Published in J Mol Biol on April 05, 2002
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Long-range RNA-RNA interactions circularize the dengue virus genome. J Virol (2005) 2.48
Single-molecule transition-state analysis of RNA folding. Proc Natl Acad Sci U S A (2003) 2.31
Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae. J Mol Biol (2006) 2.19
RNA folding: conformational statistics, folding kinetics, and ion electrostatics. Annu Rev Biophys (2008) 2.00
RNA folding: thermodynamic and molecular descriptions of the roles of ions. Biophys J (2008) 1.90
Protein folding, stability, and solvation structure in osmolyte solutions. Biophys J (2005) 1.72
RNA catalysis in model protocell vesicles. J Am Chem Soc (2005) 1.70
Effects of osmolytes on RNA secondary and tertiary structure stabilities and RNA-Mg2+ interactions. J Mol Biol (2007) 1.55
Cations and hydration in catalytic RNA: molecular dynamics of the hepatitis delta virus ribozyme. Biophys J (2006) 1.54
Mg2+-RNA interaction free energies and their relationship to the folding of RNA tertiary structures. Proc Natl Acad Sci U S A (2006) 1.54
Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution. Proc Natl Acad Sci U S A (2005) 1.46
Biomolecular electrostatics and solvation: a computational perspective. Q Rev Biophys (2012) 1.39
Molecular crowding stabilizes folded RNA structure by the excluded volume effect. J Am Chem Soc (2010) 1.30
RNA helix stability in mixed Na+/Mg2+ solution. Biophys J (2007) 1.28
Docking kinetics and equilibrium of a GAAA tetraloop-receptor motif probed by single-molecule FRET. Proc Natl Acad Sci U S A (2005) 1.27
Critical assessment of nucleic acid electrostatics via experimental and computational investigation of an unfolded state ensemble. J Am Chem Soc (2008) 1.26
Highly conserved modified nucleosides influence Mg2+-dependent tRNA folding. Nucleic Acids Res (2002) 1.26
Direct quantitation of Mg2+-RNA interactions by use of a fluorescent dye. Methods Enzymol (2009) 1.20
Do conformational biases of simple helical junctions influence RNA folding stability and specificity? RNA (2009) 1.19
Understanding nucleic acid-ion interactions. Annu Rev Biochem (2014) 1.18
A repulsive field: advances in the electrostatics of the ion atmosphere. Curr Opin Chem Biol (2008) 1.16
Metal ion dependence, thermodynamics, and kinetics for intramolecular docking of a GAAA tetraloop and receptor connected by a flexible linker. Biochemistry (2006) 1.15
Entropy-driven folding of an RNA helical junction: an isothermal titration calorimetric analysis of the hammerhead ribozyme. Biochemistry (2004) 1.14
Molecular dynamics simulations of RNA kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets. Nucleic Acids Res (2003) 1.14
Dissecting electrostatic screening, specific ion binding, and ligand binding in an energetic model for glycine riboswitch folding. RNA (2010) 1.13
Dependence of RNA tertiary structural stability on Mg2+ concentration: interpretation of the Hill equation and coefficient. Biochemistry (2010) 1.12
Mg2+-dependent folding of a Diels-Alderase ribozyme probed by single-molecule FRET analysis. Nucleic Acids Res (2007) 1.11
Characterization of a K+-induced conformational switch in a human telomeric DNA oligonucleotide using 2-aminopurine fluorescence. Biochemistry (2010) 1.10
Unwinding RNA's secrets: advances in the biology, physics, and modeling of complex RNAs. Curr Opin Struct Biol (2008) 1.10
Microenvironment analysis and identification of magnesium binding sites in RNA. Nucleic Acids Res (2003) 1.10
Metal ion specificities for folding and cleavage activity in the Schistosoma hammerhead ribozyme. RNA (2008) 1.10
Electrostatic free energy landscapes for nucleic acid helix assembly. Nucleic Acids Res (2006) 1.01
Solution structure of the K-turn and Specifier Loop domains from the Bacillus subtilis tyrS T-box leader RNA. J Mol Biol (2011) 1.01
Monovalent and divalent promoted GAAA tetraloop-receptor tertiary interactions from freely diffusing single-molecule studies. Biophys J (2008) 0.99
Magnesium fluctuations modulate RNA dynamics in the SAM-I riboswitch. J Am Chem Soc (2012) 0.98
Salt contribution to RNA tertiary structure folding stability. Biophys J (2011) 0.96
Predicting and modeling RNA architecture. Cold Spring Harb Perspect Biol (2011) 0.95
Entropic origin of Mg2+-facilitated RNA folding. Proc Natl Acad Sci U S A (2012) 0.93
Linkage between proton binding and folding in RNA: a thermodynamic framework and its experimental application for investigating pKa shifting. RNA (2005) 0.91
Cation-dependent folding of 3' cap-independent translation elements facilitates interaction of a 17-nucleotide conserved sequence with eIF4G. Nucleic Acids Res (2013) 0.89
Evidence for a thermodynamically distinct Mg2+ ion associated with formation of an RNA tertiary structure. J Am Chem Soc (2011) 0.88
Importance in catalysis of a magnesium ion with very low affinity for a hammerhead ribozyme. Nucleic Acids Res (2004) 0.86
Mapping studies of the Peach latent mosaic viroid reveal novel structural features. Mol Plant Pathol (2011) 0.86
Folding of RNA tertiary structure: Linkages between backbone phosphates, ions, and water. Biopolymers (2013) 0.85
Synthetic RNA modules for fine-tuning gene expression levels in yeast by modulating RNase III activity. Nucleic Acids Res (2011) 0.85
