bases A and T in these structures allow to partition them into three classes: partially preopened, stretched, and fully preopened. The preferable monohydration sites of the preopened, stretched, and fully preopened pairs are also determined. It is demonstrated, first, that the monohydration of the A⋅T pair at particular sites favors a base pair preopeness and, second, that a binding of the water molecule to the preopened A⋅T base pair on the major groove side enhances its stabilization. It is also shown that water molecule placing in the vicinity of the central H bond of the A⋅T pair significantly facilitates its preopening. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 82: 193–204, 2001