Rapid Formation of a Solvent-inaccessible Core in the Neurospora Varkud Satellite Ribozyme

Overview

Journal EMBO J

Specialties Biotechnology
Molecular Biology

Date 2001 Sep 28

PMID 11574478

Citations 34

Authors

S L Hiley

R A Collins

Affiliations

Soon will be listed here.

Abstract

We have used hydroxyl radicals generated by decomposition of peroxynitrous acid to study Mg(2+)-dependent structure and folding of the Varkud satellite (VS) ribozyme. Protection from radical cleavage shows the existence of a solvent-inaccessible core, which includes nucleotides near two three-helix junctions, the kissing interaction between stem-loops I and V and other nucleotides, most of which have also been implicated as important for folding or activity. Kinetic folding experiments showed that the ribozyme folds very quickly, with the observed protections completely formed within 2 s of addition of MgCl(2). In mutants that disrupt the kissing interaction or entirely remove stem-loop I, which contains the cleavage site, nucleotides in the three-helix junctions and a subset of those elsewhere remain protected. Unlike smaller ribozymes, the VS ribozyme retains a significant amount of structure in the absence of its substrate. Protections that depend on proper interaction between the substrate and the rest ribozyme map to a region previously proposed as the active site of the ribozyme and along both sides of helix II, identifying candidate sites of docking for the substrate helix.

Citing Articles

An integrative NMR-SAXS approach for structural determination of large RNAs defines the substrate-free state of a trans-cleaving Neurospora Varkud Satellite ribozyme.

Dagenais P, Desjardins G, Legault P Nucleic Acids Res. 2021; 49(20):11959-11973.

PMID: 34718697 PMC: 8599749. DOI: 10.1093/nar/gkab963.

Direct Mapping of Higher-Order RNA Interactions by SHAPE-JuMP.

Christy T, Giannetti C, Houlihan G, Smola M, Rice G, Wang J Biochemistry. 2021; 60(25):1971-1982.

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Ligand recognition and helical stacking formation are intimately linked in the SAM-I riboswitch regulatory mechanism.

Dussault A, Dube A, Jacques F, Grondin J, Lafontaine D RNA. 2017; 23(10):1539-1551.

PMID: 28701520 PMC: 5602112. DOI: 10.1261/rna.061796.117.

Insights into RNA structure and dynamics from recent NMR and X-ray studies of the Neurospora Varkud satellite ribozyme.

Dagenais P, Girard N, Bonneau E, Legault P Wiley Interdiscip Rev RNA. 2017; 8(5).

PMID: 28382748 PMC: 5573960. DOI: 10.1002/wrna.1421.

Rational engineering of the Neurospora VS ribozyme to allow substrate recognition via different kissing-loop interactions.

Lacroix-Labonte J, Girard N, Dagenais P, Legault P Nucleic Acids Res. 2016; 44(14):6924-34.

PMID: 27166370 PMC: 5001590. DOI: 10.1093/nar/gkw401.

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