Structure and function of the hairpin ribozyme

Journal of Molecular Biology

Volumn 297, Issue 2, 2000, Pages 269-291

  Fedor, Martha J ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

Antisense ribozyme; Catalysis and assembly; Catalytic mechanism; Hairpin ribozyme; RNA enzyme; Structure

Indexed keywords

RIBOZYME; RNA;

ARTICLE; CATALYSIS; KINETICS; MOLECULAR BIOLOGY; NONHUMAN; PRIORITY JOURNAL; RNA ANALYSIS; RNA CLEAVAGE; RNA CONFORMATION; RNA PROCESSING; RNA REPLICATION; RNA STRUCTURE; STRUCTURE ACTIVITY RELATION; TETRAHYMENA; THERMODYNAMICS;

NEUROSPORA; TETRAHYMENA;

EID: 0034708334     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2000.3560     Document Type: Article

References (196)

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11. Designing ribozymes for the inhibition of gene expression
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13. Replication of a plant virus satellite RNA: Evidence favors transcription of circular templates of both polarities
14. A photo-cross-linkable tertiary structure motif found in functionally distinct RNA molecules is essential for catalytic function of the hairpin ribozyme
15. Structure-mapping of the hairpin ribozyme. Magnesium-dependent folding and evidence for tertiary interactions within the ribozyme-substrate complex
16. Reconstitution of hairpin ribozyme activity following separation of functional domains
17. Solution structure of the loop B domain from the hairpin ribozyme
18. Non-enzymatic cleavage and ligation of RNAs complementary to a plant virus satellite RNA
19. Nucleotide sequence and newly formed phosphodiester bond of spontaneously ligated satellite tobacco ringspot virus RNA
20. RNA mediated formation of a phosphorothioate diester bond
21. Increase of satellite tobacco ringspot virus RNA initiated by inoculating circular RNA
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29. Extensive phosphorothioate substitution yields highly active and nuclease resistance hairpin ribozymes
30. Novel guanosine requirement for catalysis by the hairpin ribozyme
31. Four ribose 2'-hydroxyl groups essential for catalytic function of the hairpin ribozyme
32. Ionic requirements for RNA binding, cleavage, and ligation by the hairpin ribozyme
33. In vitro and in vivo comparison of hammer-head, hairpin, and hepatitis delta virus self-processing ribozyme cassettes
34. 2+(aq) binding sites
35. Relaxation kinetics of dimer formation by self complementary oligonucleotides
36. Inhibition of HIV-1 replication by ribozymes that show poor activity in vitro
37. Role of divalent metal ions in the hammerhead RNA cleavage reaction
38. Evidence for the role of solvated metal hydroxide in the hammerhead cleavage mechanism
39. Kinetic and equilibrium studies of the ribonuclease-catalyzed hydrolysis of uridine 2',3'-cyclic phosphate
40. Ribozyme mediated degradation of β-amyloid peptide precursor mRNA in COS-7 cells
41. Catalytic properties of hairpin ribozymes derived from chicory yellow mottle virus and arabis virus satellite RNAs
42. Kinetics of hairpin ribozyme cleavage in yeast
43. The kinetic mechanism of the hairpin ribozyme in vivo: Influence of RNA helix stability on intracellular cleavage kinetics
44. Ribozyme-targeted destruction of RNA associated with autosomal-dominant retinitis pigmentosa
45. Intracellular susceptibility to ribozymes in a tethered substrate-ribozyme provirus model is not predicted by secondary structures of human immunodeficiency virus type 1 RNAs in vitro
46. Progress toward the structure and therapeutic use of the hairpin ribozyme
47. Hairpin ribozyme cleavage catalyzed by aminoglycoside antibiotics and the polyamine spermine in the absence of metal ions
48. Inter-domain cross-linking and molecular modelling of the hairpin ribozyme
49. A two unit antisense RNA cassette test system for silencing of target genes
50. Kinetic mechanism of the hairpin ribozyme
51. Structural basis for heterogeneous kinetics: Reengineering the hairpin ribozyme
52. Analysis of the cleavage reaction of a transacting human hepatitis delta virus ribozyme
53. Tertiary structure stabilization promotes hairpin ribozyme ligation
