Abstract
Molecular dynamics (MD) methods have been used to study the conformation of DNA and its interaction with neighboring DNAs having the same base pair (bp) composition on a flat gold surface. Most of the simulations refer to a DNA that is surrounded by six other DNAs, with the initial distance between the DNAs chosen to be 27 A to simulate high packing conditions. A six-carbon alkylthiolate linker connects each DNA to the gold surface, and there is an A10 spacer between the alkylthiolate and an 18 bp double-stranded (ds) region for each DNA. In addition, there is a 5 base dangling end on each DNA to match recent experiments in which the dangling ends appeared to show important interactions. We performed 20 ns MD simulations in water with high salt concentration, and it is found that the ds-DNA maintains Watson−Crick B-DNA conformations. The tilt angle (relative to the surface) of the central DNA in the cluster is 27° ± 5°, whereas the tilt angle of the surrounding DNAs is 11° ± 5°. The average angle between ...
Published Version
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