Published in Methods Enzymol on January 01, 1995
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Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction. BMC Bioinformatics (2004) 3.60
Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins. Proc Natl Acad Sci U S A (2006) 3.56
MicroInspector: a web tool for detection of miRNA binding sites in an RNA sequence. Nucleic Acids Res (2005) 2.87
Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction. BMC Bioinformatics (2004) 2.57
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Predicting RNA pseudoknot folding thermodynamics. Nucleic Acids Res (2006) 1.75
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Secondary structure model of the RNA recognized by the reverse transcriptase from the R2 retrotransposable element. RNA (1997) 1.68
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Predicting structures and stabilities for H-type pseudoknots with interhelix loops. RNA (2009) 1.51
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Determination of thermodynamic parameters for HIV DIS type loop-loop kissing complexes. Nucleic Acids Res (2004) 1.21
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Interactions of Escherichia coli RNA with bacteriophage MS2 coat protein: genomic SELEX. Nucleic Acids Res (2000) 1.19
Recognition of atypical 5' splice sites by shifted base-pairing to U1 snRNA. Nat Struct Mol Biol (2009) 1.16
Rational truncation of an RNA aptamer to prostate-specific membrane antigen using computational structural modeling. Nucleic Acid Ther (2011) 1.16
Loop dependence of the stability and dynamics of nucleic acid hairpins. Nucleic Acids Res (2007) 1.15
RNA sequence and base pairing effects on insertion editing in Trypanosoma brucei. Mol Cell Biol (2002) 1.15
Proline residues within spacer peptide p1 are important for human immunodeficiency virus type 1 infectivity, protein processing, and genomic RNA dimer stability. J Virol (2002) 1.14
Specificity from steric restrictions in the guanosine binding pocket of a group I ribozyme. RNA (1999) 1.13
DotKnot: pseudoknot prediction using the probability dot plot under a refined energy model. Nucleic Acids Res (2010) 1.12
Negative and positive mRNA splicing elements act competitively to regulate human immunodeficiency virus type 1 vif gene expression. J Virol (2008) 1.11
Enthalpy-driven RNA folding: single-molecule thermodynamics of tetraloop-receptor tertiary interaction. Biochemistry (2009) 1.10
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Substrate specificity of delta ribozyme cleavage. J Biol Chem (1998) 1.09
Thermodynamics and NMR studies on Duck, Heron and Human HBV encapsidation signals. Nucleic Acids Res (2007) 1.08
Discrete state model and accurate estimation of loop entropy of RNA secondary structures. J Chem Phys (2008) 1.08
Chemical correction of pre-mRNA splicing defects associated with sequestration of muscleblind-like 1 protein by expanded r(CAG)-containing transcripts. ACS Chem Biol (2012) 1.05
Binding of aminoglycoside antibiotics to helix 69 of 23S rRNA. Nucleic Acids Res (2010) 1.05
Changes in Rous sarcoma virus RNA secondary structure near the primer binding site upon tRNATrp primer annealing. J Virol (1999) 1.04
Heat capacity changes associated with DNA duplex formation: salt- and sequence-dependent effects. Biochemistry (2006) 1.04
Efficient ligation of the Schistosoma hammerhead ribozyme. Biochemistry (2007) 1.04
Salt-dependent heat capacity changes for RNA duplex formation. J Am Chem Soc (2004) 1.03
Salt dependence of nucleic acid hairpin stability. Biophys J (2008) 1.03
A model system for investigating lineshape/structure correlations in RNA site-directed spin labeling. Biochem Biophys Res Commun (2006) 1.03
Requirement for canonical base pairing in the short pseudoknot structure of genomic hepatitis delta virus ribozyme. Nucleic Acids Res (2000) 1.02
Synthesis and investigation of the 5-formylcytidine modified, anticodon stem and loop of the human mitochondrial tRNAMet. Nucleic Acids Res (2008) 1.02
Predicting loop-helix tertiary structural contacts in RNA pseudoknots. RNA (2010) 1.02
Splicing of the meiosis-specific HOP2 transcript utilizes a unique 5' splice site. Mol Cell Biol (1999) 1.02
A versatile communication module for controlling RNA folding and catalysis. Nucleic Acids Res (2002) 1.02
Extraordinarily slow binding of guanosine to the Tetrahymena group I ribozyme: implications for RNA preorganization and function. Proc Natl Acad Sci U S A (2003) 1.01
Exploring the complex folding kinetics of RNA hairpins: I. General folding kinetics analysis. Biophys J (2005) 1.01
The Azoarcus group I intron ribozyme misfolds and is accelerated for refolding by ATP-dependent RNA chaperone proteins. J Biol Chem (2011) 1.00
Thermodynamic characterization of naturally occurring RNA tetraloops. RNA (2010) 1.00
Biphasic folding kinetics of RNA pseudoknots and telomerase RNA activity. J Mol Biol (2007) 0.99
Roles of DEAD-box proteins in RNA and RNP Folding. RNA Biol (2010) 0.99
Predicting ribosomal frameshifting efficiency. Phys Biol (2008) 0.96
A Spinach molecular beacon triggered by strand displacement. RNA (2014) 0.96
Heat capacity changes in RNA folding: application of perturbation theory to hammerhead ribozyme cold denaturation. Nucleic Acids Res (2004) 0.96
Salt contribution to RNA tertiary structure folding stability. Biophys J (2011) 0.96
Computing the conformational entropy for RNA folds. J Chem Phys (2010) 0.96
Stabilities of HIV-1 DIS type RNA loop-loop interactions in vitro and in vivo. Nucleic Acids Res (2006) 0.95
