Results 121 to 130 of about 6,175 (141)

Functional Group Requirements in the Probable Active Site of the VS Ribozyme

Journal of Molecular Biology, 2002
The VS ribozyme catalyses the site-specific cleavage of a phosphodiester linkage by a transesterification reaction that entails the attack of the neighbouring 2'-oxygen with departure of the 5'-oxygen. We have previously suggested that the A730 loop is an important component of the active site of the ribozyme, and that A756 is especially important in ...
David M.J. Lilley, Timothy J. Wilson, Zheng-yun Zhao, Daniel A. Lafontaine   +3 more
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A long-range pseudoknot is required for activity of the Neurospora VS ribozyme.

The EMBO Journal, 1996
Four small RNA self-cleaving domains, the hammerhead, hairpin, hepatitis delta virus and Neurospora VS ribozymes, have been identified previously in naturally occurring RNAs. The secondary structures of these ribozymes are reasonably well understood, but little is known about long-range interactions that form the catalytically active tertiary ...
Joan E. Olive, Tara L. Beattie, Richard A. Collins, T Rastogi   +3 more
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Effects of cobalt hexammine on folding and self-cleavage of the Neurospora VS ribozyme

Journal of Molecular Biology, 2001
We have investigated the effects of Co(NH3)6(3+), an analog of hexahydrated Mg2+, on folding and catalysis of the Neurospora VS ribozyme. Most of the metal ion-induced changes detected by chemical modification structure probing in either metal ion are similar, but occur at approximately 33-fold lower concentrations of Co(NH3)6(3+) than Mg2+.
Richard A. Collins, Jonathon L Maguire
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Smaller, faster ribozymes reveal the catalytic core of Neurospora VS RNA

Journal of Molecular Biology, 1998
We have investigated the structural requirements for cis-cleavage of the VS ribozyme by designing deletions, substitutions, and circular permutations based on the secondary structure model. Four of the six helices predicted in the model have been shortened, resulting in self-cleaving RNAs of only 121 to 126 nucleotides.
Toolika Rastogi, Richard A. Collins
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Rearrangement of Substrate Secondary Structure Facilitates Binding to the Neurospora VS Ribozyme

Journal of Molecular Biology, 2002
The Neurospora VS ribozyme differs from other small, naturally occurring ribozymes in that it recognizes for trans cleavage or ligation a substrate that consists largely of a stem-loop structure. We have previously found that cleavage or ligation by the VS ribozyme requires substantial rearrangement of the secondary structure of stem-loop I, which ...
Ricardo Zamel, Richard A. Collins
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The A730 loop is an important component of the active site of the VS ribozyme 1 1Edited by J. Karn

Journal of Molecular Biology, 2001
The core of the VS ribozyme comprises five helices, that act either in cis or in trans on a stem-loop substrate to catalyse site-specific cleavage. The structure of the 2-3-6 helical junction indicates that a cleft is formed between helices II and VI that is likely to serve as a receptor for the substrate.
Lafontaine, Daniel A., Wilson, Timothy J., Norman, David G., Lilley, David M. J.   +3 more
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The Role of Magnesium Ions and 2′-Hydroxyl Groups in the VS Ribozyme–Substrate Interaction

Journal of Molecular Biology, 2002
The minimal substrate of the trans-cleaving Neurospora VS ribozyme has a stem-loop structure and interacts with the ribozyme by RNA tertiary interactions that remain only partially defined. The magnesium ion dependence of the catalytic parameters of a trans-cleaving VS-derived ribozyme were studied. The turnover number of the catalytic RNA was found to
Jane A. Grasby, Iain A. Murray, Svetomir B. Tzokov   +2 more
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Identification of functional domains in theself-cleaving Neurospora VS ribozyme using damage selection

Journal of Molecular Biology, 1997
Varkud Satellite (VS) RNA contains a small self-cleaving RNA motif that is distinct in its sequence and secondary structure from the hammerhead, hairpin, and hepatitis delta virus ribozymes, which are found in other natural RNAs. We have used a base specific chemical damage selection (modification interference) assay to identify functionally important ...
Tara L. Beattie, Richard A. Collins
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The Solution Structure of the VS Ribozyme Active Site Loop Reveals a Dynamic “Hot-Spot”

Journal of Molecular Biology, 2004
The VS ribozyme is the largest ribozyme in its class and is also the least structurally characterized thus far. The current working model of the VS ribozyme locates the active site in stem-loop VI. The solution structure of this active site loop was determined using high resolution NMR spectroscopy.
Thorsten Dieckmann, Jeremy Flinders
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Reaction conditions and kinetics of self-cleavage of a ribozyme derived from Neurospora VS RNA

Biochemistry, 1993
We have investigated the self-cleavage reaction performed by a ribozyme that contains 164 nucleotides of Neurospora VS RNA. Self-cleavage requires a divalent cation, magnesium being more effective than manganese or calcium. Spermidine or monovalent cations stimulate the reaction but cannot replace magnesium.
Joan E. Olive, Richard A. Collins
openaire   +2 more sources