Published in Nucleic Acids Res on December 23, 1988
Improved predictions of secondary structures for RNA. Proc Natl Acad Sci U S A (1989) 11.52
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
Suppression of ribosomal reinitiation at upstream open reading frames in amino acid-starved cells forms the basis for GCN4 translational control. Mol Cell Biol (1991) 3.83
A thermodynamic study of unusually stable RNA and DNA hairpins. Nucleic Acids Res (1991) 3.59
Prediction of RNA secondary structure, including pseudoknotting, by computer simulation. Nucleic Acids Res (1990) 3.15
Substrate sequence effects on "hammerhead" RNA catalytic efficiency. Proc Natl Acad Sci U S A (1990) 2.81
Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops. Nucleic Acids Res (1992) 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
T7 RNA polymerase produces 5' end heterogeneity during in vitro transcription from certain templates. RNA (1998) 2.39
'Hairpin' catalytic RNA model: evidence for helices and sequence requirement for substrate RNA. Nucleic Acids Res (1990) 2.38
Modulating role of RNA structure in alternative splicing of a critical exon in the spinal muscular atrophy genes. Nucleic Acids Res (2006) 1.84
A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation. Nucleic Acids Res (2006) 1.67
A semiflexible polymer model applied to loop formation in DNA hairpins. Biophys J (2001) 1.54
The effect of loop size in antisense and target RNAs on the efficiency of antisense RNA control. Nucleic Acids Res (1992) 1.41
RNA hairpin loop stability depends on closing base pair. Nucleic Acids Res (1993) 1.40
The effect of base mismatches in the substrate recognition helices of hammerhead ribozymes on binding and catalysis. Nucleic Acids Res (1995) 1.39
Molecular dissection of the pseudoknot governing the translational regulation of Escherichia coli ribosomal protein S15. Nucleic Acids Res (1995) 1.35
Computational approaches for RNA energy parameter estimation. RNA (2010) 1.33
DNA hairpin loops in solution. Correlation between primary structure, thermostability and reactivity with single-strand-specific nuclease from mung bean. Nucleic Acids Res (1991) 1.26
Identification of a specific exon sequence that is a major determinant in the selection between a natural and a cryptic 5' splice site. Mol Cell Biol (1991) 1.21
A small stem loop element directs internal initiation of the URE2 internal ribosome entry site in Saccharomyces cerevisiae. J Biol Chem (2008) 1.17
Formation of Stable DNA Loops by Incorporation of Nonpolar, Non-Hydrogen-Bonding Nucleoside Isosteres. Angew Chem Int Ed Engl (1996) 1.10
Activity of hammerhead ribozymes containing non-nucleotidic linkers. Nucleic Acids Res (1993) 1.08
The i-motif in the bcl-2 P1 promoter forms an unexpectedly stable structure with a unique 8:5:7 loop folding pattern. J Am Chem Soc (2009) 1.04
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
Structural features and stability of an RNA triple helix in solution. Nucleic Acids Res (1996) 1.01
Thermodynamic characterization of naturally occurring RNA tetraloops. RNA (2010) 1.00
Structural Optimization of Non-Nucleotide Loop Replacements for Duplex and Triplex DNAs. J Am Chem Soc (1995) 0.96
Thermodynamic characterization of RNA triloops. Biochemistry (2010) 0.96
Structure of a small RNA hairpin. Nucleic Acids Res (1993) 0.94
Replacement of RNA hairpins by in vitro selected tetranucleotides. Nucleic Acids Res (1993) 0.93
