The folding of the hairpin ribozyme: Dependence on the loops and the junction

RNA

Volumn 6, Issue 12, 2000, Pages 1833-1846

  Zhao, Z Y ^a   Wilson, T J ^a   Maxwell, K ^a   Lilley, D M J ^a  

^a UNIVERSITY OF DUNDEE   (United Kingdom)

Author keywords

FRET; RNA catalysis; RNA folding

Indexed keywords

MAGNESIUM ION; RIBOZYME; RNA;

ARTICLE; CATALYSIS; CONCENTRATION RESPONSE; ENERGY TRANSFER; ENZYME ACTIVITY; MUTATION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION; RNA CONFORMATION;

BASE SEQUENCE; HYDROLYSIS; MUTAGENESIS, SITE-DIRECTED; NEPOVIRUS; NUCLEIC ACID CONFORMATION; RNA, CATALYTIC; RNA, SATELLITE; RNA, VIRAL; SPECTROMETRY, FLUORESCENCE; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 0034545071     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1017/S1355838200001230     Document Type: Article

References (69)

1. Mutagenesis of the hairpin ribozyme
2. Ion-induced folding of the hammerhead ribozyme: A fluorescence resonance energy transfer study
3. Deoxynucleoside phosphoramidites - A new class of key intermediates for deoxypolynucleotide synthesis
4. Essential nucleotide sequences and secondary structure elements of the hairpin ribozyme
5. Solution structure of the loop B domain from the hairpin ribozyme
6. Determination of metal ion binding sites within the hairpin ribozyme domains by NMR
7. Reconstitution of hairpin ribozyme activity following separation of functional domains
8. Non-enzymatic cleavage and ligation of RNAs complementary to a plant virus satellite RNA
9. Solution structure of loop A from the hairpin ribozyme from tobacco ringspot virus satellite
10. Novel guanosine requirement for catalysis by the hairpin ribozyme
11. Four ribose 2'-hydroxyl groups essential for catalytic function of the hairpin ribozyme
12. Fluorescence resonance energy transfer and nucleic acids
13. Fluorescence resonance energy transfer analysis of the structure of the four-way DNA junction
14. Observing the helical geometry of double-stranded DNA in solution by fluorescence resonance energy transfer
15. Catalytic properties of hairpin ribozymes derived from Chicory Yellow Mottle virus and Arabis Mosaic virus satellite RNAs
16. The global folding of four-way helical junctions in RNA, including that in U1 snRNA
17. Investigation of the proposed interdomain ribose zipper in ribozyme cleavage using 2'-modified nucleosides
18. Inter-domain cross-linking and molecular modelling of the hairpin ribozyme
19. The Holliday junction in an inverted repeat DNA sequence: Sequence effects on the structure of four-way junctions
20. Tertiary structure stabilization promotes hairpin ribozyme ligation
21. Structure and function of the hairpin ribozyme
22. Two sequences participating in the autolytic processing of satellite tobacco ringspot virus complementary RNA
23. Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites
24. Zwischenmolekulare Energiewanderung und Fluoreszenz
25. The kinking of DNA and RNA helices by bulged nucleotides observed by fluorescence resonance energy transfer
26. Exchange between stacking conformers in a four-way DNA junction
27. Purine functional groups in essential residues of the hairpin ribozyme required for catalytic cleavage of RNA
28. High yield selective 3'-silylation of ribonucleosides
29. RNA catalytic properties of the minimum (-)sTRSV sequence
30. 'Hairpin' catalytic RNA model: Evidence for helices and sequence requirement for substrate RNA
31. Simple RNA enzymes with new and highly specific endoribonuclease activities
32. Kinetics and thermodynamics of intermolecular catalysis by hairpin ribozymes
33. Self-cleavage of plus and minus RNA transcripts of avocado sunblotch viroid
34. 2+ binding
35. Enhanced folding of hairpin ribozymes with replaced domains
36. A new type of hairpin ribozyme consisting of three domains
37. Loop-size variation to probe a bent structure of a hairpin ribozyme
38. Construction of hairpin ribozymes with a three-way junction
39. Kinking of DNA and RNA by base bulges
40. Structure, folding and catalysis in the small nucleolytic ribozymes
41. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates
42. Uranyl photoprobing of a four-way DNA junction: Evidence for specific metal ion binding
43. Fluorescence energy transfer shows that the four-way DNA junction is a right-handed cross of antiparallel molecules
44. Folding of the hairpin ribozyme in its natural conformation achieves close physical proximity of the loops
45. The location of Cyanine-3 on double-stranded DNA: Importance for fluorescence resonance energy transfer studies
46. Crystal structure of an 82 nucleotide RNA-DNA complex formed by the 10-23 DNA enzyme
47. Mixed deoxyribo- and ribooligonucleotides with catalytic activity
48. Structural basis for the guanosine requirement of the hairpin ribozyme
49. Nucleotide analog interference mapping of the hairpin ribozyme: Implications for secondary and tertiary structure formation
50. A site-specific self-cleavage reaction performed by a novel RNA in Neurospora mitochondria
51. Base and sugar requirements for RNA cleavage of essential nucleoside residues in internal loop B of the hairpin ribozyme: Implications for secondary structure
52. Capturing the structure of a catalytic RNA intermediate: The hammerhead ribozyme
53. Antigenomic RNA of human hepatitis delta virus can undergo self-cleavage
54. The loop B domain is physically separable from the loop A domain in the hairpin ribozyme
55. Mutational analysis of loops 1 and 5 of the hairpin ribozyme
56. Analysis of hairpin ribozyme base mutations in loops 2 and 4 and their effects on cis-cleavage in vitro
57. The influence of junction conformation on RNA cleavage by the hairpin ribozyme in its natural junction form
58. In vitro selection of hammerhead ribozymes containing a bulged nucleotide in stem II
59. A small catalytic oligoribonucleotide
60. NMR structural studies on a DNA four-way junction: Stacking preference and localization of the metal-ion binding site
61. Two autolytic processing reactions of a satellite RNA proceed with inversion of configuration
62. Global structure of four-way RNA junctions studied using fluorescence resonance energy transfer
63. The folding of the four-way RNA junction of the hairpin ribozyme
64. Structure and activity of the hairpin ribozyme in its natural junction conformation: Effect of metal ions
65. Stability of hairpin ribozyme tertiary structure is governed by the interdomain junction
66. Tertiary structure formation in the hairpin ribozyme monitored by fluorescence resonance energy transfer
67. Probing non-selective cation binding in the hairpin ribozyme with Tb(III)
68. Human hepatitis δ virus RNA subfragments contain an autocleavage activity
69. The role of essential pyrimidines in the hairpin ribozyme-catalyzed reaction