Single-molecule studies of riboswitch folding. Biochim Biophys Acta (2014) 0.85
Electrostatics of nucleic acid folding under conformational constraint. J Am Chem Soc (2012) 0.85
Sequence-specific artificial ribonucleases. I. Bis-imidazole-containing oligonucleotide conjugates prepared using precursor-based strategy. Nucleic Acids Res (2004) 0.85
A counterintuitive Mg2+-dependent and modification-assisted functional folding of mitochondrial tRNAs. J Mol Biol (2006) 0.84
Specificity shifts in the rRNA and tRNA nucleotide targets of archaeal and bacterial m5U methyltransferases. RNA (2010) 0.84
RNA stem-loop enhanced expression of previously non-expressible genes. Nucleic Acids Res (2004) 0.83
A quantitative Raman spectroscopic signal for metal-phosphodiester interactions in solution. Biochemistry (2010) 0.82
Local and global effects of Mg2+ on Ago and miRNA-target interactions. J Mol Model (2012) 0.79
Many-body effect in ion binding to RNA. J Chem Phys (2014) 0.78
Reconciling ligase ribozyme activity with Fatty Acid vesicle stability. Life (Basel) (2014) 0.77
Multiscale methods for computational RNA enzymology. Methods Enzymol (2015) 0.76
Modulation of RNA metal binding by flanking bases: 15N NMR evaluation of GC, tandem GU, and tandem GA sites. Nucleosides Nucleotides Nucleic Acids (2009) 0.76
Tetracycline determines the conformation of its aptamer at physiological magnesium concentrations. Biophys J (2014) 0.76
Divalent ion competition reveals reorganization of an RNA ion atmosphere upon folding. Nucleic Acids Res (2017) 0.75
TBI server: a web server for predicting ion effects in RNA folding. PLoS One (2015) 0.75
RNA unrestrained molecular dynamics ensemble improves agreement with experimental NMR data compared to single static structure: a test case. J Comput Aided Mol Des (2006) 0.75
Counting the ions surrounding nucleic acids. Nucleic Acids Res (2016) 0.75
Deconvolution of Raman spectroscopic signals for electrostatic, H-bonding, and inner-sphere interactions between ions and dimethyl phosphate in solution. J Inorg Biochem (2010) 0.75
Inhibition of Aggregation of Mutant Huntingtin by Nucleic Acid Aptamers In Vitro and in a Yeast Model of Huntington's Disease. Mol Ther (2015) 0.75
Prebiotic Factors Influencing the Activity of a Ligase Ribozyme. Life (Basel) (2017) 0.75
Effects of osmolytes on RNA secondary and tertiary structure stabilities and RNA-Mg2+ interactions. J Mol Biol (2007) 1.55
Mg2+-RNA interaction free energies and their relationship to the folding of RNA tertiary structures. Proc Natl Acad Sci U S A (2006) 1.54
Tertiary structure of an RNA pseudoknot is stabilized by "diffuse" Mg2+ ions. Biochemistry (2007) 1.53
A thermodynamic framework for the magnesium-dependent folding of RNA. Biopolymers (2003) 1.53
Importance of partially unfolded conformations for Mg(2+)-induced folding of RNA tertiary structure: structural models and free energies of Mg2+ interactions. Biochemistry (2007) 1.49
A compact RNA tertiary structure contains a buried backbone-K+ complex. J Mol Biol (2002) 1.47
Electrostatic interactions in a peptide--RNA complex. J Mol Biol (2003) 1.31
The influence of monovalent cation size on the stability of RNA tertiary structures. J Mol Biol (2009) 1.24
Direct quantitation of Mg2+-RNA interactions by use of a fluorescent dye. Methods Enzymol (2009) 1.20
Ion-RNA interactions thermodynamic analysis of the effects of mono- and divalent ions on RNA conformational equilibria. Methods Enzymol (2009) 1.16
Dependence of RNA tertiary structural stability on Mg2+ concentration: interpretation of the Hill equation and coefficient. Biochemistry (2010) 1.12
Molecular simulation studies of monovalent counterion-mediated interactions in a model RNA kissing loop. J Mol Biol (2009) 1.04
Effects of Mg2+ on the free energy landscape for folding a purine riboswitch RNA. Biochemistry (2011) 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
The structure of free L11 and functional dynamics of L11 in free, L11-rRNA(58 nt) binary and L11-rRNA(58 nt)-thiostrepton ternary complexes. J Mol Biol (2007) 0.93
Specific interactions of the L10(L12)4 ribosomal protein complex with mRNA, rRNA, and L11. Biochemistry (2008) 0.93
A small protein unique to bacteria organizes rRNA tertiary structure over an extensive region of the 50 S ribosomal subunit. J Mol Biol (2005) 0.89
Interactions of the N-terminal domain of ribosomal protein L11 with thiostrepton and rRNA. J Biol Chem (2005) 0.88
Evidence for a thermodynamically distinct Mg2+ ion associated with formation of an RNA tertiary structure. J Am Chem Soc (2011) 0.88
Denaturation of RNA secondary and tertiary structure by urea: simple unfolded state models and free energy parameters account for measured m-values. Biochemistry (2012) 0.86
Comparison of interactions of diamine and Mg²⁺ with RNA tertiary structures: similar versus differential effects on the stabilities of diverse RNA folds. Biochemistry (2013) 0.82
Optimization of a ribosomal structural domain by natural selection. Biochemistry (2006) 0.82
Coevolution of protein and RNA structures within a highly conserved ribosomal domain. Chem Biol (2005) 0.80
Review of the sixth Annual Johns Hopkins Folding Meeting. Proteins (2002) 0.75