当前位置： SCI文献检索 > BIOCHEMISTRY期刊下所有文献 > Solution structure of the exocyclic 1,N2-propanodeoxyguanosine adduct opposite deoxyadenosine in a DNA nonamer duplex at pH 8.9. model of pH-dependent conformational transition.

Solution structure of the exocyclic 1,N2-propanodeoxyguanosine adduct opposite deoxyadenosine in a DNA nonamer duplex at pH 8.9. model of pH-dependent conformational transition.

Abstract：

:The solution structure of the complementary d(C1-A2-T3-G4-X5-G6-T7-A8-C9).d(G10-T11-A12-C13-A14-C15-A16-T17-G18) DNA duplex (designated X.A 9-mer), which contains a 1,N2-propanodeoxyguanosine exocyclic adduct X5 opposite deoxyadenosine A14 at the center, is pH dependent [Kouchakdjian, M., Eisenberg, M., Live, D., Marinelli, E., Grollman, A., & Patel, D.J. (1990) Biochemistry 29, 4456-4465]. In our previous paper [Huang, P., & Eisenberg, M. (1992) Biochemistry 31, 6518-6532] we established the three-dimensional structure of this X.A 9-mer duplex at pH 5.8 by use of restrained molecular dynamics followed by NOE-based back-calculation refinement. The present paper discusses the structure at pH 8.9 and the pH-dependent conformational transition between the structures at pH 5.8 and at pH 8.9. The structure at pH 8.9 is calculated starting from five different conformations. The final structures converge and agree well with the experimental NOE intensities. These structures are essentially B-type DNA (with X5 and A14 in the BII conformation while the other residues are in the most commonly described BI conformation) and display an approximate 27 degrees kink at the center of the helix. At the kink site, X5 is positioned in the major groove with the exocyclic ring directed toward the G6.C13 base pair, unstacked from the flanking base G6 and exposed to the solvent. A14, opposite the lesion, remains stacked with its neighbor C15, but not with C13. The kinked helix can accommodate the rotation of the bulky X5 about its glycosidic bond. We propose here a model for the pH-dependent transition. Our model explains the conformational change, which includes the anti and syn rotation of the bulky adduct around its glycosidic bond, with a minimal energy barrier and with an overall kink of the DNA helix. These new findings, fully consistent with the NMR experimental data, were revealed only after restrained dynamics refinement. Distance-restrained energy minimization by itself was insufficient, as shown by the previous NMR study.

journal_name

Biochemistry

journal_title

Biochemistry

authors

Huang P,Patel DJ,Eisenberg M

doi

10.1021/bi00066a004

subject

Has Abstract

pub_date

1993-04-20 00:00:00

pages

3852-66

issue

eissn

0006-2960

issn

1520-4995

journal_volume

pub_type

杂志文章

在线工具

Solution structure of the exocyclic 1,N2-propanodeoxyguanosine adduct opposite deoxyadenosine in a DNA nonamer duplex at pH 8.9. model of pH-dependent conformational transition.