Published in RNA on January 17, 2014
Challenge of Mimicking the Influences of the Cellular Environment on RNA Structure by PEG-Induced Macromolecular Crowding. Biochemistry (2015) 0.79
Bridging the gap between in vitro and in vivo RNA folding. Q Rev Biophys (2016) 0.78
A Highly Coupled Network of Tertiary Interactions in the SAM-I Riboswitch and Their Role in Regulatory Tuning. J Mol Biol (2015) 0.77
Structure-guided mutational analysis of gene regulation by the Bacillus subtilis pbuE adenine-responsive riboswitch in a cellular context. J Biol Chem (2014) 0.77
The structural stability and catalytic activity of DNA and RNA oligonucleotides in the presence of organic solvents. Biophys Rev (2016) 0.75
Gene Regulation Gets in Tune: How Riboswitch Tertiary-Structure Networks Adapt to Meet the Needs of Their Transcription Units. J Mol Biol (2015) 0.75
Cell-Free Systems Based on CHO Cell Lysates: Optimization Strategies, Synthesis of "Difficult-to-Express" Proteins and Future Perspectives. PLoS One (2016) 0.75
Thermal Stability of RNA Structures with Bulky Cations in Mixed Aqueous Solutions. Biophys J (2016) 0.75
Cooperative RNA Folding under Cellular Conditions Arises From Both Tertiary Structure Stabilization and Secondary Structure Destabilization. Biochemistry (2017) 0.75
The 2D Structure of the T. brucei Preedited RPS12 mRNA Is Not Affected by Macromolecular Crowding. J Nucleic Acids (2017) 0.75
Quantitative tests of a reconstitution model for RNA folding thermodynamics and kinetics. Proc Natl Acad Sci U S A (2017) 0.75
SHAPE analysis of the htrA RNA thermometer from Salmonella enterica. RNA (2017) 0.75
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RNA catalysis through compartmentalization. Nat Chem (2012) 1.20
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NMR-assisted prediction of RNA secondary structure: identification of a probable pseudoknot in the coding region of an R2 retrotransposon. J Am Chem Soc (2008) 1.14
Cooperativity in two-state protein folding kinetics. Protein Sci (2004) 1.14
The folding pathway of the genomic hepatitis delta virus ribozyme is dominated by slow folding of the pseudoknots. J Mol Biol (2002) 1.12
Folding of a stable DNA motif involves a highly cooperative network of interactions. J Am Chem Soc (2003) 1.05
Design of a highly reactive HDV ribozyme sequence uncovers facilitation of RNA folding by alternative pairings and physiological ionic strength. J Mol Biol (2004) 1.05
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Detection of innersphere interactions between magnesium hydrate and the phosphate backbone of the HDV ribozyme using Raman crystallography. J Am Chem Soc (2008) 0.99
Studies on Methanocaldococcus jannaschii RNase P reveal insights into the roles of RNA and protein cofactors in RNase P catalysis. Nucleic Acids Res (2008) 0.99
Crowding promotes the switch from hairpin to pseudoknot conformation in human telomerase RNA. J Am Chem Soc (2011) 0.98
Nonhierarchical ribonucleoprotein assembly suggests a strain-propagation model for protein-facilitated RNA folding. Biochemistry (2010) 0.98
Evidence that folding of an RNA tetraloop hairpin is less cooperative than its DNA counterpart. Biochemistry (2004) 0.98
The osmolyte TMAO stabilizes native RNA tertiary structures in the absence of Mg2+: evidence for a large barrier to folding from phosphate dehydration. J Mol Biol (2010) 0.97
Crowders perturb the entropy of RNA energy landscapes to favor folding. J Am Chem Soc (2013) 0.96
Enthalpies of DNA melting in the presence of osmolytes. Biophys Chem (2006) 0.96
Magnesium homeostasis in mammalian cells. Front Biosci (2007) 0.95
Molecular crowding favors reactivity of a human ribozyme under physiological ionic conditions. Biochemistry (2013) 0.92
