A molecular dynamics simulation of a polyamine-induced conformational change of DNA. A possible mechanism for the b to z transition

Ian S. Haworth, Alison Rodger, W. Graham Richards

Research output: Contribution to journalArticle

23 Citations (Scopus)

Abstract

A 75ps molecular dynamics simulation has been performed on a fully solvated complex of spermine with the B DNA decamer (dGdC)5o (dGdC)5. The simulation indicates a possible mechanism by which polyamines might induce the formation of a left-handed helix, the B to Z transition. Spermine was initially located in the major groove, hydrogen bonded to the helix. During the simulation the ligand migrates deeper into the DNA maintaining strong hydrogen bonding to the central guanine bases and destroying the Watson-Crick base pairing with their respective cytosines. Significant rotation of these and other cytosine bases was observed, in part due to interactions of the helix with the aminopropyl chains of spermine. An intermediate Bn conformation might be of importance in this process.

Original languageEnglish
Pages (from-to)195-211
Number of pages17
JournalJournal of Biomolecular Structure and Dynamics
Volume10
Issue number1
DOIs
Publication statusPublished - 1992
Externally publishedYes

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