Published in J Mol Biol on February 05, 1973
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res (1981) 61.59
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
Fast algorithm for predicting the secondary structure of single-stranded RNA. Proc Natl Acad Sci U S A (1980) 10.48
Method for predicting RNA secondary structure. Proc Natl Acad Sci U S A (1975) 8.39
Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proc Natl Acad Sci U S A (1994) 8.06
Computer method for predicting the secondary structure of single-stranded RNA. Nucleic Acids Res (1978) 7.55
A new principle of RNA folding based on pseudoknotting. Nucleic Acids Res (1985) 5.48
Kinetics of conformational fluctuations in DNA hairpin-loops. Proc Natl Acad Sci U S A (1998) 5.34
Prediction of hybridization and melting for double-stranded nucleic acids. Biophys J (2004) 5.11
Complementary sequences 1700 nucleotides apart form a ribonuclease III cleavage site in Escherichia coli ribosomal precursor RNA. Proc Natl Acad Sci U S A (1978) 4.90
A thermodynamic study of unusually stable RNA and DNA hairpins. Nucleic Acids Res (1991) 3.59
5'-Terminal nucleotide sequence of Escherichia coli lactose repressor mRNA: features of translational initiation and reinitiation sites. Proc Natl Acad Sci U S A (1977) 3.14
Characterization of RNA hairpin loop stability. Nucleic Acids Res (1988) 3.10
A dynamic programming algorithm for finding alternative RNA secondary structures. Nucleic Acids Res (1986) 3.09
Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops. Nucleic Acids Res (1992) 2.70
Nucleotide sequence at the 5' terminus of the avian sarcoma virus genome. Proc Natl Acad Sci U S A (1977) 2.66
Thermal denaturation of double-stranded nucleic acids: prediction of temperatures critical for gradient gel electrophoresis and polymerase chain reaction. Nucleic Acids Res (1994) 2.64
Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction. BMC Bioinformatics (2004) 2.57
The 3' terminus of 16S rRNA: secondary structure and interaction with ribosomal protein S1. Nucleic Acids Res (1979) 2.51
Discriminatory ribosome rebinding of isolated regions of protein synthesis initiation from the ribonucleic acid of bacteriophage R17. Proc Natl Acad Sci U S A (1973) 2.48
Influence of loop residues on the relative stabilities of DNA hairpin structures. Proc Natl Acad Sci U S A (1988) 2.37
Thermodynamic characterization of the stability and the melting behavior of a DNA triplex: a spectroscopic and calorimetric study. Proc Natl Acad Sci U S A (1990) 2.18
Small changes in free energy assignments for unpaired bases do not affect predicted secondary structures in single stranded RNA. Nucleic Acids Res (1982) 2.14
Configurational diffusion down a folding funnel describes the dynamics of DNA hairpins. Proc Natl Acad Sci U S A (2001) 2.08
Thermodynamics and structure of a DNA tetraplex: a spectroscopic and calorimetric study of the tetramolecular complexes of d(TG3T) and d(TG3T2G3T). Proc Natl Acad Sci U S A (1992) 2.03
Sequences of the Escherichia coli dnaG primase gene and regulation of its expression. Proc Natl Acad Sci U S A (1982) 1.98
Transcription termination: nucleotide sequence at 3' end of tryptophan operon in Escherichia coli. Proc Natl Acad Sci U S A (1978) 1.94
UGA suppression by normal tRNA Trp in Escherichia coli: codon context effects. Nucleic Acids Res (1981) 1.82
The distal end of the ribosomal RNA operon rrnD of Escherichia coli contains a tRNA1thr gene, two 5s rRNA genes and a transcription terminator. Nucleic Acids Res (1980) 1.67
RNA misfolding and the action of chaperones. Front Biosci (2008) 1.59
A semiflexible polymer model applied to loop formation in DNA hairpins. Biophys J (2001) 1.54
Nucleotide sequence surrounding a ribonuclease III processing site in bacteriophage T7 RNA. Proc Natl Acad Sci U S A (1977) 1.50
Computer-aided nucleic acid secondary structure modeling incorporating enzymatic digestion data. Nucleic Acids Res (1984) 1.46
Thermodynamics of triple helix formation: spectrophotometric studies on the d(A)10.2d(T)10 and d(C+3T4C+3).d(G3A4G3).d(C3T4C3) triple helices. Nucleic Acids Res (1990) 1.45
Fluctuations in superhelical DNA. Nucleic Acids Res (1979) 1.44
RNA hairpin loop stability depends on closing base pair. Nucleic Acids Res (1993) 1.40
