On the competition between water, sodium ions, and spermine in binding to DNA: A molecular dynamics computer simulation study

Biophysical Journal

Volumn 82, Issue 6, 2002, Pages 2860-2875

  Korolev, Nikolay ^a   Lyubartsev, Alexander P ^a   Laaksonen, Aatto ^a   Nordenskiöld, Lars ^a,b  

^a STOCKHOLM UNIVERSITY   (Sweden)

^b NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

CHLORIDE ION; DNA; POLYAMINE; SODIUM ION; SPERMINE; WATER;

ARTICLE; BINDING SITE; COMPUTER SIMULATION; DIFFUSION; DNA BINDING; DNA SEQUENCE; HYDRATION; MOLECULAR DYNAMICS;

EID: 0036106375     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(02)75628-2     Document Type: Article

References (56)

1. 12 duplexes
2. The low-temperature crystal structure of the pure-spermine form of Z-DNA reveals binding of a spermine molecule in the minor groove
3. Nucleic acids: Theory and computer simulation, Y2K
4. Localisation and dynamics of sodium counterions around DNA in solution from molecular dynamics simulations
5. Molecular dynamics simulations highlight the structural differences among DNA:DNA, RNA:RNA, and DNA:RNA structures
6. 1 Å crystal structures of B-DNA reveal sequence-specific binding and groove-specific bending of DNA by magnesium and calcium
7. Absence of minor groove monovalent cations in the crosslinked dodecamer C-G-C-G-A-A-T-T-C-G-C-G
8. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
9. Structural basis of polyamine-DNA recognition: Spermidine and spermine interactions with genomic B-DNAs of different GC content probed by Raman spectroscopy
10. Sequence-specific binding of counterions to B-DNA
11. Structure of a B-DNA dodecamer III. Geometry of hydration
12. Molecular dynamics simulation study of DNA dodecamer d(CGCGAATTCGCG) in solution: Conformation and hydration
13. X-ray crystallographic analysis of the hydration of A-and B-form DNA at atomic resolution
14. Hydration of deoxyribo-nucleic acid. I. A gravimetric study
15. A molecular simulation picture of DNA hydration around A- and B-DNA
16. Sodium and chlorine ions as part of the DNA solvation shell
17. Modeling high resolution hydration patterns in correlation with DNA sequence and conformation
18. Spermine-DNA interactions: A theoretical study
19. Molecular mechanics of the interactions of spermine with DNA: DNA bending as a result of ligand binding
20. Water and monovalent ions in the minor groove of B-DNA oligonucleotides as seen by NMR
21. Flexible structure of DNA: Ion dependence of minor-groove structure and dynamics
22. Influence of the dynamic positions of cations on the structure of the DNA minor groove: Sequence-dependent effects
23. A molecular dynamics simulation of a polyamine-induced conformational change of DNA: A possible mechanism for the B to Z transition
24. Locating monovalent cations in the grooves of B-DNA
25. DNA-cation interactions: The major and minor grooves are flexible ionophores
26. Binding sites and dynamics of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending
27. Spermine: An "invisible" component in the crystals of B-DNA. A grand canonical Monte Carlo and molecular dynamics simulation study
28. A Brillouin scattering study of the hydration of Li- and Na-DNA films
29. The origin of the A to B transition in DNA fibers and films
30. Molecular dynamics simulations of DNA in solution with different counter-ions
31. Effective potentials for ion-DNA interactions
32. M.DynaMix - A scalable portable parallel MD simulation package for arbitrary molecular mixtures
33. An all-atom empirical energy function for the simulation of nucleic-acids
34. DNA structure: What's in charge?
35. DNA structure: Cations in charge?
36. Hydration of the DNA bases is local
37. Hydration of the phosphate group in double-helical DNA
38. Spermine inhibition of the 2,5-diaziridinyl-1,4-benzoquinone (DZQ) crosslinking reaction with DNA duplexes containing poly(purine)-poly(pyrimidine) tracts
39. The B-DNA dodecamer at high resolution reveals a spine of water on sodium
40. Structure of the potassium form of CGCGAATTCGCG: DNA deformation by electrostatic collapse around inorganic cations
41. Cations mediate B-DNA conformational heterogenity
42. Water and ions in a high-resolution structure of B-DNA
43. 2 at atomic resolution
44. Measuring the geometry of DNA grooves
45. Radioprotection of DNA by spermine: A molecular modelling approach
46. The Dickerson-Drew B-DNA dodecamer revisited at atomic resolution
47. A "hydrate-ion" spine in a B-DNA minor groove
48. 5CGG) in three different conformations: Effects of spermine binding and methylation on the bending and condensation of A-DNA
49. Molecular-dynamics study of atomic motions in water
50. Reversible multiple time scale molecular-dynamics
51. B-DNA at atomic resolution reveals extended hydration pattern
52. Electrostatic mechanisms of DNA deformation
53. A 5-nanosecond molecular dynamics trajectory for B-DNA: Analysis of structure, motions, and solvation
54. Spermine binding to GC-rich DNA: Experimental and theoretical studies
55. Spermine-nucleic acid interactions: A theoretical study