Published in Science on October 10, 2002
Tools for the automatic identification and classification of RNA base pairs. Nucleic Acids Res (2003) 4.12
Tertiary contacts distant from the active site prime a ribozyme for catalysis. Cell (2006) 3.89
Ribozymes, riboswitches and beyond: regulation of gene expression without proteins. Nat Rev Genet (2007) 2.52
Peripheral regions of natural hammerhead ribozymes greatly increase their self-cleavage activity. EMBO J (2003) 2.47
Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release. EMBO J (2006) 2.23
Single-molecule enzymology of RNA: essential functional groups impact catalysis from a distance. Proc Natl Acad Sci U S A (2004) 2.11
Capturing hammerhead ribozyme structures in action by modulating general base catalysis. PLoS Biol (2008) 1.95
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Classification and energetics of the base-phosphate interactions in RNA. Nucleic Acids Res (2009) 1.43
Testing geometrical discrimination within an enzyme active site: constrained hydrogen bonding in the ketosteroid isomerase oxyanion hole. J Am Chem Soc (2008) 1.41
Water in the active site of an all-RNA hairpin ribozyme and effects of Gua8 base variants on the geometry of phosphoryl transfer. Biochemistry (2006) 1.41
Trapped water molecules are essential to structural dynamics and function of a ribozyme. Proc Natl Acad Sci U S A (2006) 1.34
A guanine nucleobase important for catalysis by the VS ribozyme. EMBO J (2007) 1.31
A rugged free energy landscape separates multiple functional RNA folds throughout denaturation. Nucleic Acids Res (2008) 1.30
Csy4 relies on an unusual catalytic dyad to position and cleave CRISPR RNA. EMBO J (2012) 1.27
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. RNA (2007) 1.27
Nucleobase catalysis in the hairpin ribozyme. RNA (2006) 1.26
Solution structure of the cap-independent translational enhancer and ribosome-binding element in the 3' UTR of turnip crinkle virus. Proc Natl Acad Sci U S A (2010) 1.23
Quantum mechanical/molecular mechanical simulation study of the mechanism of hairpin ribozyme catalysis. J Am Chem Soc (2008) 1.23
The Varkud satellite ribozyme. RNA (2004) 1.22
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
Nucleobase-mediated general acid-base catalysis in the Varkud satellite ribozyme. Proc Natl Acad Sci U S A (2010) 1.18
CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes. J Comput Chem (2007) 1.18
Structural basis for the fast self-cleavage reaction catalyzed by the twister ribozyme. Proc Natl Acad Sci U S A (2014) 1.17
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Comparison of mode analyses at different resolutions applied to nucleic acid systems. Biophys J (2005) 1.14
Use of the spliceosomal protein U1A to facilitate crystallization and structure determination of complex RNAs. Methods (2010) 1.13
Direct measurement of the ionization state of an essential guanine in the hairpin ribozyme. Nat Chem Biol (2009) 1.11
Molecular dynamics suggest multifunctionality of an adenine imino group in acid-base catalysis of the hairpin ribozyme. RNA (2009) 1.08
Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme. J Phys Chem B (2010) 1.07
General acid-base catalysis mediated by nucleobases in the hairpin ribozyme. J Am Chem Soc (2012) 1.05
Ribozyme catalysis revisited: is water involved? Mol Cell (2007) 1.05
Altered structural fluctuations in duplex RNA versus DNA: a conformational switch involving base pair opening. Nucleic Acids Res (2003) 1.05
The glmS ribozyme tunes the catalytically critical pK(a) of its coenzyme glucosamine-6-phosphate. J Am Chem Soc (2011) 1.04
The pH dependence of hairpin ribozyme catalysis reflects ionization of an active site adenine. J Biol Chem (2011) 1.01
Structural effects of nucleobase variations at key active site residue Ade38 in the hairpin ribozyme. RNA (2008) 1.00
The glmS ribozyme: use of a small molecule coenzyme by a gene-regulatory RNA. Q Rev Biophys (2010) 1.00
Chemistry and Biology of Self-Cleaving Ribozymes. Trends Biochem Sci (2015) 1.00
Catalytic importance of a protonated adenosine in the hairpin ribozyme active site. Biochemistry (2010) 0.98
Identification of an imino group indispensable for cleavage by a small ribozyme. J Am Chem Soc (2009) 0.97