Properties of a dimer of tRNA I Tyr 1 (Escherichia coli). Biochemistry (1972) 0.91
Thinking inside the box: designing, implementing, and interpreting thermodynamic cycles to dissect cooperativity in RNA and DNA folding. Methods Enzymol (2009) 0.89
Enhanced group II intron retrohoming in magnesium-deficient Escherichia coli via selection of mutations in the ribozyme core. Proc Natl Acad Sci U S A (2013) 0.88
DNA strand exchange catalyzed by molecular crowding in PEG solutions. Chem Commun (Camb) (2010) 0.81
Decrease in RNA folding cooperativity by deliberate population of intermediates in RNA G-quadruplexes. Angew Chem Int Ed Engl (2012) 0.80
Thermodynamics of ligand binding to a heterogeneous RNA population in the malachite green aptamer. Biochemistry (2011) 0.79
Analyzing RNA and DNA folding using temperature gradient gel electrophoresis (TGGE) with application to in vitro selections. Methods Enzymol (2009) 0.78
A simple molecular model for thermophilic adaptation of functional nucleic acids. Biochemistry (2007) 0.78
The double-stranded-RNA-binding motif: interference and much more. Nat Rev Mol Cell Biol (2004) 2.50
5'-triphosphate-dependent activation of PKR by RNAs with short stem-loops. Science (2007) 2.48
Exploring the energy landscape of a small RNA hairpin. J Am Chem Soc (2006) 1.62
Nucleoside modifications modulate activation of the protein kinase PKR in an RNA structure-specific manner. RNA (2008) 1.59
Continuous monitoring of enzyme reactions on a microchip: application to catalytic RNA self-cleavage. Anal Chem (2004) 1.45
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
Incorporation of pseudouridine into mRNA enhances translation by diminishing PKR activation. Nucleic Acids Res (2010) 1.42
A brilliant disguise for self RNA: 5'-end and internal modifications of primary transcripts suppress elements of innate immunity. RNA Biol (2008) 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
Activation of the protein kinase PKR by short double-stranded RNAs with single-stranded tails. RNA (2004) 1.38
Mechanistic characterization of the HDV genomic ribozyme: classifying the catalytic and structural metal ion sites within a multichannel reaction mechanism. Biochemistry (2003) 1.34
Folding thermodynamics and kinetics of YNMG RNA hairpins: specific incorporation of 8-bromoguanosine leads to stabilization by enhancement of the folding rate. Biochemistry (2004) 1.33
Regulation of innate immunity through RNA structure and the protein kinase PKR. Curr Opin Struct Biol (2010) 1.29
Isolation and characterization of a family of stable RNA tetraloops with the motif YNMG that participate in tertiary interactions. Biochemistry (2002) 1.23
RNA catalysis through compartmentalization. Nat Chem (2012) 1.20
RNA dimerization promotes PKR dimerization and activation. J Mol Biol (2009) 1.16
A catalytic metal ion interacts with the cleavage Site G.U wobble in the HDV ribozyme. Biochemistry (2009) 1.14
The folding pathway of the genomic hepatitis delta virus ribozyme is dominated by slow folding of the pseudoknots. J Mol Biol (2002) 1.12
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
Metal binding motif in the active site of the HDV ribozyme binds divalent and monovalent ions. Biochemistry (2011) 1.07
Raman crystallography of RNA. Methods (2009) 1.06
Selection for thermodynamically stable DNA tetraloops using temperature gradient gel electrophoresis reveals four motifs: d(cGNNAg), d(cGNABg),d(cCNNGg), and d(gCNNGc). Biochemistry (2002) 1.06
Folding of a stable DNA motif involves a highly cooperative network of interactions. J Am Chem Soc (2003) 1.05
Design of a highly reactive HDV ribozyme sequence uncovers facilitation of RNA folding by alternative pairings and physiological ionic strength. J Mol Biol (2004) 1.05