Straightening of bulged RNA by the double-stranded RNA-binding domain from the protein kinase PKR. Proc Natl Acad Sci U S A (2000) 0.95
A human rotavirus with rearranged genes 7 and 11 encodes a modified NSP3 protein and suggests an additional mechanism for gene rearrangement. J Virol (2001) 0.94
Predicting ion binding properties for RNA tertiary structures. Biophys J (2010) 0.93
Functional recognition of fragmented operator sites by R17/MS2 coat protein, a translational repressor. Nucleic Acids Res (1997) 0.92
Statistical thermodynamics for chain molecules with simple RNA tertiary contacts. J Chem Phys (2005) 0.91
Master equation approach to finding the rate-limiting steps in biopolymer folding. J Chem Phys (2003) 0.91
Thermodynamics and folding pathway of tetraloop receptor-mediated RNA helical packing. J Mol Biol (2008) 0.91
Analyzing the biopolymer folding rates and pathways using kinetic cluster method. J Chem Phys (2003) 0.90
Predicting kissing interactions in microRNA-target complex and assessment of microRNA activity. Nucleic Acids Res (2012) 0.90
CpG usage in RNA viruses: data and hypotheses. PLoS One (2013) 0.89
Predicting secondary structural folding kinetics for nucleic acids. Biophys J (2010) 0.89
RNAspa: a shortest path approach for comparative prediction of the secondary structure of ncRNA molecules. BMC Bioinformatics (2007) 0.89
Selection and characterization of RNAs that relieve transcriptional interference in Escherichia coli. Nucleic Acids Res (1998) 0.88
Efficient computation of optimal oligo-RNA binding. Nucleic Acids Res (2004) 0.87
Mesoscopic modeling for nucleic acid chain dynamics. Phys Rev E Stat Nonlin Soft Matter Phys (2005) 0.87
The essential role of stacking adenines in a two-base-pair RNA kissing complex. J Am Chem Soc (2013) 0.86
Exploring the complex folding kinetics of RNA hairpins: II. Effect of sequence, length, and misfolded states. Biophys J (2005) 0.85
Ion-mediated RNA structural collapse: effect of spatial confinement. Biophys J (2012) 0.85
Predicting ion-nucleic acid interactions by energy landscape-guided sampling. J Chem Theory Comput (2012) 0.84
A conserved RNA pseudoknot in a putative molecular switch domain of the 3'-untranslated region of coronaviruses is only marginally stable. RNA (2011) 0.84
A remarkably stable kissing-loop interaction defines substrate recognition by the Neurospora Varkud Satellite ribozyme. RNA (2014) 0.84
A kinetic zipper model with intrachain interactions applied to nucleic acid hairpin folding kinetics. Biophys J (2012) 0.83
Predicting electrostatic forces in RNA folding. Methods Enzymol (2009) 0.83
Probing the role of a secondary structure element at the 5'- and 3'-splice sites in group I intron self-splicing: the tetrahymena L-16 ScaI ribozyme reveals a new role of the G.U pair in self-splicing. Biochemistry (2007) 0.83
Effects of non-nearest neighbors on the thermodynamic stability of RNA GNRA hairpin tetraloops. Biochemistry (2012) 0.83
The virtues of self-binding: high sequence specificity for RNA cleavage by self-processed hammerhead ribozymes. Nucleic Acids Res (2000) 0.83
Highly conserved RNA pseudoknots at the Gag-Pol junction of HIV-1 suggest a novel mechanism of -1 ribosomal frameshifting. RNA (2014) 0.82
The long-range P3 helix of the Tetrahymena ribozyme is disrupted during folding between the native and misfolded conformations. J Mol Biol (2013) 0.82
Computational tools and algorithms for designing customized synthetic genes. Front Bioeng Biotechnol (2014) 0.81
Physics-based RNA structure prediction. Biophys Rep (2015) 0.81
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol (1999) 41.48
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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
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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
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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
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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
RNA hairpin loop stability depends on closing base pair. Nucleic Acids Res (1993) 1.40
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An NAD derivative produced during transfer RNA splicing: ADP-ribose 1"-2" cyclic phosphate. Science (1993) 1.33
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Transient ADP-ribosylation of a 2'-phosphate implicated in its removal from ligated tRNA during splicing in yeast. J Biol Chem (1999) 1.12
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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
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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
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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
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
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Recognition elements for 5' exon substrate binding to the Candida albicans group I intron. Biochemistry (2001) 0.87
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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
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
Fluorescence-detected circular dichroism. Methods Enzymol (1978) 0.85
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The crystal structure of an RNA oligomer incorporating tandem adenosine-inosine mismatches. Nucleic Acids Res (1997) 0.83
Binding enhancement by tertiary interactions and suicide inhibition of a Candida albicans group I intron by phosphoramidate and 2'-O-methyl hexanucleotides. Biochemistry (2001) 0.82