54. Substrate sequence effects on 'hammerhead' RNA catalytic efficiency
55. Kinetics of intermolecular cleavage by hammerhead ribozymes
56. Catalytically active geometry in the reversible circularization of 'mini-monomer' RNAs derived from the complementary strand of tobacco ringspot virus satellite RNA
57. Two sequences participating in the autocatalytic processing of satellite tobacco ringspot virus complementary RNA
58. Specific association between an endoribonucleolytic sequence from a satellite RNA and a substrate analogue containing a 2'-5' phosphodiester
59. The active site and mechanism of action of bovine pancreatic ribonuclease
60. Structural and ionic requirements for self-cleavage of virusoid RNAs and trans self-cleavage of viroid RNA
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62. The enthalpies of hydrolysis of acyclic, monocyclic, and glycoside cyclic phosphate diesters
63. Multigene antiviral vectors inhibit diverse human immunodeficiency virus type 1 clades
64. Gene therapy targeting peripheral blood CD34+ hematopoietic stem cells of HIV-infected individuals
65. Evidence for the metal-cofactor independence of an RNA phosphodiester-cleaving DNA enzyme
66. + on an equilibrium between alternative conformations of an RNA pseudoknot
67. Purine functional groups in essential residues of the hairpin ribozyme required for catalytic cleavage of RNA
68. Efficient trans-cleavage of a stem-loop RNA substrate by a ribozyme derived from Neurospora VS RNA
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70. A unique mechanism for RNA catalysis: The role of metal cofactors in hairpin ribozyme cleavage
71. RNA catalytic properties of the minimum (-)sTRSV sequence
72. 'Hairpin' catalytic RNA model: Evidence for helices and sequence requirement for substrate RNA
73. The solvent-protected core of the hairpin ribozyme-substrate complex
74. Simple RNA enzymes with new and highly specific endoribonuclease activities
75. Sequences required for self-catalyzed cleavage of the satellite RNA of tobacco ringspot virus
76. Kinetics and thermodynamics of intermolecular catalysis by hairpin ribozymes
77. Evidence for processivity and two-step binding of the RNA substrate from studies of J1/2 mutants of the Tetrahymena ribozyme
78. Catalysis of RNA cleavage by the Tetrahymena thermophila ribozyme. 1. Kinetic description of the reaction of an RNA substrate complementary to the active site
79. Comparison of pH dependencies of the Tetrahymena ribozyme reactions with RNA 2'-substituted and phosphorothioate substrates reveals a rate-limiting conformational step
80. The internal equilibrium of the hammerhead ribozyme reaction
81. A kinetic and thermodynamic framework for the hammerhead ribozyme reaction
82. Thermodynamic dissection of the substrate-ribozyme interaction in the hammerhead ribozyme
83. Extension of helix II of an HIV-1-directed hammerhead ribozyme with long antisense flanks does not alter kinetic parameters in vitro but causes loss of the inhibitory potential in living cells
84. Diastereomers of the nucleoside phosphorothioates as probes of the structure of metal nucleotide substrates and of the nucleotide binding site of yeast hexokinase
85. The use of ribozymes in gene therapy approaches to AIDS
86. Optimization of an anti-HIV hairpin ribozyme by in vitro selection
87. Substrate selection rules for the hairpin ribozyme determined by in vitro selection, mutation, and analysis of mismatched substrates
88. A proton-coupled conformational switch of Escherichia coli 5 S ribosomal RNA
89. 2+ binding
90. Design and anti-HIV-1 activity of hammerhead and hairpin ribozymes containing a stable loop
91. Cross-ligation and exchange reactions catalyzed by hairpin ribozymes
92. Loop-size variation to probe a bent structure of a hairpin ribozyme
93. Modification of primary structures of hairpin ribozymes for probing active conformations
94. Enhanced folding of hairpin ribozymes with replaced domains
95. A new type of hairpin ribozyme consisting of three domains
96. Construction of hairpin ribozymes with a three-way junction
97. Use of ribozymes to inhibit gene expression
98. Mechanism of ribozyme-mediated cleavage