Mechanistic strategies in the HDV ribozyme: chelated and diffuse metal ion interactions and active site protonation. J Phys Chem B (2011) 1.04
Contribution of the closing base pair to exceptional stability in RNA tetraloops: roles for molecular mimicry and electrostatic factors. J Am Chem Soc (2009) 1.03
The nuclear magnetic resonance of CCCC RNA reveals a right-handed helix, and revised parameters for AMBER force field torsions improve structural predictions from molecular dynamics. Biochemistry (2013) 1.02
Folding cooperativity in RNA and DNA is dependent on position in the helix. Biochemistry (2007) 1.00
Detection of innersphere interactions between magnesium hydrate and the phosphate backbone of the HDV ribozyme using Raman crystallography. J Am Chem Soc (2008) 0.99
Restricting the conformational heterogeneity of RNA by specific incorporation of 8-bromoguanosine. J Am Chem Soc (2003) 0.98
Evidence that folding of an RNA tetraloop hairpin is less cooperative than its DNA counterpart. Biochemistry (2004) 0.98
Thio effects and an unconventional metal ion rescue in the genomic hepatitis delta virus ribozyme. Biochemistry (2013) 0.97
Driving forces for nucleic acid pK(a) shifting in an A(+).C wobble: effects of helix position, temperature, and ionic strength. Biochemistry (2010) 0.97
Method for assigning double-stranded RNA structures. Biotechniques (2005) 0.97
Long-distance communication in the HDV ribozyme: insights from molecular dynamics and experiments. J Mol Biol (2010) 0.96
Wild-type is the optimal sequence of the HDV ribozyme under cotranscriptional conditions. RNA (2007) 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
Charged nucleobases and their potential for RNA catalysis. Acc Chem Res (2011) 0.95
Segmental motions, not a two-state concerted switch, underlie allostery in CheY. Structure (2012) 0.94
A simple fluorescence method for pK(a) determination in RNA and DNA reveals highly shifted pK(a)'s. J Am Chem Soc (2013) 0.94
TRAP-5' stem loop interaction increases the efficiency of transcription termination in the Bacillus subtilis trpEDCFBA operon leader region. RNA (2007) 0.94
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
Prevalence of syn nucleobases in the active sites of functional RNAs. RNA (2011) 0.93
Role of RNA structure in transcription attenuation in Bacillus subtilis: the trpEDCFBA operon as a model system. Methods Enzymol (2003) 0.93
A mechanistic framework for co-transcriptional folding of the HDV genomic ribozyme in the presence of downstream sequence. J Mol Biol (2002) 0.93
A Mg2+-dependent RNA tertiary structure forms in the Bacillus subtilis trp operon leader transcript and appears to interfere with trpE translation control by inhibiting TRAP binding. J Mol Biol (2003) 0.92
RNA G-Quadruplexes in the model plant species Arabidopsis thaliana: prevalence and possible functional roles. Nucleic Acids Res (2010) 0.92
Regulation of PKR by HCV IRES RNA: importance of domain II and NS5A. J Mol Biol (2010) 0.92
Mechanistic characterization of the HDV genomic ribozyme: the cleavage site base pair plays a structural role in facilitating catalysis. RNA (2008) 0.92
Molecular crowding favors reactivity of a human ribozyme under physiological ionic conditions. Biochemistry (2013) 0.92
Toward a digital gene response: RNA G-quadruplexes with fewer quartets fold with higher cooperativity. J Am Chem Soc (2011) 0.91
Competition between Co(NH(3)(6)3+ and inner sphere Mg2+ ions in the HDV ribozyme. Biochemistry (2009) 0.91
Linkage between proton binding and folding in RNA: a thermodynamic framework and its experimental application for investigating pKa shifting. RNA (2005) 0.91
A conformationally restricted guanosine analog reveals the catalytic relevance of three structures of an RNA enzyme. Chem Biol (2007) 0.91