The initial step of DNA hairpin folding: a kinetic analysis using fluorescence correlation spectroscopy. Nucleic Acids Res (2006) 1.38
Differential requirements for polypeptide chain initiation complex formation at the three bacteriophage R17 initiator regions. Nucleic Acids Res (1977) 1.37
Regulation of expression of the Escherichia coli dnaG gene and amplification of the dnaG primase. Proc Natl Acad Sci U S A (1982) 1.37
A proton-coupled conformational switch of Escherichia coli 5S ribosomal RNA. Proc Natl Acad Sci U S A (1980) 1.29
mRNA secondary structures fold sequentially but exchange rapidly in vivo. PLoS Biol (2010) 1.28
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
Pathway-dependent refolding of E. coli 5S RNA. Nucleic Acids Res (1977) 1.26
Pronounced instability of tandem IU base pairs in RNA. Nucleic Acids Res (2004) 1.23
Common structural features of different viroids: serial arrangement of double helical sections and internal loops. Nucleic Acids Res (1978) 1.22
Analysis of RNA secondary structure by photochemical reversal of psoralen crosslinks. Nucleic Acids Res (1979) 1.16
Loop dependence of the stability and dynamics of nucleic acid hairpins. Nucleic Acids Res (2007) 1.15
RNA challenges for computational chemists. Biochemistry (2005) 1.06
Sequence and secondary structure of the colicin fragment of Bacillus stearothermophilus 16S ribosomal RNA. Nucleic Acids Res (1981) 1.06
Conformation of viroids. Nucleic Acids Res (1977) 1.04
An accelerated algorithm for calculating the secondary structure of single stranded RNAs. Nucleic Acids Res (1984) 1.04
Comparative spectroscopic, calorimetric, and computational studies of nucleic acid complexes with 2',5"-versus 3',5"-phosphodiester linkages. Proc Natl Acad Sci U S A (1993) 1.02
Thermodynamics of a stable yeast 5.8S rRNA hairpin helix. Nucleic Acids Res (1978) 1.02
The solution structure of a RNA pentadecamer comprising the anticodon loop and stem of yeast tRNAPhe. A 500 MHz 1H-n.m.r. study. Biochem J (1984) 1.01
Anomalous hairpin formation in an oligodeoxyribonucleotide. Nucleic Acids Res (1985) 1.01
Secondary structure model for the complete simian virus 50 late precursor mRNA. Nucleic Acids Res (1982) 0.99
Alternating d(G-C)3 and d(C-G)3 hexanucleotides containing 7-deaza-2'-deoxyguanosine or 8-aza-7-deaza-2'-deoxyguanosine in place of dG. Nucleic Acids Res (1989) 0.98
Interconversion of the cis-5R,6S- and trans-5R,6R-thymine glycol lesions in duplex DNA. J Am Chem Soc (2008) 0.92
The regulatory region of phage fr replicase cistron. III. Initiation activity of specific fr RNA fragments. Nucleic Acids Res (1982) 0.90
A spin label study of the thermal unfolding of secondary and tertiary structure in E. colic transfer RNAs. Nucleic Acids Res (1976) 0.89
A possible role of the 5' terminal sequence of 16S ribosomal RNA in the recognition of initiation sequences for protein synthesis. Nucleic Acids Res (1975) 0.89
An intronic structure enabled by a long-distance interaction serves as a novel target for splicing correction in spinal muscular atrophy. Nucleic Acids Res (2013) 0.88
Prediction of alternative RNA secondary structures based on fluctuating thermodynamic parameters. Nucleic Acids Res (1993) 0.87
Phosphoramidites of base-modified 2'-deoxyinosine isosteres and solid-phase synthesis of d(GCI*CGC) oligomers containing an ambiguous base. Nucleic Acids Res (1986) 0.86
Analysis of multidimensional G-quadruplex melting curves. Curr Protoc Nucleic Acid Chem (2011) 0.85
Antisense oligonucleotide mediated therapy of spinal muscular atrophy. Transl Neurosci (2013) 0.85
Calorimetric and spectroscopic investigation of drug--DNA interactions: II. Dipyrandium binding to poly d(AT). Nucleic Acids Res (1983) 0.84
Thermodynamic and kinetic properties of short RNA helices: the oligomer sequence AnGCUn. Nucleic Acids Res (1974) 0.83
A kinetic zipper model with intrachain interactions applied to nucleic acid hairpin folding kinetics. Biophys J (2012) 0.83
Evidence on the conformation of HeLa-cell 5.8S ribosomal ribonucleic acid from the reaction of specific cytidine residues with sodium bisulphite. Biochem J (1978) 0.81
DNA chain flexibility and the structure of chromatin nu-bodies. Nucleic Acids Res (1977) 0.81
