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Monte-Carlo simulation of DNA duplex hydration. B and B' conformations of poly(dA).poly(dT) have different hydration shells.

Abstract：

:Monte-Carlo simulation of poly(dA).poly(dT) hydration by 30 water molecules per nucleotide pair has been performed. Two B-family conformations, both with a 36 degrees helical twist but with different minor groove widths, were considered. One conformation is Arnott's standard B form, the other one is specific for poly(dA).poly(dT) B' form with a narrowed minor groove. The mean energies and the mean numbers of water-water and water-DNA hydrogen bonds are close for the two conformations. Nevertheless, the hydration shell of the B' form differs drastically from that of the standard B form. The water arrangement in the minor groove of the B' form resembles the spine of hydration in the central part of Dickerson's dodecamer d(CGCGAATTCGCG). No such spine is formed in the hydration shell of the usual B form with a wider minor groove. In this conformation water bridges between adenine N3 or thymine O2 and oxygen of the sugar ring of the neighbouring nucleotide along the chain can be formed ("strings" in Dickerson's decamer d(CCAAGATTGG].

journal_name

J Biomol Struct Dyn

journal_title

Journal of biomolecular structure & dynamics

authors

Poltev VI,Teplukhin AV,Chuprina VP

doi

10.1080/07391102.1988.10506508

subject

Has Abstract

pub_date

1988-12-01 00:00:00

pages

575-86

issue

3

eissn

0739-1102

issn

1538-0254

journal_volume

6

pub_type

杂志文章

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