The newt ribozyme is part of a riboprotein complex. Proc Natl Acad Sci U S A (1997) 0.93
Mutational analysis of the mRNA operator for T4 DNA polymerase. Genetics (1991) 0.92
The nature of preferred hairpin structures in 16S-like rRNA variable regions. Nucleic Acids Res (1992) 0.91
A mini-RNA containing the tetraloop, wobble-pair and loop E motifs of the central conserved region of potato spindle tuber viroid is processed into a minicircle. Nucleic Acids Res (2003) 0.90
Binding of the bacteriophage T4 regA protein to mRNA targets: an initiator AUG is required. Nucleic Acids Res (1990) 0.90
Characterization of the functional role of nucleotides within the URE2 IRES element and the requirements for eIF2A-mediated repression. RNA (2009) 0.87
Exploring the complex folding kinetics of RNA hairpins: II. Effect of sequence, length, and misfolded states. Biophys J (2005) 0.85
Translation of 2'-modified mRNA in vitro and in vivo. Nucleic Acids Res (1994) 0.84
Conformationally restricted nucleotides as a probe of structure-function relationships in RNA. RNA (2008) 0.84
Effects of non-nearest neighbors on the thermodynamic stability of RNA GNRA hairpin tetraloops. Biochemistry (2012) 0.83
Molecular modelling of the 3-D structure of RNA tetraloops with different nucleotide sequences. Nucleic Acids Res (1993) 0.83
Importance of structural differences between complementary RNA molecules to control of replication of an IncB plasmid. J Bacteriol (1997) 0.82
De novo design of heat-repressible RNA thermosensors in E. coli. Nucleic Acids Res (2015) 0.81
Fluorescence competition assay measurements of free energy changes for RNA pseudoknots. Biochemistry (2010) 0.81
RNA editing by T7 RNA polymerase bypasses InDel mutations causing unexpected phenotypic changes. Nucleic Acids Res (2015) 0.81
Communication between RNA folding domains revealed by folding of circularly permuted ribozymes. J Mol Biol (2007) 0.80
Free-energy landscape of a hyperstable RNA tetraloop. Proc Natl Acad Sci U S A (2016) 0.79
Structural Effects in the Recognition of DNA by Circular Oligonucleotides. J Am Chem Soc (1992) 0.77
Influence of Two Bulge Loops on the Stability of RNA Duplexes. RNA (2016) 0.75
Capturing RNA Folding Free Energy with Coarse-Grained Molecular Dynamics Simulations. Sci Rep (2017) 0.75
Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res (1987) 25.34
Comparative anatomy of 16-S-like ribosomal RNA. Prog Nucleic Acid Res Mol Biol (1985) 16.21
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
CUUCGG hairpins: extraordinarily stable RNA secondary structures associated with various biochemical processes. Proc Natl Acad Sci U S A (1988) 5.50
Conformation of the anticodon loop intRNA. Nature (1967) 3.48
Thermodynamic studies of RNA stability. J Biomol Struct Dyn (1984) 2.75
Sequence dependence for the energetics of dangling ends and terminal base pairs in ribonucleic acid. Biochemistry (1987) 1.95
Sequences of controlling regions of the lactose operon. Cold Spring Harb Symp Quant Biol (1974) 1.76
Hairpin and duplex formation of the DNA octamer d(m5C-G-m5C-G-T-G-m5C-G) in solution. An NMR study. Nucleic Acids Res (1986) 1.31
Destabilization of secondary structure in 16S ribosomal RNA by dimethylation of two adjacent adenosines. Nucleic Acids Res (1981) 1.24
Association of complementary oligoribonucleotides in aqueous solution. Biochemistry (1968) 1.23
Effects of terminal mismatches on RNA stability: thermodynamics of duplex formation for ACCGGGp, ACCGGAp, and ACCGGCp. Biochemistry (1985) 1.13
