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Albany 2001

category image Biomolecular
Stereodynamics
SUNY at Albany
June 19-23, 2001

Water-Bridged DNA Base Pairs

The low-energy stable states of the complex of the A-T base pair with water molecule are found under examining the section of the semi-empirical PM3 potential energy surface of this DNA base pair interacting with water molecule in the vicinity of Watson-Crick configuration. The preferable monohydratation sites of the A-T base pair in the closed and preopened configurations are determined. Among the energetically favorable states of the studied complex, there are the water-bridged base pairs where water molecule mediates one of the intermolecular hydrogen bonds of the A-T base pair. The difference in energy between the most favorable states of the closed pairs with water and the water-bridged pairs are less than 1 kcal/mol (1).

Two types of base pairs bridged by water are found in the present study. One refers to the configurations with water molecule being inserted on the major groove side and bonded to the N6(A) and the O4(T). The mutual positions of the bases in this water-bridged pairs are located nearby the complementary Watson-Crick pair. An insertion of water molecule at this site results in the formation of the relatively stable and long-lived complex which might be detected experimentally. The other type covers the water-bridged pairs where water molecule disposes on the place of central H-bond of the A-T pair and connects the N1(A) and the N3(T). One of the water-bridged pair of this type appears to be extremely close to the water-bridged A-U pair reported by Poltev and Steinberg (2). Its formation may substantially facilitate the DNA opening. The present study demonstrate that water molecule is unable to intrude into the pair interior on the weak C2(A)---O2(T) bond side. We suggest that the route of the base pair preopening in the vicinity of the closed A-T pair state passes one of the local minimum energy states [3]. A possible role of the water-bridged pairs in DNA recognition processes is discussed.

References and Footnotes

  • E.S. Kryachko, S.N. Volkov, Int. J. Quant. Chem. 74, (2001).
  • V.I. Poltev, S.V. Steinberg, Mol. Biol. 21, 704-713 (1987).
  • E.S. Kryachko, S.N. Volkov, J. Biomol. Struct. Dynam.(inpreparation).
  • E.S. Kryachko and S.N. Volkov

    Bogolyubov Institute for Theoretical Physics, National Academy of Science of Ukraine, Kiev, Ukraine 03143 email: snvolkov@bitp.kiev.ua; Fax: 380 (44) 266-5998; Phone: 380 (44) 266-9159