Published in Nucleic Acids Res on August 11, 1993
Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc Natl Acad Sci U S A (2004) 10.35
Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proc Natl Acad Sci U S A (1994) 8.06
A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation. Nucleic Acids Res (2006) 1.67
Computational approaches for RNA energy parameter estimation. RNA (2010) 1.33
Transposable elements in disease-associated cryptic exons. Hum Genet (2009) 1.28
In vitro selection identifies key determinants for loop-loop interactions: RNA aptamers selective for the TAR RNA element of HIV-1. RNA (1999) 1.24
Evolutionary variation in bacterial RNase P RNAs. Nucleic Acids Res (1998) 1.24
Loop dependence of the stability and dynamics of nucleic acid hairpins. Nucleic Acids Res (2007) 1.15
Structure of the ribozyme substrate hairpin of Neurospora VS RNA: a close look at the cleavage site. RNA (2000) 1.14
DotKnot: pseudoknot prediction using the probability dot plot under a refined energy model. Nucleic Acids Res (2010) 1.12
A test of the model to predict unusually stable RNA hairpin loop stability. RNA (2000) 1.10
Evolution of CRISPR RNA recognition and processing by Cas6 endonucleases. Nucleic Acids Res (2013) 1.06
Thermodynamic analysis of 5' and 3' single- and 3' double-nucleotide overhangs neighboring wobble terminal base pairs. Nucleic Acids Res (2008) 1.00
The importance of a single G in the hairpin loop of the iron responsive element (IRE) in ferritin mRNA for structure: an NMR spectroscopy study. Nucleic Acids Res (1995) 0.99
Thermodynamic characterization of RNA triloops. Biochemistry (2010) 0.96
Correlation of RNA secondary structure statistics with thermodynamic stability and applications to folding. J Mol Biol (2009) 0.91
Probing the hammerhead ribozyme structure with ribonucleases. Nucleic Acids Res (1994) 0.85
Closing loop base pairs in RNA loop-loop complexes: structural behavior, interaction energy and solvation analysis through molecular dynamics simulations. J Mol Model (2004) 0.81
Structure of the 3'-hairpin of the TYMV pseudoknot: preformation in RNA folding. EMBO J (1998) 0.81
An innate twist between Crick's wobble and Watson-Crick base pairs. RNA (2013) 0.80
Secondary structure and stability of the selenocysteine insertion sequences (SECIS) for human thioredoxin reductase and glutathione peroxidase. Nucleic Acids Res (2004) 0.76
Structural and thermodynamic signatures that define pseudotriloop RNA hairpins. RNA (2013) 0.76
Biophysical properties, thermal stability and functional impact of 8-oxo-7,8-dihydroguanine on oligonucleotides of RNA-a study of duplex, hairpins and the aptamer for preQ1 as models. Nucleic Acids Res (2017) 0.75
Capturing RNA Folding Free Energy with Coarse-Grained Molecular Dynamics Simulations. Sci Rep (2017) 0.75
Improved estimation of secondary structure in ribonucleic acids. Nat New Biol (1973) 46.33
Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res (1987) 25.34
On finding all suboptimal foldings of an RNA molecule. Science (1989) 20.36
Improved free-energy parameters for predictions of RNA duplex stability. Proc Natl Acad Sci U S A (1986) 19.52
Improved predictions of secondary structures for RNA. Proc Natl Acad Sci U S A (1989) 11.52
Free energy of imperfect nucleic acid helices. II. Small hairpin loops. J Mol Biol (1973) 10.07
Stability of RNA hairpin loops: A 6 -C m -U 6 . J Mol Biol (1973) 8.39
Base-stacking and base-pairing contributions to helix stability: thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp. Biochemistry (1983) 6.81
Architecture of ribosomal RNA: constraints on the sequence of "tetra-loops". Proc Natl Acad Sci U S A (1990) 6.25
RNA structure prediction. Annu Rev Biophys Biophys Chem (1988) 5.75
A compilation of large subunit RNA sequences presented in a structural format. Nucleic Acids Res (1988) 4.38
A thermodynamic study of unusually stable RNA and DNA hairpins. Nucleic Acids Res (1991) 3.59
Polymer-supported RNA synthesis and its application to test the nearest-neighbor model for duplex stability. Biochemistry (1986) 3.21
Characterization of RNA hairpin loop stability. Nucleic Acids Res (1988) 3.10
Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops. Nucleic Acids Res (1992) 2.70
Contributions of dangling end stacking and terminal base-pair formation to the stabilities of XGGCCp, XCCGGp, XGGCCYp, and XCCGGYp helixes. Biochemistry (1985) 2.70