Crystal structure of the Varkud satellite ribozyme. Nat Chem Biol (2015) 0.95
Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM. Methods (2009) 0.95
Mechanisms of RNA catalysis. Philos Trans R Soc Lond B Biol Sci (2011) 0.95
Charged nucleobases and their potential for RNA catalysis. Acc Chem Res (2011) 0.95
An oxocarbenium-ion intermediate of a ribozyme reaction indicated by kinetic isotope effects. Proc Natl Acad Sci U S A (2003) 0.94
A posteriori design of crystal contacts to improve the X-ray diffraction properties of a small RNA enzyme. Acta Crystallogr D Biol Crystallogr (2007) 0.94
Prevalence of syn nucleobases in the active sites of functional RNAs. RNA (2011) 0.93
The structural basis of RNA-catalyzed RNA polymerization. Nat Struct Mol Biol (2011) 0.92
A Mini-Twister Variant and Impact of Residues/Cations on the Phosphodiester Cleavage of this Ribozyme Class. Angew Chem Int Ed Engl (2015) 0.89
Use of a coenzyme by the glmS ribozyme-riboswitch suggests primordial expansion of RNA chemistry by small molecules. Philos Trans R Soc Lond B Biol Sci (2011) 0.89
Two distinct catalytic strategies in the hepatitis δ virus ribozyme cleavage reaction. Biochemistry (2011) 0.88
A transition-state interaction shifts nucleobase ionization toward neutrality to facilitate small ribozyme catalysis. J Am Chem Soc (2012) 0.88
Engineering cooperative tecto-RNA complexes having programmable stoichiometries. Nucleic Acids Res (2010) 0.87
Shared traits on the reaction coordinates of ribonuclease and an RNA enzyme. Biochem Biophys Res Commun (2008) 0.87
The chemical versatility of RNA. Philos Trans R Soc Lond B Biol Sci (2011) 0.87
Structure-function analysis from the outside in: long-range tertiary contacts in RNA exhibit distinct catalytic roles. Biochemistry (2011) 0.86
QM/MM studies of hairpin ribozyme self-cleavage suggest the feasibility of multiple competing reaction mechanisms. J Phys Chem B (2011) 0.86
Linear free energy relationships in RNA transesterification: theoretical models to aid experimental interpretations. Phys Chem Chem Phys (2014) 0.85
The catalytic mechanism of hairpin ribozyme studied by hydrostatic pressure. Nucleic Acids Res (2005) 0.85
Single-atom imino substitutions at A9 and A10 reveal distinct effects on the fold and function of the hairpin ribozyme catalytic core. Biochemistry (2009) 0.85
Base ionization and ligand binding: how small ribozymes and riboswitches gain a foothold in a protein world. Curr Opin Struct Biol (2011) 0.84
NMR structure of the A730 loop of the Neurospora VS ribozyme: insights into the formation of the active site. Nucleic Acids Res (2011) 0.84
An in vitro evolved glmS ribozyme has the wild-type fold but loses coenzyme dependence. Nat Chem Biol (2013) 0.84
Exploring ribozyme conformational changes with X-ray crystallography. Methods (2009) 0.83
A DNAzyme requiring two different metal ions at two distinct sites. Nucleic Acids Res (2015) 0.82
The hammerhead ribozyme: structure, catalysis, and gene regulation. Prog Mol Biol Transl Sci (2013) 0.82
RNA structural motifs that entail hydrogen bonds involving sugar-phosphate backbone atoms of RNA. New J Chem (2010) 0.82
Non-canonical 3'-5' extension of RNA with prebiotically plausible ribonucleoside 2',3'-cyclic phosphates. J Am Chem Soc (2014) 0.81
Cation-specific structural accommodation within a catalytic RNA. Biochemistry (2006) 0.81
Pistol ribozyme adopts a pseudoknot fold facilitating site-specific in-line cleavage. Nat Chem Biol (2016) 0.80
Unwinding the twister ribozyme: from structure to mechanism. Wiley Interdiscip Rev RNA (2016) 0.80
Vanadate-based transition-state analog inhibitors of Cre-LoxP recombination. Biochem Biophys Res Commun (2003) 0.79
The Small Ribozymes: Common and Diverse Features Observed through the FRET Lens. Springer Ser Biophys (2009) 0.79
Nucleic acid reactivity: challenges for next-generation semiempirical quantum models. J Comput Chem (2015) 0.76
Chemical syntheses of inhibitory substrates of the RNA-RNA ligation reaction catalyzed by the hairpin ribozyme. Nucleic Acids Res (2004) 0.75
Intermolecular domain docking in the hairpin ribozyme: metal dependence, binding kinetics and catalysis. RNA Biol (2013) 0.75
