NMR structure of the A730 loop of the Neurospora VS ribozyme: insights into the formation of the active site. [PDF]
Nucleic Acids Res, 2011 The Neurospora VS ribozyme is a small nucleolytic ribozyme with unique primary, secondary and global tertiary structures, which displays mechanistic similarities to the hairpin ribozyme.
Desjardins G +4 more
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Rational engineering of the Neurospora VS ribozyme to allow substrate recognition via different kissing-loop interactions. [PDF]
Nucleic Acids Res, 2016 The Neurospora VS ribozyme is a catalytic RNA that has the unique ability to specifically recognize and cleave a stem-loop substrate through formation of a highly stable kissing-loop interaction (KLI). In order to explore the engineering potential of the
Lacroix-Labonté J +3 more
europepmc +6 more sources
Additional roles of a peripheral loop-loop interaction in the Neurospora VS ribozyme. [PDF]
Nucleic Acids Res, 2011 Many RNAs contain tertiary interactions that contribute to folding the RNA into its functional 3D structure. In the VS ribozyme, a tertiary loop–loop kissing interaction involving stem–loops I and V is also required to rearrange the secondary structure ...
DeAbreu DM, Olive JE, Collins RA.
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Helix-length compensation studies reveal the adaptability of the VS ribozyme architecture. [PDF]
Nucleic Acids Res, 2012 Compensatory mutations in RNA are generally regarded as those that maintain base pairing, and their identification forms the basis of phylogenetic predictions of RNA secondary structure.
Lacroix-Labonté J +3 more
europepmc +8 more sources
NMR localization of divalent cations at the active site of the Neurospora VS ribozyme provides insights into RNA-metal-ion interactions. [PDF]
Biochemistry, 2014 Metal cations represent key elements of RNA structure and function. In the Neurospora VS ribozyme, metal cations play diverse roles; they are important for substrate recognition, formation of the active site, and shifting the pKa’s of two key nucleobases
Bonneau E, Legault P.
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Role of SLV in SLI substrate recognition by the Neurospora VS ribozyme. [PDF]
RNA, 2008 Substrate recognition by the VS ribozyme involves a magnesium-dependent loop/loop interaction between the SLI substrate and the SLV hairpin from the catalytic domain.
Bouchard P +7 more
europepmc +7 more sources
The NMR structure of the II-III-VI three-way junction from the Neurospora VS ribozyme reveals a critical tertiary interaction and provides new insights into the global ribozyme structure. [PDF]
RNA, 2015 As part of an effort to structurally characterize the complete Neurospora VS ribozyme, NMR solution structures of several subdomains have been previously determined, including the internal loops of domains I and VI, the I/V kissing-loop interaction and ...
Bonneau E +3 more
europepmc +7 more sources
The role of phosphate groups in the VS ribozyme-substrate interaction. [PDF]
Nucleic Acids Res, 2004 The VS ribozyme trans-cleavage substrate interacts with the catalytic RNA via tertiary interactions. To study the role of phosphate groups in the ribozyme-substrate interaction, 18 modified substrates were synthesized, where an epimeric phosphorothioate ...
Kovacheva YS +3 more
europepmc +7 more sources
A guanine nucleobase important for catalysis by the VS ribozyme. [PDF]
EMBO J, 2007 A guanine (G638) within the substrate loop of the VS ribozyme plays a critical role in the cleavage reaction. Replacement by any other nucleotide results in severe impairment of cleavage, yet folding of the substrate is not perturbed, and the variant substrates bind the ribozyme with similar affinity, acting as competitive inhibitors.
Wilson TJ, McLeod AC, Lilley DM.
europepmc +9 more sources
The complete VS ribozyme in solution studied by small-angle X-ray scattering. [PDF]
Structure, 2008 We have used small-angle X-ray solution scattering to obtain ab initio shape reconstructions of the complete VS ribozyme. The ribozyme occupies an electron density envelope with an irregular shape, into which helical sections have been fitted. The ribozyme is built around a core comprising a near-coaxial stack of three helices, organized by two three ...
Lipfert J +4 more
europepmc +9 more sources