The contribution of 2′-hydroxyls to the cleavage activity of the Neurospora VS ribozyme

Nucleic Acids Research

Volumn 30, Issue 5, 2002, Pages 1132-1138

  Sood, Vanita D ^a   Yekta, Soraya ^a   Collins, Richard A ^a,b  

^a UNIVERSITY OF TORONTO   (Canada)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

2' DEOXYNUCLEOSIDE; HYDROXYL GROUP; RIBOZYME; URIDINE; DEOXYRIBONUCLEOTIDE; HYDROXIDE; NUCLEOTIDE; RIBONUCLEASE; VARKUD SATELLITE RIBOZYME;

CATALYSIS; CONTROLLED STUDY; GENE CLUSTER; NEUROSPORA; NONHUMAN; NUCLEIC ACID ANALYSIS; NUCLEIC ACID BASE SUBSTITUTION; PRIORITY JOURNAL; PROTEIN TERTIARY STRUCTURE; REVIEW; RNA CLEAVAGE; RNA STRUCTURE; ARTICLE; CHEMISTRY; CONFORMATION; ENZYMOLOGY; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE;

NEUROSPORA;

BASE SEQUENCE; DEOXYRIBONUCLEOTIDES; ENDORIBONUCLEASES; HYDROXIDES; MOLECULAR SEQUENCE DATA; NEUROSPORA; NUCLEIC ACID CONFORMATION; RNA, CATALYTIC; THIONUCLEOTIDES;

EID: 0036488944     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/30.5.1132     Document Type: Review

References (48)

1. Yeast phenylalanine transfer RNA: Atomic coordinates and torsion angles
2. Hydrogen bonding in yeast phenylalanine transfer RNA
3. Structural domains of transfer RNA molecules
4. A crystallographic study of metal-binding to yeast phenylalanine transfer RNA
5. Crystal structure of a group I ribozyme domain: Principles of RNA packing
6. The chemical basis of adenosine conservation throughout the Tetrahymena ribozyme
7. Crystal structure of a hepatitis delta virus ribozyme
8. Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis
9. Four ribose 2′-hydroxyl groups essential for catalytic function of the hairpin ribozyme
10. Nucleotide analog interference mapping of the hairpin ribozyme: Implications for secondary and tertiary structure formation
11. Inter-domain cross-linking and molecular modelling of the hairpin ribozyme
12. Tertiary structure stability of the hairpin ribozyme in its natural and minimal forms: Different energetic contributions from a ribose zipper motif
13. A site-specific self-cleavage reaction performed by a novel RNA in Neurospora mitochondria
14. RNA-mediated ligation of self-cleavage products of a Neurospora mitochondrial plasmid transcript
15. A secondary-structure model for the self-cleaving region of Neurospora VS RNA
16. Nucleotide sequence requirements for self-cleavage of Neurospora VS RNA
17. Efficient trans-cleavage of a stem-loop RNA substrate by a ribozyme derived from Neurospora VS RNA
18. A long-range pseudoknot is required for activity of the Neurospora VS ribozyme
19. Intramolecular secondary structure rearrangement by the kissing interaction of the Neurospora VS ribozyme
20. Identification of functional domains in the self-cleaving Neurospora VS ribozyme using damage selection
21. Identification of phosphate groups involved in metal binding and tertiary interactions in the core of the Neurospora VS ribozyme
22. Smaller, faster ribozymes reveal the catalytic core of Neurospora VS RNA
23. Rapid formation of a solvent-inaccessible core in the Neurospora Varkud satellite ribozyme
24. Structure, folding and activity of the VS ribozyme: Importance of the 2-3-6 helical junction
25. Functional equivalence of the uridine turn and the hairpin as building blocks of tertiary structure in the Neurospora VS ribozyme
26. The A730 loop is an important component of the active site of the VS ribozyme
27. A mutant T7 RNA polymerase as a DNA polymerase
28. Reaction conditions and kinetics of self-cleavage of a ribozyme derived from Neurospora VS RNA
29. Reactions at the termini of tRNA with T4 RNA ligase
30. DNA and RNA sequence determination based on phosphorothioate chemistry
31. Analysis of the role of phosphate oxygens in the group I intron from Tetrahymena
32. Defining the chemical groups essential for Tetrahymena group I intron function by nucleotide analog interference mapping
33. RNA tertiary structure mediation by adenosine platforms
34. Antisense RNA regulation in prokaryotes: Rapid RNA/RNA interaction facilitated by a general U-turn loop structure
35. Rearrangement of a stable RNA secondary structure during VS ribozyme catalysis
36. Three metal ions at the active site of the Tetrahymena group I ribozyme
37. Probing the role of metal ions in RNA catalysis: Kinetic and thermodynamic characterization of a metal ion interaction with the 2′-moiety of the guanosine nucleophile in the Tetrahymena group I ribozyme
38. Relationship between 2′-hydroxyls and magnesium binding in the hammerhead RNA domain: A model for ribozyme catalysis
39. Minimum ribonucleotide requirement for catalysis by the RNA hammerhead domain
40. Function of specific 2′-hydroxyl groups of guanosines in a hammerhead ribozyme probed by 2′-modifications
41. Nuclease-resistant chimeric ribozymes containing deoxyribonucleotides and phosphorothioate linkages
42. Comparison of binding of mixed ribose-deoxyribose analogues of CUCU to a ribozyme and to GGAGAA by equilibrium dialysis: Evidence for ribozyme specific interactions with 2′-OH groups
43. RNA substrate binding site in the catalytic core of the Tetrahymena ribozyme
44. Complementary sets of noncanonical base pairs mediate RNA helix packing in the group I intron active site
45. Identifying RNA minor groove tertiary contacts by nucleotide analogue interference mapping with N2-methylguanosine
46. A minor groove RNA triple helix within the catalytic core of a group I intron
47. Defining functional groups, core structural features and inter-domain tertiary contacts essential for group II intron self-splicing: A NAIM analysis