Transition State Features in the Hepatitis Delta Virus Ribozyme Reaction Revealed by Atomic Perturbations. J Am Chem Soc (2015) 0.75
Cobalt(III)hexaammine-dependent photocrosslinks in the hairpin ribozyme. J Inorg Biochem (2013) 0.75
Ternary borate-nucleoside complex stabilization by ribonuclease A demonstrates phosphate mimicry. J Biol Inorg Chem (2007) 0.75
Crystal structure of Pistol, a class of self-cleaving ribozyme. Proc Natl Acad Sci U S A (2017) 0.75
Thermodynamics and kinetics of RNA tertiary structure formation in the junctionless hairpin ribozyme. Biophys Chem (2017) 0.75
Structural basis of glmS ribozyme activation by glucosamine-6-phosphate. Science (2006) 3.94
Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch. Nat Struct Mol Biol (2009) 3.05
Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition. Structure (2006) 2.85
Structure of protein L7Ae bound to a K-turn derived from an archaeal box H/ACA sRNA at 1.8 A resolution. Structure (2004) 2.68
Rapid construction of empirical RNA fitness landscapes. Science (2010) 2.52
The structure and function of small nucleolar ribonucleoproteins. Nucleic Acids Res (2007) 2.50
Riboswitches: small-molecule recognition by gene regulatory RNAs. Curr Opin Struct Biol (2007) 2.11
Cocrystal structure of a class I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase. Nat Struct Mol Biol (2009) 1.88
Pseudouridine synthases. Chem Biol (2006) 1.73
Idiosyncratically tuned switching behavior of riboswitch aptamer domains revealed by comparative small-angle X-ray scattering analysis. RNA (2010) 1.58
Ribozymes and riboswitches: modulation of RNA function by small molecules. Biochemistry (2010) 1.58
Structural basis of specific tRNA aminoacylation by a small in vitro selected ribozyme. Nature (2008) 1.55
Riboswitches: discovery of drugs that target bacterial gene-regulatory RNAs. Acc Chem Res (2011) 1.52
The Cbf5-Nop10 complex is a molecular bracket that organizes box H/ACA RNPs. Nat Struct Mol Biol (2005) 1.52
Thermodynamic analysis of ligand binding and ligand binding-induced tertiary structure formation by the thiamine pyrophosphate riboswitch. RNA (2009) 1.48
Essential role of an active-site guanine in glmS ribozyme catalysis. J Am Chem Soc (2007) 1.45
Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA. Nature (2013) 1.45
Requirement of helix P2.2 and nucleotide G1 for positioning the cleavage site and cofactor of the glmS ribozyme. J Mol Biol (2007) 1.43
Crystal structure of pseudouridine synthase RluA: indirect sequence readout through protein-induced RNA structure. Mol Cell (2006) 1.42
Gold nanoparticles as a versatile platform for optimizing physicochemical parameters for targeted drug delivery. Macromol Biosci (2006) 1.38
Structural basis for specific, high-affinity tetracycline binding by an in vitro evolved aptamer and artificial riboswitch. Chem Biol (2008) 1.35
Isolation and characterization of a thermostable RNA ligase 1 from a Thermus scotoductus bacteriophage TS2126 with good single-stranded DNA ligation properties. Nucleic Acids Res (2005) 1.32
The box H/ACA ribonucleoprotein complex: interplay of RNA and protein structures in post-transcriptional RNA modification. J Biol Chem (2009) 1.21
Riboswitch function: flipping the switch or tuning the dimmer? RNA Biol (2010) 1.18
YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops. RNA (2012) 1.16
Relative orientation of rigid nitroxides by PELDOR: beyond distance measurements in nucleic acids. Angew Chem Int Ed Engl (2009) 1.15
Allosteric tertiary interactions preorganize the c-di-GMP riboswitch and accelerate ligand binding. ACS Chem Biol (2012) 1.09
A nucleoside that contains a rigid nitroxide spin label: a fluorophore in disguise. Angew Chem Int Ed Engl (2007) 1.08
Crystallization of the hairpin ribozyme: illustrative protocols. Methods Mol Biol (2004) 1.07
The glmS ribozyme tunes the catalytically critical pK(a) of its coenzyme glucosamine-6-phosphate. J Am Chem Soc (2011) 1.04
Studying RNA using site-directed spin-labeling and continuous-wave electron paramagnetic resonance spectroscopy. Methods Enzymol (2009) 1.03
Folding of the cocaine aptamer studied by EPR and fluorescence spectroscopies using the bifunctional spectroscopic probe Ç. Nucleic Acids Res (2009) 1.01
