Results 1 to 10 of about 6,175 (141)
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 +7 more sources
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
europepmc +7 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 of stem-loop I such that nucleotides at the base of stem I, which contains the cleavage-ligation site,
DeAbreu DM, Olive JE, Collins RA.
europepmc +5 more sources
A split ribozyme system for in vivo plant RNA imaging and genetic engineering. [PDF]
Plant Biotechnol JSummary RNA plays a central role in plants, governing various cellular and physiological processes. Monitoring its dynamic abundance provides a discerning understanding of molecular mechanisms underlying plant responses to internal (developmental) and external (environmental) stimuli, paving the way for advances in plant biotechnology to engineer crops
Liu Y +11 more
europepmc +2 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 +6 more sources
Activation of Caged Functional RNAs by An Oxidative Transformation. [PDF]
ChembiochemRNAs containing 2‐thiouridine (2sUrd) in place of uridine (Urd) can exhibit loss of function. Treatment with hydrogen peroxide can convert 2sUrd to Urd. We show that a 2sUrd‐containing aptamer and ribozyme can exhibit recovery of function upon treatment with hydrogen peroxide, allowing for redox‐switched functional behavior.
Heili JM, Adamala KP, Engelhart AE.
europepmc +2 more sources
Crystal structure of the Varkud satellite ribozyme. [PDF]
Nat Chem Biol, 2015 Varkud Satellite (VS) ribozyme mediates rolling circle replication of a plasmid found in the Neurospora mitochondria. We report crystal structures of this ribozyme at 3.1Å resolution, revealing an intertwined dimer formed by an exchange of substrate helices.
Suslov NB +6 more
europepmc +2 more sources
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 VS ribozyme to cleave alternate substrates, we substituted the wild-type KLI by other known KLIs ...
Lacroix-Labonté J +3 more
europepmc +4 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 replaces one of the phosphate diester linkages.
Kovacheva YS +3 more
europepmc +5 more sources
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. Recent NMR studies of SLV demonstrated that magnesium ions stabilize a U-turn loop structure and trigger a conformational change for the extruded loop residue U700, suggesting a role for ...
Bouchard P +7 more
europepmc +5 more sources