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Single-molecule enzymology of RNA: essential functional groups impact catalysis from a distance

Single-molecule enzymology of RNA: essential functional groups impact catalysis from a distance

http://www.wikidata.org/entity/Q35971022

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Novel cyanine-AMP conjugates for efficient 5' RNA fluorescent labeling by one-step transcription and replacement of [gamma-32P]ATP in RNA structural investigation Single molecule fluorescence approaches shed light on intracellular RNAs The Shine-Dalgarno sequence of riboswitch-regulated single mRNAs shows ligand-dependent accessibility bursts A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization A posterioridesign of crystal contacts to improve the X-ray diffraction properties of a small RNA enzyme Comparison of a PreQ1 Riboswitch Aptamer in Metabolite-bound and Free States with Implications for Gene Regulation Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure Conformational dynamics of single pre-mRNA molecules during in vitro splicing.Single VS ribozyme molecules reveal dynamic and hierarchical folding toward catalysis.Construction of bacteriophage phi29 DNA packaging motor and its applications in nanotechnology and therapy Biased Brownian ratcheting leads to pre-mRNA remodeling and capture prior to first-step splicing.BOBA FRET: bootstrap-based analysis of single-molecule FRET data Single-molecule enzymology of chymotrypsin using water-in-oil emulsion.Exploring ribozyme conformational changes with X-ray crystallography.Construction of a laser combiner for dual fluorescent single molecule imaging of pRNA of phi29 DNA packaging motor.Design and application of single fluorophore dual-view imaging system containing both the objective- and prism-type TIRF.Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape.Thermodynamic and kinetic analysis of an RNA kissing interaction and its resolution into an extended duplex.Comparative analysis of RNA/protein dynamics for the arginine-rich-binding motif and zinc-finger-binding motif proteins encoded by HIV-1.Dual-channel single-molecule fluorescence resonance energy transfer to establish distance parameters for RNA nanoparticles.Single-molecule tools for enzymology, structural biology, systems biology and nanotechnology: an update.Analysis of single-molecule FRET trajectories using hidden Markov modeling.Mg2+-induced compaction of single RNA molecules monitored by tethered particle microscopy Molecular crowding accelerates ribozyme docking and catalysis Do-it-yourself guide: how to use the modern single-molecule toolkit Allostery and cooperativity revisited.Removal of covalent heterogeneity reveals simple folding behavior for P4-P6 RNA.Trapped water molecules are essential to structural dynamics and function of a ribozyme.Cation-induced kinetic heterogeneity of the intron-exon recognition in single group II introns.Counting of six pRNAs of phi29 DNA-packaging motor with customized single-molecule dual-view system.Single-molecule FRET of protein-nucleic acid and protein-protein complexes: surface passivation and immobilization.Dissecting the multistep reaction pathway of an RNA enzyme by single-molecule kinetic "fingerprinting".Coupling of fast and slow modes in the reaction pathway of the minimal hammerhead ribozyme cleavage.Instrumentation and metrology for single RNA counting in biological complexes or nanoparticles by a single-molecule dual-view system.Single-molecule biophysics: at the interface of biology, physics and chemistry Single-molecule Förster resonance energy transfer reveals an innate fidelity checkpoint in DNA polymerase I Viral nanomotors for packaging of dsDNA and dsRNA Single-molecule nonequilibrium periodic Mg2+-concentration jump experiments reveal details of the early folding pathways of a large RNA.Engineered holliday junctions as single-molecule reporters for protein-DNA interactions with application to a MerR-family regulator.Single-molecule studies of group II intron ribozymes

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P2860

Single-molecule enzymology of RNA: essential functional groups impact catalysis from a distance

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Proceedings of the National Academy of Sciences of the United States of America

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Single-molecule enzymology of ...... pact catalysis from a distance

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David Rueda

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Gregory Bokinsky

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Maria M Rhodes

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Michael J Rust

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Nils G Walter

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Xiaowei Zhuang

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P2860

Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis

Transition state stabilization by a catalytic RNA

Early events in RNA folding

Single-molecule enzymatic dynamics

Functional involvement of G8 in the hairpin ribozyme cleavage mechanism.

Tertiary structure formation in the hairpin ribozyme monitored by fluorescence resonance energy transfer

A perspective on enzyme catalysis.

The hairpin ribozyme. Discovery, mechanism, and development for gene therapy.

Structure and function of the hairpin ribozyme.

Correlating structural dynamics and function in single ribozyme molecules.

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