Modulation of quaternary structure and enhancement of ligand binding by the K-turn of tandem glycine riboswitches. RNA (2012) 0.98
Trityl radicals: spin labels for nanometer-distance measurements. Chemistry (2012) 0.98
Rigid spin-labeled nucleoside C: a nonperturbing EPR probe of nucleic acid conformation. Nucleic Acids Res (2008) 0.97
Structural investigation of a high-affinity MnII binding site in the hammerhead ribozyme by EPR spectroscopy and DFT calculations. Effects of neomycin B on metal-ion binding. Chembiochem (2003) 0.97
Electron paramagnetic resonance dynamic signatures of TAR RNA-small molecule complexes provide insight into RNA structure and recognition. Biochemistry (2002) 0.96
Structure-guided engineering of the regioselectivity of RNA ligase ribozymes. J Am Chem Soc (2009) 0.96
Precursor complex structure of pseudouridine synthase TruB suggests coupling of active site perturbations to an RNA-sequestering peripheral protein domain. Protein Sci (2005) 0.96
Monitoring tat peptide binding to TAR RNA by solid-state 31P-19F REDOR NMR. Nucleic Acids Res (2005) 0.94
Investigation of RNA-protein and RNA-metal ion interactions by electron paramagnetic resonance spectroscopy. The HIV TAR-Tat motif. Chem Biol (2002) 0.94
Site-specific incorporation of nitroxide spin-labels into 2'-positions of nucleic acids. Nat Protoc (2007) 0.94
Determination of DNA minor groove width in distamycin-DNA complexes by solid-state NMR. Nucleic Acids Res (2003) 0.93
EPR spectroscopic analysis of U7 hammerhead ribozyme dynamics during metal ion induced folding. Biochemistry (2005) 0.92
U1A RNA-binding domain at 1.8 A resolution. Acta Crystallogr D Biol Crystallogr (2003) 0.91
Orientation selection in distance measurements between nitroxide spin labels at 94 GHz EPR with variable dual frequency irradiation. Phys Chem Chem Phys (2013) 0.90
Conformational flexibility of DNA. J Am Chem Soc (2011) 0.89
SEWAL: an open-source platform for next-generation sequence analysis and visualization. Nucleic Acids Res (2010) 0.89
Single base interrogation by a fluorescent nucleotide: each of the four DNA bases identified by fluorescence spectroscopy. Chem Commun (Camb) (2008) 0.89
Zinc-dependent cleavage in the catalytic core of the hammerhead ribozyme: evidence for a pH-dependent conformational change. Nucleic Acids Res (2003) 0.89
Noncovalent and site-directed spin labeling of nucleic acids. Angew Chem Int Ed Engl (2010) 0.89
W-band PELDOR with 1 kW microwave power: molecular geometry, flexibility and exchange coupling. J Magn Reson (2012) 0.88
Crystallization of the glmS ribozyme-riboswitch. Methods Mol Biol (2009) 0.88
Solution structure of a nitrous acid induced DNA interstrand cross-link. Nucleic Acids Res (2004) 0.88
Site-directed spin-labeling of nucleic acids by click chemistry: detection of abasic sites in duplex DNA by EPR spectroscopy. J Am Chem Soc (2010) 0.85
A nonafluoro nucleoside as a sensitive 19f NMR probe of nucleic acid conformation. Org Lett (2008) 0.85
Identification of amino acids that promote specific and rigid TAR RNA-tat protein complex formation. Chem Biol (2005) 0.84
EPR spectroscopic analysis of TAR RNA-metal ion interactions. Biochem Biophys Res Commun (2003) 0.84
An in vitro evolved glmS ribozyme has the wild-type fold but loses coenzyme dependence. Nat Chem Biol (2013) 0.84
How RNA closes a Diel. Nat Struct Mol Biol (2005) 0.84
Measurements of short distances between trityl spin labels with CW EPR, DQC and PELDOR. Phys Chem Chem Phys (2013) 0.83
Conformational equilibria of bulged sites in duplex DNA studied by EPR spectroscopy. J Phys Chem B (2009) 0.83
Glucosamine and glucosamine-6-phosphate derivatives: catalytic cofactor analogues for the glmS ribozyme. J Org Chem (2013) 0.82
Investigation of Mg2+- and temperature-dependent folding of the hairpin ribozyme by photo-crosslinking: effects of photo-crosslinker tether length and chemistry. Nucleic Acids Res (2005) 0.81
Using solid-state 31P{19F} REDOR NMR to measure distances between a trifluoromethyl group and a phosphodiester in nucleic acids. J Magn Reson (2005) 0.81
Analytical method to determine the orientation of rigid spin labels in DNA. Phys Rev E Stat Nonlin Soft Matter Phys (2010) 0.81
