Results 131 to 140 of about 1,849,598 (165)

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 ...
R. Zamel, Richard A. Collins
semanticscholar   +5 more sources

Catalytic cleave of an RNA substrate that bypasses the reorganization of its secondary structure during substrate recognition by a trans -acting VS ribozyme

Nucleosides, Nucleotides & Nucleic Acids
Varkud satellite ribozyme (VS ribozyme) is a class of catalytic RNA with self-cleavage activity. The wild-type VS ribozyme has structural modularity with a relatively large catalytic module (H2-H6 elements) and a small substrate module (H1 element).
Yuki Miyzaki, Ryohei Nakane, Shogo Tanishi, Shigeyoshi Matsumura, Yoshiya Ikawa   +4 more
openalex   +2 more sources

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
Svetomir B. Tzokov, Iain A. Murray, Jane A. Grasby   +2 more
semanticscholar   +5 more sources

Identification of the Catalytic Subdomain of the VS Ribozyme and Evidence for Remarkable Sequence Tolerance in the Active Site Loop

Journal of Molecular Biology, 2002
We show here that the ribozyme domain of the Neurospora VS ribozyme consists of separable upper and lower subdomains. Deletion analysis demonstrates that the entire upper subdomain (helices III/IV/V) is dispensable for site-specific cleavage activity, providing experimental evidence that the active site is contained within the lower subdomain and ...
Vanita D. Sood, Richard A. Collins
semanticscholar   +5 more sources

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Identification of phosphate groups involved in metal binding and tertiary interactions in the core of the Neurospora VS ribozyme.

Journal of Molecular Biology, 1998
We have used ethylation protection experiments and modification interference using phosphorothioate nucleosides to identify phosphate groups involved in the magnesium-dependent tertiary structure and function of the VS ribozyme, a small, self-cleaving ...
V. Sood, Tara L. Beattie, Richard A. Collins   +2 more
semanticscholar   +4 more sources

Spermine switches a Neurospora VS ribozyme from slow Cis cleavage to fast trans cleavage.

Biochemistry, 1998
In keeping with the known role of polyamines as counterions in RNA folding, we have found that concentrations of spermine as low as 1 microM facilitate first-order Cis cleavage and decrease the concentration of magnesium required for optimal cleavage of ...
J. Olive, R. Collins
semanticscholar   +3 more sources

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 ...
T. Rastogi, Tara L. Beattie, J. Olive, Richard A. Collins   +3 more
semanticscholar   +4 more sources

Folding and catalysis by the VS ribozyme.

Biochimie, 2002
The VS ribozyme is a 154 nt self-cleaving RNA molecule that can be divided into a trans-acting five-helix ribozyme and stem-loop substrate. The structure of the ribozyme is organised by two three-way helical junctions, the structure of which has been determined by a combination of comparative gel electrophoresis and fluorescence resonance energy ...
D. Lafontaine, D. Norman, D. Lilley
semanticscholar   +5 more sources

Focus on Function: Single Molecule Enzymology of the VS ribozyme

The FASEB Journal, 2008
Non‐coding RNAs of complex structure are involved in numerous aspects of the replication and processing of genetic information. Within the mitochondria of the bread mold Neurospora, the Varkud satellite (VS) RNA replicates parasitically by cycling between DNA and multimeric RNA forms.
Nils Walter, Miguel J. B. Pereira, R. A. Collins   +2 more
semanticscholar   +3 more sources

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
openalex   +4 more sources