Published in Biochemistry on March 23, 2015
Chemistry and Biology of Self-Cleaving Ribozymes. Trends Biochem Sci (2015) 1.00
Ambient-Potential Composite Ewald Method for ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation. J Chem Theory Comput (2016) 0.78
Assessment of metal-assisted nucleophile activation in the hepatitis delta virus ribozyme from molecular simulation and 3D-RISM. RNA (2015) 0.76
Thermal Stability of RNA Structures with Bulky Cations in Mixed Aqueous Solutions. Biophys J (2016) 0.75
Understanding in-line probing experiments by modeling cleavage of nonreactive RNA nucleotides. RNA (2017) 0.75
The GlcN6P cofactor plays multiple catalytic roles in the glmS ribozyme. Nat Chem Biol (2017) 0.75
A Two-Metal-Ion-Mediated Conformational Switching Pathway for HDV Ribozyme Activation. ACS Catal (2016) 0.75
VR-SCOSMO: A smooth conductor-like screening model with charge-dependent radii for modeling chemical reactions. J Chem Phys (2016) 0.75
Advances in methods and algorithms in a modern quantum chemistry program package. Phys Chem Chem Phys (2006) 6.51
Tertiary contacts distant from the active site prime a ribozyme for catalysis. Cell (2006) 3.89
A magnesium ion core at the heart of a ribozyme domain. Nat Struct Biol (1997) 3.68
The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone. Chem Biol (1998) 3.01
Solvent isotope effects of enzyme systems. Methods Enzymol (1982) 3.01
General acid catalysis by the hepatitis delta virus ribozyme. Nat Chem Biol (2005) 2.88
A genomewide search for ribozymes reveals an HDV-like sequence in the human CPEB3 gene. Science (2006) 2.82
Imidazole rescue of a cytosine mutation in a self-cleaving ribozyme. Science (1999) 2.77
General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme. Science (2000) 2.59
Structural basis of the enhanced stability of a mutant ribozyme domain and a detailed view of RNA--solvent interactions. Structure (2001) 2.49
Sites and thermodynamic quantities associated with proton and metal ion interaction with ribonucleic acid, deoxyribonucleic acid, and their constituent bases, nucleosides, and nucleotides. Chem Rev (1971) 2.30
Mechanistic considerations for general acid-base catalysis by RNA: revisiting the mechanism of the hairpin ribozyme. Biochemistry (2003) 1.94
An unusual pH-independent and metal-ion-independent mechanism for hairpin ribozyme catalysis. Chem Biol (1997) 1.88
Characteristics of the glmS ribozyme suggest only structural roles for divalent metal ions. RNA (2006) 1.81
Small self-cleaving ribozymes. Cold Spring Harb Perspect Biol (2010) 1.79
Widespread occurrence of self-cleaving ribozymes. Science (2009) 1.74
A unique mechanism for RNA catalysis: the role of metal cofactors in hairpin ribozyme cleavage. Chem Biol (1997) 1.67
Evidence that genomic and antigenomic RNA self-cleaving elements from hepatitis delta virus have similar secondary structures. Nucleic Acids Res (1991) 1.63
Comparison of the hammerhead cleavage reactions stimulated by monovalent and divalent cations. RNA (2001) 1.51
Nucleobase catalysis in ribozyme mechanism. Curr Opin Chem Biol (2006) 1.46
The hammerhead cleavage reaction in monovalent cations. RNA (2001) 1.44
Mechanistic characterization of the HDV genomic ribozyme: assessing the catalytic and structural contributions of divalent metal ions within a multichannel reaction mechanism. Biochemistry (2001) 1.44
Direct measurement of a pK(a) near neutrality for the catalytic cytosine in the genomic HDV ribozyme using Raman crystallography. J Am Chem Soc (2007) 1.43
A widespread self-cleaving ribozyme class is revealed by bioinformatics. Nat Chem Biol (2013) 1.42
Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulations. J Am Chem Soc (2011) 1.42
A 1.9 A crystal structure of the HDV ribozyme precleavage suggests both Lewis acid and general acid mechanisms contribute to phosphodiester cleavage. Biochemistry (2010) 1.39
Mechanistic characterization of the HDV genomic ribozyme: classifying the catalytic and structural metal ion sites within a multichannel reaction mechanism. Biochemistry (2003) 1.34
