Paper Citing NAMD - Abstract
Lee, One-Sun; Schatz, George C.
Conformation of DNA Between Gold Surfaces
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 7:2568-2573, DEC 2010
The distance between gold nanoparticles that are connected by DNA to form a face centered cubic crystal is significantly shorter than the value based on the B-DNA conformer. This has generated debate as to the correct conformation of DNA. To answer this question, we performed atomistic molecular dynamics simulations (with explicit solvent and added salt) to explore the DNA structure that links the gold surfaces, with the observed gold gold distance imposed as constraint in the simulations. We found that the short distance is accommodated by two effects that allow DNA to maintain a B-DNA structure. First, a 10 base ss-DNA region that is used as a spacer between the ss-DNA linker and the surface is partially adsorbed on the gold surface. Second, 30 degrees bending of the ds-DNA is found in the 4 bp linker region such that the 15 bp ds-DNAs on either side of the linker region have an almost straight structure.