A carbon-13 nuclear magnetic resonance study of the 3'-terminus of 16S ribosomal RNA of Escherichia coli specifically labeled with carbon-13 in the methylgroups of the m6(2)Am6(2)A sequence. Nucleic Acids Res (1982) 0.97
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
Estimation of secondary structure in ribonucleic acids. Nature (1971) 20.52
Stability of ribonucleic acid double-stranded helices. J Mol Biol (1974) 16.35
Synthesis of small RNAs using T7 RNA polymerase. Methods Enzymol (1989) 10.82
3'-terminal labelling of RNA with T4 RNA ligase. Nature (1978) 10.69
A small catalytic oligoribonucleotide. Nature (1987) 8.73
Stability of RNA hairpin loops: A 6 -C m -U 6 . J Mol Biol (1973) 8.39
Biochemical and physical characterization of an unmodified yeast phenylalanine transfer RNA transcribed in vitro. Proc Natl Acad Sci U S A (1988) 7.76
Specific labeling of 3' termini of RNA with T4 RNA ligase. Methods Enzymol (1980) 7.55
Reactions at the termini of tRNA with T4 RNA ligase. Nucleic Acids Res (1978) 5.93
CUUCGG hairpins: extraordinarily stable RNA secondary structures associated with various biochemical processes. Proc Natl Acad Sci U S A (1988) 5.50
Self-complementary oligoribonucleotides: effects of helix defects and guanylic acid-cytidylic acid base pairs. J Mol Biol (1971) 4.54
RNA binding site of R17 coat protein. Biochemistry (1987) 4.20
Sequence-specific interaction of R17 coat protein with its ribonucleic acid binding site. Biochemistry (1983) 4.09
Enzymatic oligoribonucleotide synthesis with T4 RNA ligase. Biochemistry (1978) 3.99
3'-Phosphatase activity in T4 polynucleotide kinase. Biochemistry (1977) 3.86
Sequence requirements of the hammerhead RNA self-cleavage reaction. Biochemistry (1990) 3.64
Uniform binding of aminoacyl-tRNAs to elongation factor Tu by thermodynamic compensation. Science (2001) 3.54
Role of divalent metal ions in the hammerhead RNA cleavage reaction. Biochemistry (1991) 3.31
Evidence for the role of solvated metal hydroxide in the hammerhead cleavage mechanism. Biochemistry (1993) 2.91
Specific interaction between RNA phage coat proteins and RNA. Prog Nucleic Acid Res Mol Biol (1991) 2.84
T4-induced RNA ligase joins single-stranded oligoribonucleotides. Proc Natl Acad Sci U S A (1975) 2.84
Substrate sequence effects on "hammerhead" RNA catalytic efficiency. Proc Natl Acad Sci U S A (1990) 2.81
Kinetics of intermolecular cleavage by hammerhead ribozymes. Biochemistry (1992) 2.79
Self-complementary oligoribonucleotides: adenylic acid-uridylic acid block copolymers. J Mol Biol (1971) 2.78
Numbering system for the hammerhead. Nucleic Acids Res (1992) 2.74
In vitro selection of RNAs that undergo autolytic cleavage with Pb2+. Biochemistry (1992) 2.60
Role of a bulged A residue in a specific RNA-protein interaction. Biochemistry (1987) 2.52
A kinetic and thermodynamic framework for the hammerhead ribozyme reaction. Biochemistry (1994) 2.39
T7 RNA polymerase produces 5' end heterogeneity during in vitro transcription from certain templates. RNA (1998) 2.39
Nucleotides in yeast tRNAPhe required for the specific recognition by its cognate synthetase. Science (1989) 2.36
Equimolar addition of oligoribonucleotides with T4 RNA ligase. Nucleic Acids Res (1977) 2.32
Interaction of R17 coat protein with synthetic variants of its ribonucleic acid binding site. Biochemistry (1983) 2.30
An RNA mutation that increases the affinity of an RNA-protein interaction. Nucleic Acids Res (1987) 2.25
