Role of counterion condensation in folding of the Tetrahymena ribozyme. I. Equilibrium stabilization by cations

Journal of Molecular Biology

Volumn 306, Issue 5, 2001, Pages 1157-1166

  Heilman Miller, Susan L ^a,b,c   Thirumalai, D ^a,b   Woodson, Sarah A ^b,c  

^a University of Maryland   (United States)

^b UNIVERSITY OF MARYLAND   (United States)

^c JOHNS HOPKINS UNIVERSITY   (United States)

Author keywords

Counterion condensation; Group I ribozyme; Metal ion; Native gel electrophoresis; RNA structure

Indexed keywords

METAL ION; RIBOZYME;

ARTICLE; BINDING KINETICS; CONFORMATIONAL TRANSITION; ENZYME ACTIVITY; EQUILIBRIUM CONSTANT; GEL ELECTROPHORESIS; INCUBATION TIME; ION TRANSPORT; MOLECULAR STABILITY; NONHUMAN; POLYMERIZATION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DEGRADATION; PROTEIN FOLDING; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; TETRAHYMENA;

TETRAHYMENA;

EID: 0035830964     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2001.4437     Document Type: Article

References (52)

1. Hierarchy and dynamics of RNA folding
2. RNA folds: Insights from recent crystal structures
3. Ribozymes: A distinct class of metalloenzymes
4. On the role of magnesium ions in RNA stability
5. Tertiary structure in transfer ribonucleic acids
6. Conformational changes of transfer ribonucleic acid. Equilibrium phase diagrams
7. Cooperative binding of magnesium to transfer ribonucleic acid studied by a fluorescent probe
8. Conformational changes of transfer RNA. The role of magnesium(II)
9. Metal ions and RNA
10. The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides
11. 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
12. Interactions of DNA with divalent metal ions. II. Proton relaxation enhancement studies
13. Interaction of manganese with fragments, complementary fragment recombinations, and whole molecules of yeast phenylalanine specific transfer RNA
14. Equilibrium binding of magnesium(II) by Escherichia coli tRNAfMet
15. 2+ to tRNA
16. Role of divalent ions in folding of tRNA
17. 2+ binding isotherms for nucleic acids using Poisson-Boltzmann theory
18. Calculating the electrostatic properties of RNA provides new insights into molecular interactions and function
19. Building a catalytic active site using only RNA
20. Self-splicing of group I introns
21. Visualizing the higher order folding of a catalytic RNA molecule
22. Metal ion requirements for sequence-specific endoribonuclease activity of the Tetrahymena ribozyme
23. Effects of divalent metal ions on individual steps of the Tetrahymena ribozyme reaction
24. Time-resolved synchrotron X-ray "foot-printing", a new approach to the study of nucleic acid structure and function: Application to protein- DNA interactions and RNA folding
25. RNA folding at millisecond intervals by synchrotron hydroxyl radical foot-printing
26. Kinetic intermediates in RNA folding
27. Kinetics of folding of protein and RNA
28. Folding of RNA involves parallel pathways
29. A field-dissociation relation for polyelectrolytes with an application to field-induced conformational changes of polynucleotides
30. Small angle X-ray scattering reveals a compact intermediate in RNA folding
31. Flexibility of RNA
32. Counterion-induced condensation of deoxyribonucleic acid. A light-scattering study
33. Fast folding of a ribozyme by stabilizing core interactions: Evidence for multiple folding pathways in RNA
34. Fingerprinting the folding of a group I precursor RNA
35. Magnesium-dependent folding of self-splicing RNA: Exploring the link between cooperativity, thermodynamics, and kinetics
36. DNA condensation by multivalent cations
37. Catalysis of RNA cleavage by the Tetrahymena thermophila ribozyme. 1. Kinetic description of the reaction of an RNA substrate complementary to the active site
38. Folding intermediates of a self-splicing RNA: Mispairing of the catalytic core
39. Salt effects on nucleic acids
40. Exploration of metal ion binding sites in RNA folds by Brownian-dynamics simulations
41. 2+, and in the presence of substrate
42. Heat capacity effects on the melting of DNA. 1. General aspects
43. The interactions that shape RNA structure
44. Metal-binding sites in the major groove of a large ribozyme domain
45. Solution structure of a metal-binding site in the major groove of RNA complexed with cobalt (III) hexammine
46. A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor
47. Stabilization of RNA tertiary structure by monovalent cations
48. Sequence-specific endoribonuclease activity of the Tetrahymena ribozyme: Enhanced cleavage of certain oligonucleotide substrates that form mismatched ribozyme-substrate complexes
49. Self-splicing of the Tetrahymena pre-rRNA is decreased by misfolding during transcription
50. Synthesis of small RNAs using T7 RNA polymerase