The linkage between magnesium binding and RNA folding

Journal of Molecular Biology

Volumn 317, Issue 4, 2002, Pages 507-521

  Misra, Vinod K ^a   Draper, David E ^a  

^a JOHNS HOPKINS UNIVERSITY   (United States)

Author keywords

Electrostatics, energetics; Magnesium binding; Poisson Boltzmann equation; RNA folding

Indexed keywords

MAGNESIUM; RIBOSOME RNA; TRANSFER RNA;

ARTICLE; BINDING SITE; CHEMICAL BINDING; COMPARATIVE STUDY; ELECTRIC POTENTIAL; GENETIC STABILITY; HYDRATION; MATHEMATICAL ANALYSIS; PRIORITY JOURNAL; RNA ANALYSIS; RNA STRUCTURE; STOICHIOMETRY; SURFACE PROPERTY; THEORETICAL MODEL; YEAST;

EID: 0036295964     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2002.5422     Document Type: Article

References (69)

1. Structural motifs in RNA
2. RNA folds: Insights from recent crystal structures
3. RNA: Versatility in form and function
4. On the role of magnesium ions in RNA stability
5. 2+ binding to tRNA revisited: The non-linear Poisson-Boltzmann model
6. 2+ binding isotherms for nucleic acids using Poisson-Boltzmann theory
7. 2+ binding to RNA
8. Hierarchy and dynamics of RNA folding
9. Strategies for RNA folding
10. How RNA folds
11. Early events in RNA folding
12. Small angle X-ray scattering reveals a compact intermediate in RNA folding
13. A collapsed non-native RNA folding state
14. Phe and the catalytic domain of the B. subtilis RNase P RNA determined by small-angle X-ray scattering
15. 2+ ions
16. The mode of binding to oligo-nucleotides. Inner sphere complexes as markers for recognition?
17. 2+ (aq) to DNA
18. Hydration effects accompanying the substitution of counterions in the ionic atmosphere of poly(rA)·poly(rU) and poly(rA)·2poly(rU) helices
19. Raman spectroscopy of DNA-metal complexes. I. Interactions and conformational effects of the divalent cations: Mg, Ca, Sr, Ba, Mn, Co, Ni, Cu, Pd, and Cd
20. Interactions of polyelectrolytes with simple electrolytes. III. The binding of magnesium ion by deoxyribonucleic acid
21. The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides
22. Theory of the delocalized binding of Mg(II) to DNA: Preliminary analysis for low binding levels
23. Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: The roles of ion association or release, screening, and ion effects on water activity
24. 2+ ions
25. Competitive electrostatic binding of charged ligands to polyelectrolytes: Practical approach using the non-linear Poisson-Boltzmann equation
26. Comparison of polyelectrolyte theories of the binding of cations to DNA
27. Effect of finite ionic size on the solution of the Poisson-Boltzmann equation: Application to the binding of divalent metal ions to DNA
28. Polyelectrolyte theory. 3. The surface potential in mixed-salt solutions
29. Divalent cations and the electrostatic potential around DNA: Monte Carlo and Poisson-Boltzmann calculations
30. Counterion exchange reactions on DNA: Monte Carlo and Poisson-Boltzmann analysis
31. Monte Carlo studies of counterion-DNA interactions: Comparison of the radial distribution of counterions with predictions of other polyelectrolyte theories
32. Ionic distributions and competitive association in DNA/mixed salt solutions
33. 2+ ions to polyadenylate, polyuridylate, and their complexes
34. A universal mode of helix packing in RNA
35. 2+-dependent ribozyme
36. Role of counterion condensation in folding of the Tetrahymena ribozyme. I. Equilibrium stabilization by cations
37. Visualizing the higher order folding of a catalytic RNA molecule
38. Transfer RNA in solution: Selected topics
39. Interaction of manganese with fragments, complementary fragment recombinations, and whole molecules of yeast phenylalanine specific transfer RNA
40. Electrostatic interactions in macromolecules: Theory and applications
41. Classical electrostatics in biology and chemistry
42. Polyelectrolyte electrostatics: Salt dependence, entropic, and enthalpic contributions to free energy in the non-linear Poisson-Boltzmann model
43. Monovalent and divalent salt effects on electrostatic free energies defined by the non-linear Poisson-Boltzmann equation: Application to DNA binding reactions
44. Salt dependence of oligoion-polyion binding: A thermodynamic description based on preferential interaction coefficients
45. Interpretation of preferential interaction coefficients of nonelectrolytes and of electrolyte ions in terms of a two-domain model
46. Salt effects on polyelectrolyte-ligand binding: Comparison of Poisson-Boltzmann, and limiting law/counterion binding models
47. tRNA conformation and magnesium binding. A study of yeast phenylalanine-specific tRNA by a fluorescent indicator and differential melting curves
48. Salt effects on ligand-DNA binding: Minor groove binding antibiotics
49. Thermodynamic studies of transfer ribonucleic acids. I. Magnesium binding to yeast phenylalanine transfer ribonucleic acid
50. Conformational transitions of an unmodified tRNA: Implications for RNA folding
51. Thermodynamic analysis of transfer RNA unfolding
52. Crystal structure of a conserved ribosomal protein-RNA complex
53. Stabilization of RNA structure by Mg ions. Specific and nonspecific effects
54. Affinities and selectivities of divalent cation binding sites within an RNA tertiary structure
55. Thermodynamics of RNA folding in a conserved ribosomal RNA domain
56. Stabilization of RNA tertiary structure by monovalent cations
57. Specific ammonium ion requirement for functional ribosomal RNA tertiary structure
58. + complex
59. Calculating the electrostatic properties of RNA provides new insights into molecular interactions and function
60. Restrained refinement of the monoclinic form of yeast phenyl-alanine transfer RNA. Temperature factors and dynamics, coordinated waters, and base-pair propeller twist angles
61. Restrained refinement of two crystalline forms of yeast aspartic acid and phenylalanine transfer RNA crystals
62. The protein data bank
63. The dielectric constant of a folded protein
64. Electrostatic contributions to the binding free energy of the lcI repressor to DNA
65. A second generation force-field For the simulation of proteins, nucleic acids, and organic-molecules
66. Calculating the electrostatic potential of molecules in solution: Method and error assessment