Quantitative in situ hybridization of ribosomal RNA species to polytene chromosomes of Drosophila melanogaster. J Mol Biol (1977) 2.18
Folding of circularly permuted transfer RNAs. Science (1991) 2.14
Complementary oligonucleotide binding to the anticodon loop of fMet-transfer RNA. Nature (1970) 2.13
Hammerhead ribozyme kinetics. RNA (1998) 2.08
Kinetic and thermodynamic characterization of the R17 coat protein-ribonucleic acid interaction. Biochemistry (1983) 2.07
Ribonucleoprotein complexes of R17 coat protein and a translational operator analog. J Mol Biol (1988) 1.99
RNA template-directed RNA synthesis by T7 RNA polymerase. Proc Natl Acad Sci U S A (1994) 1.98
Dinucleoside pyrophosphate are substrates for T4-induced RNA ligase. Proc Natl Acad Sci U S A (1977) 1.94
Enzymatic replacement of the anticodon of yeast phenylalanine transfer ribonucleic acid. Biochemistry (1982) 1.94
Lead-catalyzed cleavage of yeast tRNAPhe mutants. Biochemistry (1990) 1.87
Tetraloops and RNA folding. Nature (1990) 1.87
Chemical and enzymatic synthesis of tRNAs for high-throughput crystallization. RNA (2001) 1.81
Thiophosphate interference experiments locate phosphates important for the hammerhead RNA self-cleavage reaction. Nucleic Acids Res (1990) 1.76
Photocrosslinking of 5-iodouracil-substituted RNA and DNA to proteins. Science (1993) 1.73
Mutants of the bacteriophage MS2 coat protein that alter its cooperative binding to RNA. Biochemistry (1995) 1.72
Structure of an unmodified tRNA molecule. Biochemistry (1989) 1.71
Inhibition of the hammerhead ribozyme cleavage reaction by site-specific binding of Tb. Science (1998) 1.66
Synthesis of modified nucleoside 3',5'-bisphosphates and their incorporation into oligoribonucleotides with T4 RNA ligase. Biochemistry (1978) 1.62
Joining of RNA molecules with RNA ligase. Methods Enzymol (1983) 1.62
Nucleoside and nucleotide inactivation of R17 coat protein: evidence for a transient covalent RNA-protein bond. Biochemistry (1985) 1.62
Role of the tertiary nucleotides in the interaction of yeast phenylalanine tRNA with its cognate synthetase. Biochemistry (1990) 1.60
Determination of RNA-protein contacts using thiophosphate substitutions. Biochemistry (1989) 1.60
The self-splicing RNA of Tetrahymena is trapped in a less active conformation by gel purification. Biochemistry (1990) 1.58
Escherichia coli DbpA is an RNA helicase that requires hairpin 92 of 23S rRNA. EMBO J (2001) 1.58
Involvement of a specific metal ion in the transition of the hammerhead ribozyme to its catalytic conformation. J Biol Chem (1997) 1.55
Studies on the hammerhead RNA self-cleaving domain. Gene (1989) 1.52
Comparison of the hammerhead cleavage reactions stimulated by monovalent and divalent cations. RNA (2001) 1.51
Specificity of hammerhead ribozyme cleavage. EMBO J (1996) 1.49
Complementary oligonucleotide binding to transfer RNA. J Mol Biol (1972) 1.49
Sequence-dependent structural variations of hammerhead RNA enzymes. Nucleic Acids Res (1990) 1.47
Proton NMR and structural features of a 24-nucleotide RNA hairpin. Biochemistry (1995) 1.47
Intact aminoacyl-tRNA is required to trigger GTP hydrolysis by elongation factor Tu on the ribosome. Biochemistry (2000) 1.47
A small metalloribozyme with a two-step mechanism. Nature (1992) 1.46
Specific RNA binding by Q beta coat protein. Biochemistry (1989) 1.45
Kinetic characterization of intramolecular and intermolecular hammerhead RNAs with stem II deletions. Proc Natl Acad Sci U S A (1994) 1.42