Identification of single-base mismatches in duplex DNA by EPR spectroscopy. J Am Chem Soc (2009) 0.81
Theory for spin-lattice relaxation of spin probes on weakly deformable DNA. J Phys Chem B (2008) 0.81
Sequence context effect on the structure of nitrous acid induced DNA interstrand cross-links. Nucleic Acids Res (2004) 0.80
Synthesis and characterization of RNA containing a rigid and nonperturbing cytidine-derived spin label. J Org Chem (2012) 0.80
Distance measurements between manganese(II) and nitroxide spin-labels by DEER determine a binding site of Mn(2+) in the HP92 loop of ribosomal RNA. Phys Chem Chem Phys (2015) 0.80
A single-stranded junction modulates nanosecond motional ordering of the substrate recognition duplex of a group I ribozyme. Chembiochem (2013) 0.80
Conformationally restricted isoindoline-derived spin labels in duplex DNA: distances and rotational flexibility by pulsed electron-electron double resonance spectroscopy. Chemistry (2014) 0.78
Interactions of the antibiotics neomycin B and chlortetracycline with the hammerhead ribozyme as studied by Zn2+-dependent RNA cleavage. Bioorg Med Chem (2004) 0.78
Simulating electron spin resonance spectra of macromolecules labeled with two dipolar-coupled nitroxide spin labels from trajectories. Phys Chem Chem Phys (2011) 0.78
Structural changes of an abasic site in duplex DNA affect noncovalent binding of the spin label ç. Nucleic Acids Res (2011) 0.78
tert-Butyldimethylsilyl O-protected chitosan and chitooligosaccharides: useful precursors for N-modifications in common organic solvents. Carbohydr Res (2008) 0.77
Protein-induced changes in DNA structure and dynamics observed with noncovalent site-directed spin labeling and PELDOR. Nucleic Acids Res (2012) 0.77
Large flanking sequence effects in single nucleotide mismatch detection using fluorescent nucleoside C(f). Bioorg Med Chem (2010) 0.77
Structure-function relationships of phenoxazine nucleosides for identification of mismatches in duplex DNA by fluorescence spectroscopy. Chembiochem (2011) 0.77
Experimental and theoretical study of the metastable decay of negatively charged nucleosides in the gas phase. Phys Chem Chem Phys (2011) 0.77
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Protein synthesis: Stop the nonsense. Nature (2011) 0.76
Analysis of riboswitch structure and ligand binding using small-angle X-ray scattering (SAXS). Methods Mol Biol (2014) 0.76
Syntheses and photophysical properties of 5'-6-locked fluorescent nucleosides. Org Biomol Chem (2013) 0.76
Hydrogen-bonding controlled rigidity of an isoindoline-derived nitroxide spin label for nucleic acids. Chem Commun (Camb) (2012) 0.76
Stereospecific syntheses of 3'-deuterated pyrimidine nucleosides and their site-specific incorporation into DNA. Org Lett (2003) 0.76
Nitroxide-labeled pyrimidines for non-covalent spin-labeling of abasic sites in DNA and RNA duplexes. Org Biomol Chem (2014) 0.76
Site-directed spin labeling of 2'-amino groups in RNA with isoindoline nitroxides that are resistant to reduction. Chem Commun (Camb) (2015) 0.76
Synthetic biology: an RNP switch raises a roadblock. Nat Chem Biol (2010) 0.75
Crystal structure of a DNA containing the planar, phenoxazine-derived bi-functional spectroscopic probe C. Nucleic Acids Res (2011) 0.75
Chemical syntheses of inhibitory substrates of the RNA-RNA ligation reaction catalyzed by the hairpin ribozyme. Nucleic Acids Res (2004) 0.75
TMIO-PyrImid hybrids are profluorescent, site-directed spin labels for nucleic acids. Org Lett (2014) 0.75
Post-crystallization Improvement of RNA Crystal Diffraction Quality. Methods Mol Biol (2015) 0.75
Conformation and dynamics of nucleotides in bulges and symmetric internal loops in duplex DNA studied by EPR and fluorescence spectroscopies. Biochem Biophys Res Commun (2012) 0.75
Structural features and dynamics of a cold-adapted alkaline phosphatase studied by EPR spectroscopy. FEBS J (2009) 0.75
Rigid 5'-6-locked phenanthroline-derived nucleosides chelated to ruthenium and europium ions. Bioorg Med Chem Lett (2012) 0.75
Correction: Distance measurements between manganese(ii) and nitroxide spin-labels by DEER determine a binding site of Mn(2+) in the HP92 loop of ribosomal RNA. Phys Chem Chem Phys (2015) 0.75