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
This publication has 23 references indexed in Scilit:
- A molecular dynamics simulation of double-helical B-DNA including counterions and water.Proceedings of the National Academy of Sciences of the United States of America, 1985
- Molecular dynamics simulations of d(C-G-C-G-A) X d(T-C-G-C-G) with and without "hydrated" counterions.Proceedings of the National Academy of Sciences of the United States of America, 1985
- Aqueous Hydration of Nucleic Acid Constituents: Monte Carlo Computer Simulation StudiesJournal of Biomolecular Structure and Dynamics, 1984
- Structure of hydrated Na+ ions around a region of A- or B-DNA helixPeptide Science, 1984
- Molecular Dynamics of Phenylalanine Transfer RNAJournal of Biomolecular Structure and Dynamics, 1983
- Dynamics of DNA OligomersJournal of Biomolecular Structure and Dynamics, 1983
- Monte Carlo Studies on Water in the dCpG/Proflavin Crystal HydrateJournal of Biomolecular Structure and Dynamics, 1983
- Computer Simulation of DNA Double-helix DynamicsPublished by Cold Spring Harbor Laboratory ,1983
- Simulations of the solvent structure for macromolecules. III. Determination of the Na+ counter ion structurePeptide Science, 1982
- Structure of a B-DNA dodecamer: conformation and dynamics.Proceedings of the National Academy of Sciences of the United States of America, 1981