RNA helical imperfections regulate activation of the protein kinase PKR: effects of bulge position, size, and geometry. RNA (2011) 0.89
Thermodynamic coupling of the loop and stem in unusually stable DNA hairpins closed by CG base pairs. J Am Chem Soc (2003) 0.89
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
Thinking inside the box: designing, implementing, and interpreting thermodynamic cycles to dissect cooperativity in RNA and DNA folding. Methods Enzymol (2009) 0.89
Role of unsatisfied hydrogen bond acceptors in RNA energetics and specificity. J Am Chem Soc (2010) 0.88
The human HDV-like CPEB3 ribozyme is intrinsically fast-reacting. Biochemistry (2010) 0.87
A residual structure in unfolded intestinal fatty acid binding protein consists of amino acids that are neighbors in the native state. Biochemistry (2006) 0.87
pKa shifting in double-stranded RNA is highly dependent upon nearest neighbors and bulge positioning. Biochemistry (2013) 0.86
Structural and energetic consequences of expanding a highly cooperative stable DNA hairpin loop. J Am Chem Soc (2004) 0.86
Colocalization of fast and slow timescale dynamics in the allosteric signaling protein CheY. J Mol Biol (2013) 0.86
Molecular basis of TRAP-5'SL RNA interaction in the Bacillus subtilis trp operon transcription attenuation mechanism. RNA (2008) 0.86
Swapping core residues in homologous proteins swaps folding mechanism. Biochemistry (2005) 0.85
Effect of loop sequence and loop length on the intrinsic fluorescence of G-quadruplexes. Biochemistry (2013) 0.85
Activation of PKR by RNA misfolding: HDV ribozyme dimers activate PKR. RNA (2012) 0.84
Mechanism of catalytic RNA. Biopolymers (2004) 0.83
Native tertiary structure and nucleoside modifications suppress tRNA's intrinsic ability to activate the innate immune sensor PKR. PLoS One (2013) 0.83
A hybridization-based approach for quantitative and low-bias single-stranded DNA ligation. Anal Biochem (2013) 0.82
Specificity of the double-stranded RNA-binding domain from the RNA-activated protein kinase PKR for double-stranded RNA: insights from thermodynamics and small-angle X-ray scattering. Biochemistry (2012) 0.82
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
Decrease in RNA folding cooperativity by deliberate population of intermediates in RNA G-quadruplexes. Angew Chem Int Ed Engl (2012) 0.80
PKR and the ribosome compete for mRNA. Nat Chem Biol (2009) 0.80
Thermodynamics of ligand binding to a heterogeneous RNA population in the malachite green aptamer. Biochemistry (2011) 0.79
Phylogenetic conservation of RNA secondary and tertiary structure in the trpEDCFBA operon leader transcript in Bacillus. RNA (2003) 0.79
Portability of the GN(R)A hairpin loop motif between RNA and DNA. Biochemistry (2009) 0.78
Analyzing RNA and DNA folding using temperature gradient gel electrophoresis (TGGE) with application to in vitro selections. Methods Enzymol (2009) 0.78
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
A simple molecular model for thermophilic adaptation of functional nucleic acids. Biochemistry (2007) 0.78
Comparison of the folding mechanism of highly homologous proteins in the lipid-binding protein family. Proteins (2009) 0.77
Analysis of RNA folding and ligand binding by conventional and high-throughput calorimetry. Methods Mol Biol (2012) 0.77
Relative humidity sensors based on an environment-sensitive fluorophore in hydrogel films. Anal Chem (2010) 0.77
Assessing the Potential Effects of Active Site Mg(2+) Ions in the glmS Ribozyme-Cofactor Complex. J Phys Chem Lett (2016) 0.77
Editorial overview: exploring the vast dynamic range of RNA dynamics. Curr Opin Chem Biol (2008) 0.76
Access to human, animal, and environmental journals is still limited for the One Health community. J Med Libr Assoc (2016) 0.75
Prospecting for aptamers in the human genome. Chem Biol (2012) 0.75