A Molecular Dynamics Simulation of a Polyamine-Induced Conformational Change of DNA. A Possible Mechanism for the B to Z Transition |
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| Authors: | Ian S. Haworth Alison Rodger W. Graham Richards |
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| Affiliation: | 1. School of Pharmacy University of Southern California , 1985 Zonal Avenue, Los Angeles , CA , 90033 , U.S.A.;2. Physical Chemistry Laboratory , Oxford University , South Parks Road, Oxford , 0X1 3QZ , U.K. |
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| Abstract: | Abstract A 75ps molecular dynamics simulation has been performed on a fully solvated complex of spermine with the B DNA decamer (dGdC)5 · (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 BII conformation might be of importance in this process. |
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