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

  • One-Sun Lee (a1) and George C. Schatz (a2)

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.

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