Roles of operator and non-operator RNA sequences in bacteriophage R17 capsid assembly. J Mol Biol (1988) 1.41
The Escherichia coli DEAD protein DbpA recognizes a small RNA hairpin in 23S rRNA. RNA (2001) 1.40
In vitro analysis of translational rate and accuracy with an unmodified tRNA. Biochemistry (1993) 1.40
A thermodynamic analysis of the sequence-specific binding of RNA by bacteriophage MS2 coat protein. Proc Natl Acad Sci U S A (1998) 1.40
The effect of base mismatches in the substrate recognition helices of hammerhead ribozymes on binding and catalysis. Nucleic Acids Res (1995) 1.39
Self-cleaving catalytic RNA. FASEB J (1993) 1.39
Cloning and biochemical characterization of Bacillus subtilis YxiN, a DEAD protein specifically activated by 23S rRNA: delineation of a novel sub-family of bacterial DEAD proteins. Nucleic Acids Res (1999) 1.35
A specific, UV-induced RNA-protein cross-link using 5-bromouridine-substituted RNA. Biochemistry (1991) 1.34
Specific interaction of anticodon loop residues with yeast phenylalanyl-tRNA synthetase. Biochemistry (1982) 1.32
Determination of recognition nucleotides for Escherichia coli phenylalanyl-tRNA synthetase. Biochemistry (1992) 1.31
Enzymatic synthesis of a 21-nucleotide coat protein binding fragment of R17 ribonucleic acid. Biochemistry (1982) 1.31
Inhibition of the hammerhead ribozyme by neomycin. RNA (1995) 1.31
Cooperative binding of R17 coat protein to RNA. Biochemistry (1990) 1.30
Quantitative assessment of EF-1alpha.GTP binding to aminoacyl-tRNAs, aminoacyl-viral RNA, and tRNA shows close correspondence to the RNA binding properties of EF-Tu. J Biol Chem (1999) 1.29
Kinetic analysis of the RNA-dependent adenosinetriphosphatase activity of DbpA, an Escherichia coli DEAD protein specific for 23S ribosomal RNA. Biochemistry (1998) 1.28
Polynucleotide kinase from a T4 mutant which lacks the 3' phosphatase activity. Nucleic Acids Res (1978) 1.27
Binding of yeast tRNAPhe anticodon arm to Escherichia coli 30 S ribosomes. J Mol Biol (1983) 1.27
Properties of an in vitro selected Pb2+ cleavage motif. Biochemistry (1994) 1.27
Guanosine modifications in runoff transcripts of synthetic transfer RNA-Phe genes microinjected into Xenopus oocytes. Biochim Biophys Acta (1990) 1.25
Hammerhead ribozymes with a faster cleavage rate. Biochemistry (1997) 1.25
Many of the conserved nucleotides of tRNA(Phe) are not essential for ternary complex formation and peptide elongation. EMBO J (1994) 1.24
Interaction of Escherichia coli host factor protein with oligoriboadenylates. Biochemistry (1980) 1.21
Aminoacylation of anticodon loop substituted yeast tyrosine transfer RNA. Biochemistry (1985) 1.20
A re-investigation of the thio effect at the hammerhead cleavage site. Nucleic Acids Res (1999) 1.20
A new assay for tRNA aminoacylation kinetics. RNA (1998) 1.19
Interactions of Escherichia coli RNA with bacteriophage MS2 coat protein: genomic SELEX. Nucleic Acids Res (2000) 1.19
Effect of replacing uridine 33 in yeast tRNAPhe on the reaction with ribosomes. J Biol Chem (1986) 1.17
The role of 2'-hydroxyl groups in an RNA-protein interaction. Biochemistry (1995) 1.15
Identification of thermodynamically relevant interactions between EF-Tu and backbone elements of tRNA. J Mol Biol (2001) 1.13
Recognition of yeast tRNA(Phe) by its cognate yeast phenylalanyl-tRNA synthetase: an analysis of specificity. Biochemistry (1992) 1.12