Localisation and dynamics of sodium counterions around DNA in solution from molecular dynamics simulation

European Biophysics Journal

Volumn 29, Issue 1, 2000, Pages 57-60

  Bonvin, A M J J ^a  

^a UTRECHT UNIVERSITY   (Netherlands)

Author keywords

DNA; Dynamics; Localisation; Molecular dynamics simulation; Sodium counterions

Indexed keywords

DOUBLE STRANDED DNA; SODIUM ION;

ARTICLE; BINDING AFFINITY; CRYSTAL STRUCTURE; DENSITY; DNA SEQUENCE; DNA STRUCTURE; DYNAMICS; MOLECULAR DYNAMICS; SIMULATION; SOLVATION;

EID: 0033801089     PISSN: 01757571     EISSN: None     Source Type: Journal    
DOI: 10.1007/s002490050251     Document Type: Article

References (27)

1. Atomic coordinates and molecular conformations for DNA-DNA, RNA-RNA, and DNA-RNA helices
2. Interaction models for water in relation to protein hydration
3. Molecular dynamics with coupling to an external bath
4. The Protein Data Bank: A computer-based archival file for macromolecular structures
5. Water molecules in DNA recognition II: A molecular dynamics view of the structure and hydration of the trp operator
6. Helix packing in proteins: Prediction and energetic analysis of dimeric, trimeric and tetrameric GCN4 coiled coil structures
7. Sodium ions and solvent nuclear relaxation results in aqueous solutions of DNA
8. SETOR: Hardware lighted three-dimensional solid model representations of macromolecules
9. Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending
10. VMD - Visual molecular dynamics
11. 23Na relaxation in isotropic and anisotropic liquid-crystalline DNA solutions
12. Computer simulation of molecular dynamics: Methodology, applications and perspectives in chemistry
13. The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids
14. Tandem binding in crystals of a trp repressor/operator half-site complex
15. Molecular dynamics simulations of DNA in solution with different counter-ions
16. The molecular theory of polyelectrolyte solutions with application to the electrostatic properties of polynucleotides
17. DNA bending by small, mobile multivalent cations
18. Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
19. 4NN)(n): Sequence elements responsible for curvature
20. The GROMOS biomolecular simulation program package
21. Structure of the potassium form of CGCGAATTCGCG: DNA deformation by electrostatic collapse around inorganic cations
22. 5): Effects of sequence polarity on DNA curvature
23. Water molecules in DNA recognition I: Hydration lifetimes of the trp operator in solution measured by NMR spectroscopy
24. A generalized reaction field method for molecular dynamics simulations
25. A 5-nanosecond molecular dynamics trajectory for B-DNA: Analysis of structure, motions and solvation