Preopening of the DNA base pairs

The lower-energy stable structures of the AT 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 a nd the mutual position of the nucleic acid bases A and T in these structure s allow to partition them into three classes: partially preopened, stretche d, and fully preopened. The preferable monohydration sites of the preopened , stretched, and fully preopened pairs are also determined. It is demonstra ted, first, that the monohydration of the AT pair at particular sites favor s a base Fair preopeness and, second, that a binding of the water molecule to the preopened AT base pair on the major groove side enhances its stabili zation. It is also shown that water molecule placing in the vicinity of the central H bond of the AT pair significantly facilitates its preopening. (C ) 2001 John Wiley & Sons, Inc. Int J Quantum Chem 82: 193-204, 2001.