Structure, folding and activity of the VS ribozyme: Importance of the 2-3-6 helical junction

EMBO Journal

Volumn 20, Issue 6, 2001, Pages 1415-1424

  Lafontaine, D A ^a   Norman, D G ^a   Lilley, D M J ^a  

^a UNIVERSITY OF DUNDEE   (United Kingdom)

Author keywords

Fluorescence resonance energy transfer; Metal ions; RNA catalysis; RNA folding

Indexed keywords

NUCLEOTIDE; RIBOZYME;

AMINO ACID SEQUENCE; ARTICLE; CATALYSIS; ENERGY TRANSFER; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DEGRADATION; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN STRUCTURE;

ADENINE; BASE SEQUENCE; CATALYSIS; COMPUTER SIMULATION; ENERGY TRANSFER; FLUORESCENCE; GUANINE; MITOCHONDRIA; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NEUROSPORA; NUCLEIC ACID CONFORMATION; RNA, CATALYTIC;

EID: 0035869008     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/20.6.1415     Document Type: Article

References (40)

1. Rearrangement of a stable RNA secondary structure during VS ribozyme catalysis
2. The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution
3. Ionic interactions and the global conformations of the hammerhead ribozyme
4. The ion-induced folding of the hammerhead ribozyme: Core sequence changes that perturb folding into the active conformation
5. Ion-induced folding of the hammerhead ribozyme: A fluorescence resonance energy transfer study
6. RNA folding and misfolding of the hammerhead ribozyme
7. Identification of functional domains in the self-cleaving Neurospora VS ribozyme using damage selection
8. A secondary-structure model for the self-cleaving region of Neurospora VS RNA
9. Deoxynucleoside phosphoramidites - A new class of key intermediates for deoxypolynucleotide synthesis
10. Fluorescence resonance energy transfer and nucleic acids
11. Fluorescence resonance energy transfer analysis of the structure of the four-way DNA junction
12. Observing the helical geometry of double-stranded DNA in solution by fluorescence resonance energy transfer
13. The global folding of four-way helical junctions in RNA, including that in U1 snRNA
14. Crystal structure of a hepatitis delta virus ribozyme
15. Zwischenmolekulare Energiewanderung und Fluoreszenz
16. Binding of U1A protein to the 3′ untranslated region of its pre-mRNA
17. Efficient trans-cleavage of a stem-loop RNA substrate by a ribozyme derived from Neurospora VS RNA
18. Nucleotide sequence requirements for self-cleavage of Neurospora VS RNA
19. The VS catalytic RNA replicates by reverse transcription as a satellite of a retroplasmid
20. Analysis of the global conformation of branched RNA species by a combined electrophoresis and fluorescence approach
21. Nomenclature Committee of the International Union of Biochemistry: A nomenclature of junctions and branchpoints in nucleic acids. Recommendations 1994
22. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates
23. Fluorescence energy transfer shows that the four-way DNA junction is a right-handed cross of antiparallel molecules
24. Folding of the hairpin ribozyme in its natural conformation achieves close physical proximity of the loops
25. The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone
26. The location of Cyanine-3 on double-stranded DNA; importance for fluorescence resonance energy transfer studies
27. Smaller, faster ribozymes reveal the catalytic core of Neurospora VS RNA
28. A long-range pseudoknot is required for activity of the Neurospora VS ribozyme
29. A site-specific self-cleavage reaction performed by a novel RNA in Neurospora mitochondria
30. RNA-mediated ligation of self-cleavage products of a Neurospora mitochondrial plasmid transcript
31. The crystal structure of an all-RNA hammerhead ribozyme: A proposed mechanism for RNA catalytic cleavage
32. Capturing the structure of a catalytic RNA intermediate: The hammerhead ribozyme
33. Identification of phosphate groups involved in metal binding and tertiary interactions in the core of the Neurospora VS ribozyme
34. Hammerhead ribozyme kinetics
35. Tertiary structure formation in the hairpin ribozyme monitored by fluorescence resonance energy transfer
36. Stability of hairpin ribozyme tertiary structure is governed by the interdomain junction
37. Structures of bulged three-way DNA junctions