99. Stabilization of RNA structure by Mg ions. Specific and non-specific effects
100. In situ probing of adenine protonation in RNA by 13C NMR
101. A common motif organizes the structure of multi-helix loops in 16 S and 23 S ribosomal RNAs
102. Ribozyme rescue of photo-receptor cells in a transgenic rat model of autosomal dominant retinitis pigmentosa
103. Efficacy of hammerhead ribozymes targeting α-lactalbumin transcripts: Experiments in cells and transgenic mice
104. 4+ cells from HIV-exposed infants: Preclinical studies
105. Thermodynamic and activation parameters for binding of a pyrene-labeled substrate by the Tetrahymena ribozyme: Docking is not diffusion-controlled and is driven by a favorable entropy change
106. Kinetics of RNA degradation by specific base catalysis of transesterification involving the 2'-hydroxyl group
107. The sCYMV1 hairpin ribozyme: Targeting rules and cleavage of heterologous RNA
108. Structure, folding and catalysis of the small nucleolytic ribozymes
109. Self-cleaving RNA
110. Folding of the hairpin ribozyme in its natural conformation achieves close physical proximity of the loops
111. The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone
112. Characterization of a local folding event of the Tetrahymena group I ribozyme: Effects of oligonucleotide substrate length, pH, and temperature on the two substrate binding steps
113. An unusual pH-independent and metal-ion-independent mechanism for hairpin ribozyme catalysis
114. The internal equilibrium of the hairpin ribozyme: Temperature, ion and pH effects
115. Facilitation of group I splicing in vivo: Misfolding of the Tetrahymena IVS and the role of ribosomal RNA exons
116. Two histidine residues are essential for ribonuclease T1 activity as is the case for ribonuclease A
117. Inhibition of human immunodeficiency virus type 1 expression by a hairpin ribozyme
118. A small metalloribozyme with a two-step mechanism
119. Divalent metal ions in RNA folding and catalysis
120. 2+ cleavage motif
121. 2+ complexes of adenine nucleotides and thionucleotides and rate constants for formation and dissociation of MgATP and MgADP
122. Specificity of the hairpin ribozyme. Sequence requirements surrounding the cleavage site
123. Imidazole rescue of a cytosine mutation in a self-cleaving ribozyme
124. Metal ion catalysis in the Tetrahymena ribozyme reaction
125. Alignment of the two domains of the hairpin ribozyme-substrate complex defined by interdomain photoaffinity crosslinking
126. Structural basis for the guanosine requirement of the hairpin ribozyme
127. Thermodynamics and kinetics of the helix-coil transition of oligomers containing GC base-pairs
128. Global structure and flexibility of hairpin ribozymes with extended terminal helices
129. Ribozymes: A distinct class of metalloenzymes
130. Building a kinetic framework for group II intron ribozyme activity: Quantitation of interdomain binding and reaction rate
131. Thermodynamic and kinetic properties of short RNA helices: The oligomer sequence AnGCUn
132. Bovine pancreatic ribonuclease
133. Intracellular immunization of rhesus CD34+ hematopoietic progenitor cells with a hairpin ribozyme protects T cells and macrophages from simian immunodeficiency virus infection
134. Nucleotide sequence and structural analysis of two satellite RNAs associated with chicory yellow mottle virus
135. Nucleotide analog interference mapping of the hairpin ribozyme: Implications for secondary and tertiary structure formation
136. A small nucleolar RNA: Ribozyme hybrid cleaves a nucleolar RNA target in vivo with near-perfect efficiency
137. An improved version of the hairpin ribozyme functions as a ribonucleoprotein complex
138. Base and sugar requirements for RNA cleavage of essential nucleoside residues in internal loop B of the hairpin ribozyme: Implications for secondary structure
139. A re-investigation of the thio effect at the hammerhead cleavage site
140. RNA catalysis
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146. Three metal ions at the active site of the Tetrahymena group I ribozyme
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148. Mutational analysis of loops 1 and 5 of the hairpin ribozyme