Silk gland-specific tRNA(Ala) genes are tightly clustered in the silkworm genome. Mol Cell Biol (1988) 0.81
Communication between RNA folding domains revealed by folding of circularly permuted ribozymes. J Mol Biol (2007) 0.80
The transmission of stability or instability from site specific protein-DNA complexes. Nucleic Acids Res (1977) 0.79
Characterization of double-stranded ribonucleic acid sequences present in the initial transcription products of rat liver chromatin. Biochem J (1977) 0.77
Influence of a hairpin loop on the thermodynamic stability of a DNA oligomer. J Nucleic Acids (2011) 0.77
Melting of local ordered structures in yeast 5S ribosomal RNA in aqueous salts. Nucleic Acids Res (1983) 0.76
Secondary structure of Tetrahymena thermophilia 5S ribosomal RNA as revealed by enzymatic digestion and microdensitometric analysis. Nucleic Acids Res (1986) 0.76
Human glutamate tRNA forms stable hybrids in vitro with 28S ribosomal RNA. Nucleic Acids Res (1987) 0.76
The binding of T4 gene 32 protein to MS2 virus RNA and transfer RNA. Nucleic Acids Res (1980) 0.75
Improved estimation of secondary structure in ribonucleic acids. Nat New Biol (1973) 46.33
Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis. Nucleic Acids Res (1981) 35.39
The locus of sequence-directed and protein-induced DNA bending. Nature (1984) 15.05
DNA bending at adenine . thymine tracts. Nature (1986) 9.25
Free energy of imperfect nucleic acid helices. 3. Small internal loops resulting from mismatches. J Mol Biol (1973) 8.74
Bent helical structure in kinetoplast DNA. Proc Natl Acad Sci U S A (1982) 6.43
Prediction of RNA secondary structure. Proc Natl Acad Sci U S A (1971) 5.68
Relaxation kinetics of dimer formation by self complementary oligonucleotides. J Mol Biol (1971) 4.77
Fragments of the HIV-1 Tat protein specifically bind TAR RNA. Science (1990) 4.33
Calculation of binding isotherms for heterogenous polymers. Biopolymers (1968) 4.26
The DNA binding domain and bending angle of E. coli CAP protein. Cell (1986) 3.99
Intermediates in transcription initiation from the E. coli lac UV5 promoter. Cell (1985) 3.88
RNA recognition by Tat-derived peptides: interaction in the major groove? Cell (1991) 3.83
On the physical basis for ambiguity in genetic coding interactions. Proc Natl Acad Sci U S A (1978) 3.71
Stability and properties of double and triple helices: dramatic effects of RNA or DNA backbone composition. Science (1992) 3.53
Artificial nucleosome positioning sequences. Proc Natl Acad Sci U S A (1989) 3.38
DNA-ethidium reaction kinetics: demonstration of direct ligand transfer between DNA binding sites. J Mol Biol (1975) 3.35
Studies of the binding of actinomycin and related compounds to DNA. J Mol Biol (1968) 3.35
The molecular mechanism of thermal unfolding of Escherichia coli formylmethionine transfer RNA. J Mol Biol (1974) 3.25
DNA sequence determinants of CAP-induced bending and protein binding affinity. Nature (1988) 3.22
Calibration of DNA curvature and a unified description of sequence-directed bending. Proc Natl Acad Sci U S A (1988) 3.09
DNA bend direction by phase sensitive detection. Nature (1987) 3.01
Viscosity and sedimentation of the DNA from bacteriophages T2 and T7 and the relation to molecular weight. J Mol Biol (1965) 2.90
Determination of the extent of DNA bending by an adenine-thymine tract. Biochemistry (1990) 2.72
The influence of polyvalency on the binding properties of antibodies. Immunochemistry (1972) 2.67
CAP and RNA polymerase interactions with the lac promoter: binding stoichiometry and long range effects. Nucleic Acids Res (1983) 2.60
The 3' terminus of 16S rRNA: secondary structure and interaction with ribosomal protein S1. Nucleic Acids Res (1979) 2.51
Equilibrium studies of the cyclic AMP receptor protein-DNA interaction. J Mol Biol (1984) 2.49
Kinetics and mechanism in the reaction of gene regulatory proteins with DNA. J Mol Biol (1984) 2.43
Identification and characterization of genomic nucleosome-positioning sequences. J Mol Biol (1997) 2.41
Is there a discriminator site in transfer RNA? Proc Natl Acad Sci U S A (1972) 2.37
Direct physical evidence for secondary structure in an isolated fragment of R17 bacteriophage mRNA. Nature (1974) 2.28
Conformational changes of transfer ribonucleic acid. Equilibrium phase diagrams. Biochemistry (1972) 2.27