A comparison of optimal and suboptimal RNA secondary structures predicted by free energy minimization with structures determined by phylogenetic comparison. Nucleic Acids Res (1991) 2.51
Stabilities of consecutive A.C, C.C, G.G, U.C, and U.U mismatches in RNA internal loops: Evidence for stable hydrogen-bonded U.U and C.C.+ pairs. Biochemistry (1991) 2.44
Context dependence of hydrogen bond free energy revealed by substitutions in an RNA hairpin. Science (1992) 2.44
Influence of loop residues on the relative stabilities of DNA hairpin structures. Proc Natl Acad Sci U S A (1988) 2.37
Free energy contributions of G.U and other terminal mismatches to helix stability. Biochemistry (1986) 1.92
Enzymatic and NMR analysis of oligoribonucleotides synthesized with 2'-tert-butyldimethylsilyl protected cyanoethylphosphoramidite monomers. Nucleic Acids Res (1990) 1.28
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol (1999) 41.48
Improved free-energy parameters for predictions of RNA duplex stability. Proc Natl Acad Sci U S A (1986) 19.52
Improved predictions of secondary structures for RNA. Proc Natl Acad Sci U S A (1989) 11.52
Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry (1998) 9.75
Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proc Natl Acad Sci U S A (1994) 8.06
Predicting optimal and suboptimal secondary structure for RNA. Methods Enzymol (1990) 7.08
Base-stacking and base-pairing contributions to helix stability: thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp. Biochemistry (1983) 6.81
Predicting thermodynamic properties of RNA. Methods Enzymol (1995) 3.38
Thermodynamics of (dG--dC)3 double-helix formation in water and deuterium oxide. Biochemistry (1981) 3.30
Polymer-supported RNA synthesis and its application to test the nearest-neighbor model for duplex stability. Biochemistry (1986) 3.21
Investigation of the structural basis for thermodynamic stabilities of tandem GU mismatches: solution structure of (rGAGGUCUC)2 by two-dimensional NMR and simulated annealing. Biochemistry (1996) 2.96
Thermodynamic studies of RNA stability. J Biomol Struct Dyn (1984) 2.75
Contributions of dangling end stacking and terminal base-pair formation to the stabilities of XGGCCp, XCCGGp, XGGCCYp, and XCCGGYp helixes. Biochemistry (1985) 2.70
Predicting oligonucleotide affinity to nucleic acid targets. RNA (1999) 2.67
A comparison of optimal and suboptimal RNA secondary structures predicted by free energy minimization with structures determined by phylogenetic comparison. Nucleic Acids Res (1991) 2.51
Stabilities of consecutive A.C, C.C, G.G, U.C, and U.U mismatches in RNA internal loops: Evidence for stable hydrogen-bonded U.U and C.C.+ pairs. Biochemistry (1991) 2.44
Context dependence of hydrogen bond free energy revealed by substitutions in an RNA hairpin. Science (1992) 2.44
Thermodynamics of single mismatches in RNA duplexes. Biochemistry (1999) 2.36
Stability of XGCGCp, GCGCYp, and XGCGCYp helixes: an empirical estimate of the energetics of hydrogen bonds in nucleic acids. Biochemistry (1986) 2.32
Expanded CUG repeat RNAs form hairpins that activate the double-stranded RNA-dependent protein kinase PKR. RNA (2000) 2.25
Thermal unfolding of a group I ribozyme: the low-temperature transition is primarily disruption of tertiary structure. Biochemistry (1993) 2.13
Laser temperature-jump, spectroscopic, and thermodynamic study of salt effects on duplex formation by dGCATGC. Biochemistry (1989) 2.13
Laser temperature-jump study of stacking in adenylic acid polymers. Biochemistry (1979) 2.12
Sequence dependence for the energetics of dangling ends and terminal base pairs in ribonucleic acid. Biochemistry (1987) 1.95
Energetics of internal GU mismatches in ribooligonucleotide helixes. Biochemistry (1986) 1.92
Free energy contributions of G.U and other terminal mismatches to helix stability. Biochemistry (1986) 1.92
Thermodynamics of three-way multibranch loops in RNA. Biochemistry (2001) 1.78
Effects of GA mismatches on the structure and thermodynamics of RNA internal loops. Biochemistry (1990) 1.76
Solvent effects on the stability of A7U7p. Biochemistry (1985) 1.73
Thermodynamic study of internal loops in oligoribonucleotides: symmetric loops are more stable than asymmetric loops. Biochemistry (1991) 1.71
Nearest-neighbor parameters for G.U mismatches: [formula; see text] is destabilizing in the contexts [formula; see text] and [formula; see text] but stabilizing in [formula; see text]. Biochemistry (1991) 1.70
