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Vaish NK, Heaton PA, Fedorova O, Eckstein F: In vitro selection of a purine nucleotide-specific hammerhead-like ribozyme. Proc Natl Acad Sci USA 1998, 95:2158-2162. By randomising 22 nucleotides in the catalytic core, this in vitro selection experiment provided a ribozyme with good cleavage activity 3′ to AUG, extending the range of cleavable triplets for the hammerhead ribozyme.
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Proc Natl Acad Sci USA
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NMR solution structure of the lead-dependent ribozyme: Evidence for dynamics in RNA catalysis
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Hoogstraten CG, Legault P, Pardi A: NMR solution structure of the lead-dependent ribozyme: Evidence for dynamics in RNA catalysis. J Mol Biol 1998, 284:337-350.
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A core folding model for catalysis by the hammerhead ribozyme accounts for its extraordinary sensitivity to abasic mutations
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Peracchi A, Karpeisky A, Maloney L, Beigelman L, Herschlag D: A core folding model for catalysis by the hammerhead ribozyme accounts for its extraordinary sensitivity to abasic mutations. Biochemistry 1998, 37:14765-14775. This is an interesting discussion on the difference between small and large ribozymes and proteins in terms of preorganisation for substrate binding.
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Molecular dynamics study to display near inline attack conformations in the hammerhead ribozyme self-cleavage reaction
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2+ ion with the pro-R oxygen of the scissile phosphate in the transition state of a hammerhead ribozyme-catalysed reaction
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Scott EC, Uhlenbeck OC: A re-investigation of the thio effect at the hammerhead cleavage sue. Nucleic Acids Res 1999, 27:479-484. This paper describes how careful the chosen experimental set-up has to be in order to analyse the phosphorothioate effect. It sets a standard for future work on this subject.
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Murray JB, Seyhan AA, Walter NG, Burke JM, Scott WG: The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone. Chem Biol 1998, 5:587-595. This paper shows that, contrary to a widely held notion, divalent metal ions are not required for the catalytic activity of the hammerhead, hairpin and Neurospora VS ribozyme. What is fundamental is the presence of a global positive charge whose specific catalytic involvment remains undetermined.
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Esteban JA, Walter NG, Kotzorek G, Heckman JE, Burke JM: Structural basis for heterogeneous kinetics: Reengineering the hairpin ribozyme. Proc Natl Acad Sci USA 1998, 95:6091-6096.
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Walter NG, Hampel KJ, Brown KM, Burke JM: Tertiary structure formation in the hairpin ribozyme monitored by fluorescence resonance energy transfer. EMBO J 1998, 17:2378-2391. Fluorescence resonance energy transfer is used to study the dynamics of the formation of the catalytically competent form of the hairpin-ribozyme-substrate complex by bringing loops A and B in proximity.
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Walter F, Murchie AIH, Thompson JB, Lilley DMJ: Structure and activity of the hairpin ribozyme in its natural junction conformation: Effect of metal ions. Biochemistry 1998, 37:14195-14203. This is a study of the hairpin ribozyme activity in its natural four-way junction form under different metal-ion conditions, using fluorescent resonance energy transfer to monitor the conformational changes.
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Earnshaw DJ, Gait MJ: Hairpin ribozyme cleavage catalysed by aminoglycoside antibiotics and the polyamine spermine in the absence of metal ions. Nucleic Acid Res 1998, 26:5551-5561. This paper shows that in the absence of metal ions, a number of aminoglycoside antibiotics promote hairpin ribozyme cleavage with comparable rates to the magnesium-dependent reaction.
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Science
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Sclavi B, Sullivan M, Chance MR, Brenowitz M, Woodson SA: RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting. Science 1998, 279:1940-1943. Folding of the Tetrahymena ribozyme at millisecond intervals is monitored by hydroxyl radical footprinting using a synchrotron X-ray beam to generate the radicals. This improved time resolution gave new insight into the hierarchy of RNA folding.
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Science
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Sclavi, B.1
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••] this paper reports the characterisation of a kinetically trapped intermediate during RNA folding. Mutants have been isolated which increase folding by destabilising the kinetically trapped intermediate.
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Science
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Pan J, Woodson SA: Folding intermediates of a self-splicing RNA: Mispairing of the catalytic core. J Mol Biol 1998, 280:597-609.
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Uhlenbeck OC: Keeping RNA happy. RNA 1995, 1:4-6.
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Hoch I, Berens C, Westhof E, Schroeder R: Antibiotic inhibition of RNA catalysis: Neomycin B binds to the catalytic core of the td group I intron displacing essential metal ions. J Mol Biol 1998, 282:557-569.
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Qin PZ, Pyle AM: The architectural organization and mechanistic function of group II intron structural elements. Curr Opin Struct Biol 1998, 8:301-308.
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Xiang Q, Qin PZ, Michels WJ, Freeland K, Pyle AM: Sequence specificity of a group II intron ribozyme: Multiple mechansisms for promoting unusually high discrimination against mismatched targets. Biochemistry 1998, 37:3839-3849. This is a detailed and thorough kinetic and thermodynamic study which reveals and explains the high sequence specificity of a group II intron ribozyme towards a substrate.
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Konforti BB, Abramowitz DL, Duarte CM, Karpeisky A, Beigelman L, Pyle AM: Ribozyme catalysis from the major groove of group II intron domain 5. Mol Cell 1998, 1:433-441. By modifying the functional groups of the essential guanine residue in domain 5 of a group II intron, it is shown that the major groove atoms of this ribozyme might be involved in catalysis despite their presumed inaccessibility.
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Mol Cell
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Konforti, B.B.1
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Differential chemical probing of a group II self-splicing intron identifies bases involved in tertiary interactions and supports an alternative secondary structure model of domain 5
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Costa M, Christian EL, Michel F: Differential chemical probing of a group II self-splicing intron identifies bases involved in tertiary interactions and supports an alternative secondary structure model of domain 5. RNA 1998, 4:1055-1068.
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A map of the binding for catalytic domain 5 in the core of group II intron ribozyme
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Konforti BB, Liu Q, Pyle AM: A map of the binding for catalytic domain 5 in the core of group II intron ribozyme. EMBO J 1998, 17:7105-7117.
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Boudvillain M, Pyle AM: Defining functional groups, core structural features and inter-domain tertiary contacts essential for group II intron self-splicing: A NAIM analysis. EMBO J 1998, 17:7091-7104.
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Podar M, Perlman PS, Padgett RA: The two steps of group II intron self-splicing are mechanistically distinguishable. RNA 1998, 4:890-900. This article describes the use of the diastereomers of phosphorothioates at the 3′ and 5′ splice sites of a group II intron to analyse and compare the stereochemistry of these two transesterification reactions, which turn out to be different.
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RNA
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