Constant pressure molecular dynamics simulations of the dodecamers: d(GCGCGCGCGCGC)2 and r(GCGCGCGCGCGC)2

Here we report constant pressure molecular dynamics simulations of the B‐DNA dodecamer d(GCGCGCGCGCGC)2 and the A‐RNA dodecamer r(GCGCGCGCGCGC)2 in aqueous solution. The molecular dynamics simulations were performed at reference pressures of 1 and 6000 atm. We obtained stable trajectories, especially for the A‐RNA dodecamer, using the standard atom based truncation cutoff method. For the B‐DNA dodecamer, a tendency to transform to the A‐DNA form was obtained. The atomic mean square fluctuations were lower for the A‐RNA dodecamer than for the B‐DNA, and were further reduced by increased pressure for the A‐RNA dodecamer. The backbone and glycosidic torsion angles were well preserved for the A‐RNA dodecamer and only small changes were observed for the B‐DNA dodecamer. In both dodecamers the Watson–Crick hydrogen bonds were preserved without any constraints. The differences in the exposed surface area between the dodecamers were mainly due to the 2′OH group and to the cytosine base being more exposed in the B...

[1]  N C Seeman,et al.  RNA double-helical fragments at atomic resolution. II. The crystal structure of sodium guanylyl-3',5'-cytidine nonahydrate. , 1976, Journal of molecular biology.

[2]  L. Verlet.  Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules , 1967 .

[3]  B. Lee,et al.  The interpretation of protein structures: estimation of static accessibility. , 1971, Journal of molecular biology.

[4]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

[5]  D W Hukins,et al.  Optimised parameters for A-DNA and B-DNA. , 1972, Biochemical and biophysical research communications.

[6]  R. Levy,et al.  Molecular dynamics simulation of solvated protein at high pressure. , 1992, Biochemistry.

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

[8]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

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

[10]  W. V. van Gunsteren,et al.  Dynamical properties of bovine pancreatic trypsin inhibitor from a molecular dynamics simulation at 5000 atm , 1993, FEBS letters.

[11]  Alexander D. MacKerell,et al.  An all-atom empirical energy function for the simulation of nucleic acids , 1995 .

[12]  Harel Weinstein,et al.  Molecular dynamics simulation of the hydrated d(CGCGAATTCGCG)2 dodecamer , 1993 .

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

[14]  L. Nilsson,et al.  High-pressure molecular dynamics of a nucleic acid fragment , 1994 .

[15]  S. Swaminathan,et al.  Molecular dynamics of B-DNA including water and counterions: a 140-ps trajectory for d(CGCGAATTCGCG) based on the GROMOS force field , 1991 .

[16]  E. Lesnik,et al.  Relative thermodynamic stability of DNA, RNA, and DNA:RNA hybrid duplexes: relationship with base composition and structure. , 1995, Biochemistry.

[17]  T. Darden,et al.  Toward the Accurate Modeling of DNA: The Importance of Long-Range Electrostatics , 1995 .

[18]  P. Kollman,et al.  Molecular Dynamics Simulations on Solvated Biomolecular Systems: The Particle Mesh Ewald Method Leads to Stable Trajectories of DNA, RNA, and Proteins , 1995 .

[19]  G. Ciccotti,et al.  Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .

[20]  H R Drew,et al.  Structure of a B-DNA dodecamer: conformation and dynamics. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[21]  D W Hukins,et al.  Refinement of the structure of B-DNA and implications for the analysis of x-ray diffraction data from fibers of biopolymers. , 1973, Journal of molecular biology.

[22]  B. Montgomery Pettitt,et al.  Structural and energetic effects of truncating long ranged interactions in ionic and polar fluids , 1985 .

[23]  R Lavery,et al.  The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. , 1988, Journal of biomolecular structure & dynamics.

[24]  S. Swaminathan,et al.  Toward a dynamical structure of DNA: comparison of theoretical and experimental NOE intensities. , 1992, Science.

[25]  David L. Beveridge,et al.  Molecular dynamics studies of DNA , 1994 .

[26]  D. Beveridge,et al.  A Nanosecond Molecular Dynamics Trajectory for a B DNA Double Helix: Evidence for Substates , 1994 .

[27]  J. Barciszewski,et al.  B–Z DNA reversible conformation changes effected by high pressure , 1991, FEBS letters.

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