Published in Biochemistry on March 14, 1995
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
On the wobble GoU and related pairs. RNA (2000) 2.47
TectoRNA: modular assembly units for the construction of RNA nano-objects. Nucleic Acids Res (2001) 2.31
A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation. Nucleic Acids Res (2006) 1.67
Effects of magnesium ions on the stabilization of RNA oligomers of defined structures. RNA (2002) 1.49
Rich RNA Structure Landscapes Revealed by Mutate-and-Map Analysis. PLoS Comput Biol (2015) 1.44
Computational approaches for RNA energy parameter estimation. RNA (2010) 1.33
Pronounced instability of tandem IU base pairs in RNA. Nucleic Acids Res (2004) 1.23
New insights into the structure of abasic DNA from molecular dynamics simulations. Nucleic Acids Res (2000) 1.11
Structure and thermodynamics of a conserved U2 snRNA domain from yeast and human. RNA (2007) 1.08
RNA challenges for computational chemists. Biochemistry (2005) 1.06
Non-nearest-neighbor dependence of the stability for RNA bulge loops based on the complete set of group I single-nucleotide bulge loops. Biochemistry (2007) 1.04
NMR structures of (rGCUGAGGCU)2 and (rGCGGAUGCU)2: probing the structural features that shape the thermodynamic stability of GA pairs. Biochemistry (2007) 1.01
The electrostatic characteristics of G.U wobble base pairs. Nucleic Acids Res (2007) 0.95
Positional and neighboring base pair effects on the thermodynamic stability of RNA single mismatches. Biochemistry (2010) 0.95
Genome-wide analyses of Epstein-Barr virus reveal conserved RNA structures and a novel stable intronic sequence RNA. BMC Genomics (2013) 0.93
Yeast ribosomal protein L32 recognizes an RNA G:U juxtaposition. RNA (1996) 0.92
The NMR structure of an internal loop from 23S ribosomal RNA differs from its structure in crystals of 50s ribosomal subunits. Biochemistry (2006) 0.92
The thermal stability of DNA fragments with tandem mismatches at a d(CXYG).d(CY'X'G) site. Nucleic Acids Res (1996) 0.92
Minimum-energy path for a u6 RNA conformational change involving protonation, base-pair rearrangement and base flipping. J Mol Biol (2009) 0.90
Ensemble analysis of primary microRNA structure reveals an extensive capacity to deform near the Drosha cleavage site. Biochemistry (2013) 0.87
In vitro selection of hammerhead ribozymes containing a bulged nucleotide in stem II. Nucleic Acids Res (1996) 0.85
Thermodynamic characterization of tandem mismatches found in naturally occurring RNA. Nucleic Acids Res (2009) 0.84
Synthesis and crystal structure of an octamer RNA r(guguuuac)/r(guaggcac) with G.G/U.U tandem wobble base pairs: comparison with other tandem G.U pairs. Nucleic Acids Res (2000) 0.83
The crystal structure of an RNA oligomer incorporating tandem adenosine-inosine mismatches. Nucleic Acids Res (1997) 0.83
Isoenergetic microarrays to study the structure and interactions of DsrA and OxyS RNAs in two- and three-component complexes. Biochemistry (2011) 0.82
The Neurospora crassa CYT-18 protein C-terminal RNA-binding domain helps stabilize interdomain tertiary interactions in group I introns. RNA (2004) 0.82
Crystal structure of an RNA helix recognized by a zinc-finger protein: an 18-bp duplex at 1.6 A resolution. RNA (2002) 0.82
An innate twist between Crick's wobble and Watson-Crick base pairs. RNA (2013) 0.80
Biochemical Methods To Investigate lncRNA and the Influence of lncRNA:Protein Complexes on Chromatin. Biochemistry (2016) 0.77
Thermodynamic characterization of RNA 2 × 3 nucleotide internal loops. Biochemistry (2012) 0.77
Hairpins in a DNA site for topoisomerase II studied by 1H- and 31P-NMR. Nucleic Acids Res (1995) 0.77
Noncanonical registers and base pairs in human 5' splice-site selection. Nucleic Acids Res (2016) 0.77
Thermodynamic examination of the pyrophosphate sensor helix in the thiamine pyrophosphate riboswitch. RNA (2011) 0.77
Secondary structure and stability of the selenocysteine insertion sequences (SECIS) for human thioredoxin reductase and glutathione peroxidase. Nucleic Acids Res (2004) 0.76
Advancing viral RNA structure prediction: measuring the thermodynamics of pyrimidine-rich internal loops. RNA (2017) 0.75
Pseudouridine Modification Inhibits Muscleblind-like 1 (MBNL1) Binding to CCUG Repeats and Minimally Structured RNA through Reduced RNA Flexibility. J Biol Chem (2017) 0.75
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
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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
Ordering and administration of sedatives and analgesics during the withholding and withdrawal of life support from critically ill patients. JAMA (1992) 1.79
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
Validation of the University of Washington quality of life questionnaires for head and neck cancer patients in India. Indian J Cancer (2008) 1.57
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
RNA hairpin loop stability depends on closing base pair. Nucleic Acids Res (1993) 1.40
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
Safety and pharmacokinetics of abacavir (1592U89) following oral administration of escalating single doses in human immunodeficiency virus type 1-infected adults. Antimicrob Agents Chemother (1999) 1.39
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
Single-dose pharmacokinetics and safety of abacavir (1592U89), zidovudine, and lamivudine administered alone and in combination in adults with human immunodeficiency virus infection. Antimicrob Agents Chemother (1999) 1.29
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
Safety and single-dose pharmacokinetics of abacavir (1592U89) in human immunodeficiency virus type 1-infected children. Antimicrob Agents Chemother (1999) 1.19
Thermodynamics of coaxially stacked helixes with GA and CC mismatches. Biochemistry (1996) 1.18
Solution structure of (rGGCAGGCC)2 by two-dimensional NMR and the iterative relaxation matrix approach. Biochemistry (1997) 1.17
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
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
Solvent effects on thermodynamics of double-helix formation in (dG-dC)3. Biochemistry (1981) 1.08
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
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
A phase I study of abacavir (1592U89) alone and in combination with other antiretroviral agents in infants and children with human immunodeficiency virus infection. AIDS Clinical Trials Group 330 Team. Pediatrics (1999) 0.96
Abacavir: absolute bioavailability, bioequivalence of three oral formulations, and effect of food. Pharmacotherapy (1999) 0.95
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
Substrate recognition by a yeast 2'-phosphotransferase involved in tRNA splicing and by its Escherichia coli homolog. Biochemistry (2001) 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
C5-(1-propynyl)-2'-deoxy-pyrimidines enhance mismatch penalties of DNA:RNA duplex formation. Biochemistry (2001) 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
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
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
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
Nonsurgical treatment of Hemophilus influenzae pericarditis in an adult. Am Heart J (1984) 0.89
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
Randomized trial of amplification strategies. Arch Otolaryngol Head Neck Surg (2001) 0.87
Long-range cooperativity in molecular recognition of RNA by oligodeoxynucleotides with multiple C5-(1-propynyl) pyrimidines. J Am Chem Soc (2001) 0.87