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Molecular dynamics simulation of ds-DNA on a gold surface at low surface coverage

Published online by Cambridge University Press:  31 January 2011

One-Sun Lee  and
George C. Schatz
One-Sun Lee
Affiliation:
[email protected], Northwestern University, Chemistry, Evanston, Illinois, United States
George C. Schatz
Affiliation:
[email protected], Northwestern University, Chemistry, Evanston, Illinois, United States
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Abstract

Molecular dynamics methods have been used to study the conformation of ds-DNA on a gold surface for low surface coverage at the atomistic level. Each ds-DNA strand, which is attached to the [111] surface of gold with a -S(CH2)6- linker, is found to be nearly perpendicular to the surface and maintaining the Watson-Crick B-DNA conformation. The tilt angle between the ds-DNA and an axis normal to the gold surface is 7.3 (+/-) 2.2 degree. The concentration of counterions around the ds-DNA is increased by a factor of 1.8 relative to the bulk, which is significantly lower than in our previous simulations of ds-DNA at high surface coverage.

Keywords

simulationsurface chemistryadsorption
Type
Research Article
Information
MRS Online Proceedings Library (OPL) , Volume 1177: Symposium Z – Computational Nanoscience–How to Exploit Synergy between Predictive Simulations and Experiment , 2009 , 1177-Z09-33
Copyright
Copyright © Materials Research Society 2009

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