Structure of (rGGCGAGCC)2 in solution from NMR and restrained molecular dynamics. Biochemistry (1993) 1.70
Dynamics of ribozyme binding of substrate revealed by fluorescence-detected stopped-flow methods. Science (1992) 1.69
Secondary structure model of the RNA recognized by the reverse transcriptase from the R2 retrotransposable element. RNA (1997) 1.68
Thermodynamic and spectroscopic study of bulge loops in oligoribonucleotides. Biochemistry (1990) 1.63
A model for the stabilities of RNA hairpins based on a study of the sequence dependence of stability for hairpins of six nucleotides. Biochemistry (1994) 1.58
A periodic table of symmetric tandem mismatches in RNA. Biochemistry (1995) 1.55
Comparison of binding of mixed ribose-deoxyribose analogues of CUCU to a ribozyme and to GGAGAA by equilibrium dialysis: evidence for ribozyme specific interactions with 2' OH groups. Biochemistry (1991) 1.50
Measuring the thermodynamics of RNA secondary structure formation. Biopolymers (1997) 1.43
Melting and chemical modification of a cyclized self-splicing group I intron: similarity of structures in 1 M Na+, in 10 mM Mg2+, and in the presence of substrate. Biochemistry (1990) 1.40
Thermodynamics of RNA-RNA duplexes with 2- or 4-thiouridines: implications for antisense design and targeting a group I intron. Biochemistry (1999) 1.36
Solvent effects on the kinetics and thermodynamics of stacking in poly(cytidylic acid). Biochemistry (1981) 1.36
The stability and structure of tandem GA mismatches in RNA depend on closing base pairs. Biochemistry (1994) 1.35
Kinetics for reaction of a circularized intervening sequence with CU, UCU, CUCU, and CUCUCU: mechanistic implications from the dependence on temperature and on oligomer and Mg2+ concentrations. Biochemistry (1988) 1.35
Factors affecting the thermodynamic stability of small asymmetric internal loops in RNA. Biochemistry (2000) 1.35
An NAD derivative produced during transfer RNA splicing: ADP-ribose 1"-2" cyclic phosphate. Science (1993) 1.33
Solvent effects on the dynamics of (dG-dC)3. Biopolymers (1983) 1.33
The kinetics of codon-anticodon interaction in yeast phenylalanine transfer RNA. J Mol Biol (1975) 1.32
Solution structure of (rGCGGACGC)2 by two-dimensional NMR and the iterative relaxation matrix approach. Biochemistry (1996) 1.31
Improved free energies for G.C base-pairs. J Mol Biol (1985) 1.31
Enzymatic and NMR analysis of oligoribonucleotides synthesized with 2'-tert-butyldimethylsilyl protected cyanoethylphosphoramidite monomers. Nucleic Acids Res (1990) 1.28
Sequence dependence of stability for coaxial stacking of RNA helixes with Watson-Crick base paired interfaces. Biochemistry (1994) 1.20
Thermodynamics of unpaired terminal nucleotides on short RNA helixes correlates with stacking at helix termini in larger RNAs. J Mol Biol (1999) 1.20
Thermodynamics of coaxially stacked helixes with GA and CC mismatches. Biochemistry (1996) 1.18
Association of 2'-5' oligoribonucleotides. Nucleic Acids Res (1992) 1.17
Evidence that 5-hydroxytryptamine3 receptors mediate cytotoxic drug and radiation-evoked emesis. Br J Cancer (1987) 1.17
Solution structure of (rGGCAGGCC)2 by two-dimensional NMR and the iterative relaxation matrix approach. Biochemistry (1997) 1.17
Laser crosslinking of E. coli RNA polymerase and T7 DNA. Nucleic Acids Res (1982) 1.14
Effects of terminal mismatches on RNA stability: thermodynamics of duplex formation for ACCGGGp, ACCGGAp, and ACCGGCp. Biochemistry (1985) 1.13
Thermodynamics of nonsymmetric tandem mismatches adjacent to G.C base pairs in RNA. Biochemistry (1997) 1.13
Transient ADP-ribosylation of a 2'-phosphate implicated in its removal from ligated tRNA during splicing in yeast. J Biol Chem (1999) 1.12
NMR structures of r(GCAGGCGUGC)2 and determinants of stability for single guanosine-guanosine base pairs. Biochemistry (2000) 1.12
Thermodynamic stabilities of internal loops with GU closing pairs in RNA. Biochemistry (2001) 1.12
Binding of guanosine and 3' splice site analogues to a group I ribozyme: interactions with functional groups of guanosine and with additional nucleotides. Biochemistry (1993) 1.10
The energetics of small internal loops in RNA. Biopolymers (2001) 1.09
Replacement of the conserved G.U with a G-C pair at the cleavage site of the Tetrahymena ribozyme decreases binding, reactivity, and fidelity. Biochemistry (1994) 1.08