Direct Raman measurement of an elevated base pKa in the active site of a small ribozyme in a precatalytic conformation. J Am Chem Soc (2009) 1.20
Identification of catalytic metal ion ligands in ribozymes. Methods (2009) 1.18
Mechanistic characterization of the HDV genomic ribozyme: a mutant of the C41 motif provides insight into the positioning and thermodynamic linkage of metal ions and protons. Biochemistry (2007) 1.11
Mechanistic characterization of the HDV genomic ribozyme: solvent isotope effects and proton inventories in the absence of divalent metal ions support C75 as the general acid. J Am Chem Soc (2008) 1.10
HDV ribozyme activity in monovalent cations. Biochemistry (2006) 1.07
Metal binding motif in the active site of the HDV ribozyme binds divalent and monovalent ions. Biochemistry (2011) 1.07
Mechanistic strategies in the HDV ribozyme: chelated and diffuse metal ion interactions and active site protonation. J Phys Chem B (2011) 1.04
The glmS ribozyme tunes the catalytically critical pK(a) of its coenzyme glucosamine-6-phosphate. J Am Chem Soc (2011) 1.04
Proton inventory of the genomic HDV ribozyme in Mg(2+)-containing solutions. J Am Chem Soc (2001) 1.02
A novel calcium-dependent bacterial phosphatidylinositol-specific phospholipase C displaying unprecedented magnitudes of thio effect, inverse thio effect, and stereoselectivity. J Am Chem Soc (2003) 1.00
Distinct reaction pathway promoted by non-divalent-metal cations in a tertiary stabilized hammerhead ribozyme. RNA (2007) 1.00
Nucleic acid catalysis: metals, nucleobases, and other cofactors. Chem Rev (2014) 1.00
Characterization of the Structure and Dynamics of the HDV Ribozyme at Different Stages Along the Reaction Path. J Phys Chem Lett (2011) 0.98
Thio effects and an unconventional metal ion rescue in the genomic hepatitis delta virus ribozyme. Biochemistry (2013) 0.97
Long-distance communication in the HDV ribozyme: insights from molecular dynamics and experiments. J Mol Biol (2010) 0.96
Identification of the catalytic Mg²⁺ ion in the hepatitis delta virus ribozyme. Biochemistry (2013) 0.95
Simple method for determining nucleobase pK(a) values by indirect labeling and demonstration of a pK(a) of neutrality in dsDNA. J Am Chem Soc (2004) 0.95
Role of the active site guanine in the glmS ribozyme self-cleavage mechanism: quantum mechanical/molecular mechanical free energy simulations. J Am Chem Soc (2015) 0.93
Cobalt hexammine inhibition of the hammerhead ribozyme. Biochemistry (2000) 0.92
Comparisons of phosphorothioate with phosphate transfer reactions for a monoester, diester, and triester: isotope effect studies. J Am Chem Soc (2003) 0.92
Competition between Co(NH(3)(6)3+ and inner sphere Mg2+ ions in the HDV ribozyme. Biochemistry (2009) 0.91
Quantum mechanical/molecular mechanical free energy simulations of the self-cleavage reaction in the hepatitis delta virus ribozyme. J Am Chem Soc (2014) 0.89
Evidence for the role of active site residues in the hairpin ribozyme from molecular simulations along the reaction path. J Am Chem Soc (2014) 0.84
Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape. RNA (2014) 0.83
Characterization of the trans Watson-Crick GU base pair located in the catalytic core of the antigenomic HDV ribozyme. PLoS One (2012) 0.83
New tools provide a second look at HDV ribozyme structure, dynamics and cleavage. Nucleic Acids Res (2014) 0.81
Quantum Mechanical/Molecular Mechanical Study of the HDV Ribozyme: Impact of the Catalytic Metal Ion on the Mechanism. J Phys Chem Lett (2011) 0.81
The thermodynamics of phosphate versus phosphorothioate ester hydrolysis. J Org Chem (2005) 0.80
HDV family of self-cleaving ribozymes. Prog Mol Biol Transl Sci (2013) 0.79
Mechanistic analysis of the hepatitis delta virus (HDV) ribozyme: methods for RNA preparation, structure mapping, solvent isotope effects, and co-transcriptional cleavage. Methods Mol Biol (2012) 0.78