A Molecular Dynamics Computer Simulation of an Eight‐Base‐Pair DNA Fragment in Aqueous Solution: Comparison with Experimental Two‐Dimensional NMR Dataa
- 16 December 1986
- journal article
- Published by Wiley in Annals of the New York Academy of Sciences
- Vol. 482 (1) , 287-303
- https://doi.org/10.1111/j.1749-6632.1986.tb20962.x
Abstract
The structure and dynamics of an 8-base-pair DNA fragment (dCGCAACGC/dGCGTTGCG) in aqueous solution (14 Na+ ions, 1231 water molecules) have been simulated by using the molecular-dynamics method. Interproton distances have been calculated for various structures and are compared with a set of 174 distances which have been derived from 2D NOE experiments. The averaged MD structures are compared with ideal A-DNA and B-DNA structures in terms of helix parameters, dihedral angles, and so forth. The hydration of various atoms of the DNA fragment and of the Na+ ions is analyzed by calculating coordination numbers and first-neighbor shell residence times.Keywords
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