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A Molecular Dynamics Computer Simulation of an Eight‐Base‐Pair DNA Fragment in Aqueous Solution: Comparison with Experimental Two‐Dimensional NMR Data a
Author(s) -
GUNSTEREN W. F.,
BERENDSEN H. J. C.,
GEURTSEN R. G.,
ZWINDERMAN H. R. J.
Publication year - 1986
Publication title -
annals of the new york academy of sciences
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.712
H-Index - 248
eISSN - 1749-6632
pISSN - 0077-8923
DOI - 10.1111/j.1749-6632.1986.tb20962.x
Subject(s) - molecular dynamics , chemistry , dihedral angle , dna , aqueous solution , molecule , ion , base pair , fragment (logic) , crystallography , base (topology) , solvation shell , computational chemistry , algorithm , solvation , hydrogen bond , mathematics , mathematical analysis , biochemistry , organic chemistry
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.