Solvent effects on thermodynamics of double-helix formation in (dG-dC)3. Biochemistry (1981) 1.08
Effects of substrate structure on the kinetics of circle opening reactions of the self-splicing intervening sequence from Tetrahymena thermophila: evidence for substrate and Mg2+ binding interactions. Nucleic Acids Res (1989) 1.07
Fluorescence detected circular dichroism study of the anticodon loop of yeast tRNAPhe. Biochemistry (1975) 1.07
The time dependence of chemical modification reveals slow steps in the folding of a group I ribozyme. Biochemistry (1995) 1.07
Thermodynamic and activation parameters for binding of a pyrene-labeled substrate by the Tetrahymena ribozyme: docking is not diffusion-controlled and is driven by a favorable entropy change. Biochemistry (1995) 1.06
G.A and U.U mismatches can stabilize RNA internal loops of three nucleotides. Biochemistry (1996) 1.02
Structural features of a six-nucleotide RNA hairpin loop found in ribosomal RNA. Biochemistry (1996) 1.01
A Pneumocystis carinii group I intron ribozyme that does not require 2' OH groups on its 5' exon mimic for binding to the catalytic core. Biochemistry (1997) 0.98
Laser temperature jump study of solvent effects of poly(adenylic acid) stacking. Biochemistry (1980) 0.97
Thermodynamics of RNA internal loops with a guanosine-guanosine pair adjacent to another noncanonical pair. Biochemistry (2001) 0.97
Proton magnetic resonance melting studies of CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp. Biochemistry (1983) 0.95
Nuclear overhauser studies of CCGGAp, ACCGGp, and ACCGGUp. Biochemistry (1983) 0.93
Site-specific incorporation of nonnatural residues during in vitro protein biosynthesis with semisynthetic aminoacyl-tRNAs. Biochemistry (1991) 0.93
Substrate recognition by a yeast 2'-phosphotransferase involved in tRNA splicing and by its Escherichia coli homolog. Biochemistry (2001) 0.92
C5-(1-propynyl)-2'-deoxy-pyrimidines enhance mismatch penalties of DNA:RNA duplex formation. Biochemistry (2001) 0.92
Design, synthesis, and evaluation of latent alkylating agents activated by glutathione S-transferase. J Med Chem (1996) 0.92
A mechanistic framework for the second step of splicing catalyzed by the Tetrahymena ribozyme. Biochemistry (1996) 0.92
Cooperative and anticooperative binding to a ribozyme. Proc Natl Acad Sci U S A (1993) 0.92
Fluorescence-detected stopped flow with a pyrene labeled substrate reveals that guanosine facilitates docking of the 5' cleavage site into a high free energy binding mode in the Tetrahymena ribozyme. Biochemistry (1994) 0.92
Antisense binding enhanced by tertiary interactions: binding of phosphorothioate and N3'-->P5' phosphoramidate hexanucleotides to the catalytic core of a group I ribozyme from the mammalian pathogen Pneumocystis carinii. Biochemistry (1998) 0.91
Investigation of the structural basis for thermodynamic stabilities of tandem GU wobble pairs: NMR structures of (rGGAGUUCC)2 and (rGGAUGUCC)2. Biochemistry (1997) 0.91
Stability and structure of RNA duplexes containing isoguanosine and isocytidine. J Am Chem Soc (2001) 0.91
Effects of Mg2+ and the 2' OH of guanosine on steps required for substrate binding and reactivity with the Tetrahymena ribozyme reveal several local folding transitions. Biochemistry (1997) 0.90
In vitro suicide inhibition of self-splicing of a group I intron from Pneumocystis carinii by an N3' --> P5' phosphoramidate hexanucleotide. Proc Natl Acad Sci U S A (1999) 0.88
Long-range cooperativity in molecular recognition of RNA by oligodeoxynucleotides with multiple C5-(1-propynyl) pyrimidines. J Am Chem Soc (2001) 0.87
Recognition elements for 5' exon substrate binding to the Candida albicans group I intron. Biochemistry (2001) 0.87
Effect of a 5'-phosphate on the stability of triple helix. Nucleic Acids Res (1993) 0.86
Sequence dependence for the energetics of terminal mismatches in ribooligonucleotides. Biochemistry (1987) 0.85
Guanosine binds to the Tetrahymena ribozyme in more than one step, and its 2'-OH and the nonbridging pro-Sp phosphoryl oxygen at the cleavage site are required for productive docking. Biochemistry (1997) 0.85
Long-range cooperativity due to C5-propynylation of oligopyrimidines enhances specific recognition by uridine of ribo-adenosine over ribo-guanosine. J Am Chem Soc (2001) 0.85
Fluorescence-detected circular dichroism. Methods Enzymol (1978) 0.85