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150. Analysis of hairpin ribozyme base mutations in loops 2 and 4 and their effects on cis-cleavage in vitro
151. Screening for important base identities in the hairpin ribozyme by in vitro selection for cleavage
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153. Ribozyme-mediated inhibition of a Philadelphia chromosome-positive acute lymphoblastic leukemia cell line expressing the p190 bcr-abl oncogene
154. Synthetic catalytic oligonucleotides based on the hammerhead ribozyme
155. A general two-metal mechanism for catalytic RNA
156. Unusual metal ion catalysis in an acyl-transferase ribozyme
157. The use of ribozymes to inhibit HIV replication
158. The sarcin/ricin loop, a modular RNA
159. A minor groove RNA triple helix within the catalytic core of a group I intron
160. An important base-triple anchors the substrate helix recognition surface within the Tetrahymena ribozyme active site
161. Ribozyme mediated destruction of influenza A virus in vitro and in vivo
162. The influence of junction conformation on RNA cleavage by the hairpin ribozyme in its natural junction form
163. Keeping RNA happy
164. Tertiary structure of tRNA(Phe) (yeast): Kinetics and electrostatic repulsion
165. Design, synthesis, and function of therapeutic hammerhead ribozymes
166. Hammerhead ribozyme engineering
167. Recent developments in the hammerhead ribozyme field
168. Two autolytic processing reactions of a satellite RNA proceed with inversion of configuration
169. Evidence for spontaneous circle formation in the replication of the satellite RNA of tobacco ringspot virus
170. Flexibility of the bulge formed between a hairpin ribozyme and deoxy-substrate analogues
171. Global structure of four-way RNA junctions studied using fluorescence resonance energy transfer
172. Folding of the four-way RNA junction of the hairpin ribozyme
173. Structure and activity of the hairpin ribozyme in its natural junction conformation: Effect of metal ions
174. Real-time monitoring of hairpin ribozyme kinetics through base-specific quenching of fluorescein-labeled substrates
175. The hairpin ribozyme: Structure, assembly and catalysis
176. Tertiary structure formation in the hairpin ribozyme monitored by fluorescence resonance energy transfer
177. Stability of hairpin ribozyme tertiary structure is governed by the interdomain junction
178. Crystallographic structures of the hammerhead ribozyme: Relationship to ribozyme folding and catalysis
179. A second catalytic metal ion in group I ribozyme
180. Inhibition of HIV replication by the hairpin ribozyme
181. A potential therapeutic application of hairpin ribozymes: In vitro and in vivo studies of gene therapy for hepatitis C virus infection
182. Intracellular application of hairpin ribozyme genes against hepatitis B virus
183. Expression of ribozymes in gene transfer systems to modulate target RNA levels
184. Kinetics of renaturation of DNA
185. The conformation of loop E of eukaryotic 5 S ribosomal RNA
186. A controlled, phase 1 clinical trial to evaluate the safety and effects in HIV-1 infected humans of autologous lymphocytes transduced with a ribozyme that cleaves HIV-1 RNA
187. Conservation of a hairpin ribozyme sequence in HIV-1 is required for efficient viral replication
188. How many catalytic RNAs? Ions and the Cheshire cat conjecture
189. Metal ions play a passive role in the hairpin ribozyme catalysed reaction
190. The role of essential pyrimidines in the hairpin ribozyme-catalysed reaction
191. A hairpin ribozyme inhibits expression of diverse strains of human immunodeficiency virus type 1
192. In vitro and in vivo characterization of a second functional hairpin ribozyme against HIV-1
193. Cleavage of highly structured viral RNA molecules by combinatorial libraries of hairpin ribozymes. The most effective ribozymes are not predicted by substrate selection rules
194. In vivo facilitation of Tetrahymena group I inton splicing in Escherichia coli pre-ribosomal RNA
195. Combinatorial screening and intracellular antiviral activity of hairpin ribozymes directed against hepatitis B virus