Premium
Preopening of the DNA base pairs
Author(s) -
Kryachko Eugene S.,
Volkov Sergey N.
Publication year - 2001
Publication title -
international journal of quantum chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.484
H-Index - 105
eISSN - 1097-461X
pISSN - 0020-7608
DOI - 10.1002/qua.1040
Subject(s) - base pair , chemistry , base (topology) , molecule , molecular structure of nucleic acids: a structure for deoxyribose nucleic acid , nucleic acid , dna , groove (engineering) , crystallography , stereochemistry , materials science , mathematics , mathematical analysis , biochemistry , metallurgy , organic chemistry
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