Related references
Note: Only part of the references are listed.Confluence of theory and experiment reveals the catalytic mechanism of the Varkud satellite ribozyme
Abir Ganguly et al.
NATURE CHEMISTRY (2020)
An Ontology for Facilitating Discussion of Catalytic Strategies of RNA-Cleaving Enzymes
Philip C. Bevilacqua et al.
ACS CHEMICAL BIOLOGY (2019)
Cleaning Up Mechanistic Debris Generated by Twister Ribozymes Using Computational RNA Enzymology
Colin S. Gaines et al.
ACS CATALYSIS (2019)
Elucidation of Catalytic Strategies of Small Nucleolytic Ribozymes from Comparative Analysis of Active Sites
Daniel D. Seith et al.
ACS CATALYSIS (2018)
Evidence That Nucleophile Deprotonation Exceeds Bond Formation in the HDV Ribozyme Transition State
Jun Lu et al.
BIOCHEMISTRY (2018)
Enzymatic Transition States and Drug Design
Vern L. Schramm
CHEMICAL REVIEWS (2018)
Directed Evolution: Bringing New Chemistry to Life
Frances H. Arnold
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2018)
Biomedical applications of RNA-based devices
Cameron M. Kim et al.
CURRENT OPINION IN BIOMEDICAL ENGINEERING (2017)
How RNA acts as a nuclease: some mechanistic comparisons in the nucleolytic ribozymes
David M. J. Lilley
BIOCHEMICAL SOCIETY TRANSACTIONS (2017)
From the RNA world to the clinic
Bruce A. Sullenger et al.
SCIENCE (2016)
A Two-Metal-Ion-Mediated Conformational Switching Pathway for HDV Ribozyme Activation
Tai-Sung Lee et al.
ACS CATALYSIS (2016)
Inverse Thio Effects in the Hepatitis Delta Virus Ribozyme Reveal that the Reaction Pathway Is Controlled by Metal Ion Charge Density
Pallavi Thaplyal et al.
BIOCHEMISTRY (2015)
Integration of kinetic isotope effect analyses to elucidate ribonuclease mechanism
Michael E. Harris et al.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS (2015)
Effect of Zn2+ binding and enzyme active site on the transition state for RNA 2′-O-transphosphorylation interpreted through kinetic isotope effects
Haoyuan Chen et al.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS (2015)
Transition State Features in the Hepatitis Delta Virus Ribozyme Reaction Revealed by Atomic Perturbations
Selene C. Koo et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2015)
New classes of self-cleaving ribozymes revealed by comparative genomics analysis
Zasha Weinberg et al.
NATURE CHEMICAL BIOLOGY (2015)
The role of an active site Mg2+ in HDV ribozyme self-cleavage: insights from QM/MM calculations
Vojtech Mlynsky et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2015)
Mechanistic Insights into RNA Transphosphorylation from Kinetic Isotope Effects and Linear Free Energy Relationships of Model Reactions
Haoyuan Chen et al.
CHEMISTRY-A EUROPEAN JOURNAL (2014)
Quantum Mechanical/Molecular Mechanical Free Energy Simulations of the Self-Cleavage Reaction in the Hepatitis Delta Virus Ribozyme
Abir Ganguly et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2014)
New tools provide a second look at HDV ribozyme structure, dynamics and cleavage
Gary J. Kapral et al.
NUCLEIC ACIDS RESEARCH (2014)
Thio Effects and an Unconventional Metal Ion Rescue in the Genomic Hepatitis Delta Virus Ribozyme
Pallavi Thaplyal et al.
BIOCHEMISTRY (2013)
Experimental and computational analysis of the transition state for ribonuclease A-catalyzed RNA 2′-O-transphosphorylation
Hong Gu et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
Characterization of the Reaction Path and Transition States for RNA Transphosphorylation Models from Theory and Experiment
Kin-Yiu Wong et al.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2012)
Biological Phosphoryl-Transfer Reactions: Understanding Mechanism and Catalysis
Jonathan K. Lassila et al.
ANNUAL REVIEW OF BIOCHEMISTRY, VOL 80 (2011)
Quantum Mechanical/Molecular Mechanical Study of the HDV Ribozyme: Impact of the Catalytic Metal Ion on the Mechanism
Abir Ganguly et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2011)
Characterization of the Structure and Dynamics of the HDV Ribozyme in Different Stages Along the Reaction Path
Tai-Sung Lee et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2011)
A two-step chemical mechanism for ribosome-catalysed peptide bond formation
David A. Hiller et al.
NATURE (2011)
A 1.9 Å Crystal Structure of the HDV Ribozyme Precleavage Suggests both Lewis Acid and General Acid Mechanisms Contribute to Phosphodiester Cleavage
Jui-Hui Chen et al.
BIOCHEMISTRY (2010)
Kinetic Isotope Effects for RNA Cleavage by 2′-O-Transphosphorylation: Nucleophilic Activation by Specific Base
Michael E. Harris et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2010)
A Catalytic Metal Ion Interacts with the Cleavage Site G•U Wobble in the HDV Ribozyme
Jui-Hui Chen et al.
BIOCHEMISTRY (2009)
Competition between Co(NH3)63+ and Inner Sphere Mg2+ Ions in the HDV Ribozyme
Bo Gong et al.
BIOCHEMISTRY (2009)
Functional Nucleic Acid Sensors
Juewen Liu et al.
CHEMICAL REVIEWS (2009)
Probing General Acid Catalysis in the Hammerhead Ribozyme
Jason M. Thomas et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2009)
Detection of innersphere interactions between magnesium hydrate and the phosphate backbone of the HDV ribozyme using Raman crystallography
Bo Gong et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2008)
Altered Transition State for the Reaction of an RNA Model Catalyzed by a Dinuclear Zinc(II) Catalyst
Tim Humphry et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2008)
Direct measurement of a pKa near neutrality for the catalytic cytosine in the genomic HDV ribozyme using Raman crystallography
Bo Gong et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2007)
The mechanism of RNA strand scission: An experimental measure of the Bronsted coefficient, beta(nuc)
Jing-Dong Ye et al.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2007)
Artificially expanded genetic information system: a new base pair with an alternative hydrogen bonding pattern
Zunyi Yang et al.
NUCLEIC ACIDS RESEARCH (2006)
Chemical rescue, multiple ionizable groups, and general acid-base catalysis in the HDV genomic ribozyme
Anne T. Perrotta et al.
RNA (2006)
General acid catalysis by the hepatitis delta virus ribozyme
SR Das et al.
NATURE CHEMICAL BIOLOGY (2005)
The structure-function dilemma of the hammer head ribozyme
KE Blount et al.
ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE (2005)
How enzymes work: Analysis by modern rate theory and computer simulations
M Garcia-Viloca et al.
SCIENCE (2004)
Altered mechanisms of reactions of phosphate esters bridging a dinuclear metal center
T Humphry et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2004)
An oxocarbenium-ion intermediate of a ribozyme reaction indicated by kinetic isotope effects
PJ Unrau et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)
Isotope effects in the study of phosphoryl and sulfuryl transfer reactions
AC Hengge
ACCOUNTS OF CHEMICAL RESEARCH (2002)