Molecular dynamics studies of the behaviour of water molecules and small ions in concentrated solutions of polymeric B-DNA

Molecular dynamics calculations are carried out for systems of hexagonally packed B-DNA molecules in aqueous solutions containing Na+, Ca2+ and Cl- ions. Attention is focussed on the static ordering and dynamics of water molecules and small ions in the vicinity of the DNA. Results are reported for hydration numbers, solvent molecule mobilities and DNA-counterion distributions, and comparison is made with the available experimental data and with simulations of related systems.

[1]  I. R. Mcdonald,et al.  The role of molecular flexibility in simulations of water , 1990 .

[2]  A. Laaksonen,et al.  Molecular dynamics simulation of double helix Z-DNA in solution , 1989 .

[3]  William L. Jorgensen,et al.  Energy component analysis for dilute aqueous solutions of lithium(1+), sodium(1+), fluoride(1-), and chloride(1-) ions , 1984 .

[4]  G. C. Levy,et al.  Spontaneous ordering of DNA. Effects of intermolecular interactions on DNA motional dynamics monitored by 13C and 31P nuclear magnetic resonance spectroscopy. , 1983, The Journal of biological chemistry.

[5]  S. Hanlon,et al.  Structural transitions of deoxyribonucleic acid in aqueous electrolyte solutions. II. The role of hydration. , 1975, Biochemistry.

[6]  B. H. Pheiffer,et al.  Helical parameters of DNA do not change when DNA fibers are wetted: X-ray diffraction study. , 1979, Proceedings of the National Academy of Sciences of the United States of America.

[7]  E. Clementi,et al.  Simulations of the solvent structure for macromolecules. III. Determination of the Na+ counter ion structure , 1982, Biopolymers.

[8]  K. A. Hartman,et al.  Hydration of Deoxyribonucleic Acid. III. A Spectroscopic Study of the Effect of Hydration on the Structure of Deoxyribonucleic Acid , 1963 .

[9]  H. Magdelenat,et al.  Study of the self‐diffusion coefficients of cations in the presence of an acidic polysaccharide , 1974, Biopolymers.

[10]  H. Berendsen,et al.  A Molecular Dynamics Computer Simulation of an Eight‐Base‐Pair DNA Fragment in Aqueous Solution: Comparison with Experimental Two‐Dimensional NMR Data a , 1986, Annals of the New York Academy of Sciences.

[11]  P. Kollman,et al.  An all atom force field for simulations of proteins and nucleic acids , 1986, Journal of computational chemistry.

[12]  R. Lynden-Bell,et al.  Distribution and dynamics of mobile ions in systems of ordered B-DNA , 1989 .

[13]  Mauro Ferrario,et al.  Molecular-dynamics simulation of liquid methanol , 1987 .

[14]  J. Mccammon,et al.  Dynamics of Proteins and Nucleic Acids , 2018 .

[15]  H. Berendsen,et al.  Interaction Models for Water in Relation to Protein Hydration , 1981 .

[16]  F. Crick,et al.  Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid , 1953, Nature.

[17]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[18]  J. Banavar,et al.  Computer Simulation of Liquids , 1988 .

[19]  Roger Impey,et al.  Spectroscopic and transport properties of water , 1982 .

[20]  Wolfram Saenger,et al.  Principles of Nucleic Acid Structure , 1983 .

[21]  Michael L. Klein,et al.  Effective pair potentials and the properties of water , 1989 .

[22]  G. Fasman,et al.  Handbook of biochemistry and molecular biology. Nucleic acids - v. 1 - 3. ed. , 1975 .

[23]  M. Gruwel,et al.  Sodium ion and solvent nuclear relaxation results in aqueous solutions of DNA , 1987, Biopolymers.

[24]  U. Singh,et al.  A NEW FORCE FIELD FOR MOLECULAR MECHANICAL SIMULATION OF NUCLEIC ACIDS AND PROTEINS , 1984 .

[25]  H R Drew,et al.  Ordered water structure around a B-DNA dodecamer. A quantitative study. , 1983, Journal of molecular biology.

[26]  G L Seibel,et al.  A molecular dynamics simulation of double-helical B-DNA including counterions and water. , 1985, Proceedings of the National Academy of Sciences of the United States of America.