Major groove accessibility of RNA. Science (1993) 2.19
Detection of localized DNA flexibility. Nature (1994) 2.18
Protein-induced bending and DNA cyclization. Proc Natl Acad Sci U S A (1992) 2.12
Synergy between Escherichia coli CAP protein and RNA polymerase in the lac promoter open complex. J Mol Biol (1989) 2.11
Studies of the complex between transfer RNAs with complementary anticodons. I. Origins of enhanced affinity between complementary triplets. J Mol Biol (1976) 2.05
Transient electric dichroism of rod-like DNA molecules. Proc Natl Acad Sci U S A (1978) 2.05
Lac repressor is a transient gene-activating protein. Cell (1987) 2.04
SIMPLIFIED ROTATING CYLINDER VISCOMETER FOR DNA. Proc Natl Acad Sci U S A (1962) 2.04
Synthetic DNA bending sequences increase the rate of in vitro transcription initiation at the Escherichia coli lac promoter. J Mol Biol (1991) 2.01
The Leptomonas collosoma spliced leader RNA can switch between two alternate structural forms. Biochemistry (1993) 2.00
A stressed intermediate in the formation of stably initiated RNA chains at the Escherichia coli lac UV5 promoter. J Mol Biol (1987) 2.00
31P NMR studies of the solution structure and dynamics of nucleosomes and DNA. Nucleic Acids Res (1979) 1.98
Specificity and stringency in DNA triplex formation. Proc Natl Acad Sci U S A (1991) 1.96
Relaxation studies of the proflavine-DNA complex: the kinetics of an intercalation reaction. J Mol Biol (1969) 1.95
Conformational changes of transfer RNA. The role of magnesium(II). Biochemistry (1976) 1.95
A computer graphics study of sequence-directed bending in DNA. J Biomol Struct Dyn (1983) 1.94
Effects of DNA sequence and histone-histone interactions on nucleosome placement. J Mol Biol (1990) 1.91
Interactions of heteroaromatic compounds with nucleic acids. 1. The influence of heteroatoms and polarizability on the base specificity of intercalating ligands. Eur J Biochem (1975) 1.83
Molecular characterization of the GCN4-DNA complex. Proc Natl Acad Sci U S A (1990) 1.82
Climate change and the integrity of science. Science (2010) 1.80
The dimensions of DNA in solution. J Mol Biol (1981) 1.80
Equilibrium studies of ethidium--polynucleotide interactions. Biochemistry (1981) 1.75
DNA sequence directs placement of histone cores on restriction fragments during nucleosome formation. Biochemistry (1979) 1.69
Studies on interaction of anthracycline antibiotics and deoxyribonucleic acid: equilibrium binding studies on interaction of daunomycin with deoxyribonucleic acid. Biochemistry (1982) 1.68
Bent helix formation between RNA hairpins with complementary loops. Science (1995) 1.66
RNA binding assays for Tat-derived peptides: implications for specificity. Biochemistry (1992) 1.65
Bending and flexibility of kinetoplast DNA. Biochemistry (1986) 1.65
Free energy of imperfect nucleic acid helices. I. The bulge defect. J Mol Biol (1972) 1.63
Statistical thermodynamics of nucleic acid melting transitions with coupled binding equilibria. Biopolymers (1971) 1.62
Structural basis for DNA bending. Proc Natl Acad Sci U S A (1989) 1.61
The major adduct of the antitumor drug cis-diamminedichloroplatinum(II) with DNA bends the duplex by approximately equal to 40 degrees toward the major groove. Proc Natl Acad Sci U S A (1988) 1.61
Does 5S RNA function by a switch between two secondary structures? Nature (1977) 1.57
Ring closure probabilities for DNA fragments by Monte Carlo simulation. J Mol Biol (1986) 1.56
A bent helix in kinetoplast DNA. Cold Spring Harb Symp Quant Biol (1983) 1.55
Safety of endovascular treatment beyond the 6-h time window in 205 patients. Eur J Neurol (2013) 1.53
The position of site-directed cleavage of RNA using RNase H and 2'-O-methyl oligonucleotides is dependent on the enzyme source. RNA (1997) 1.50
Equilibrium binding of magnesium(II) by Escherichia coli tRNAfMet. Biochemistry (1976) 1.49
Lac UV5 transcription in vitro. Rate limitation subsequent to formation of an RNA polymerase-DNA complex. Biochemistry (1979) 1.45
RNase H cleavage for processing of in vitro transcribed RNA for NMR studies and RNA ligation. RNA (1996) 1.44
Transmission of allosteric effects in DNA. Nature (1979) 1.44
Catabolite activator protein-induced DNA bending in transcription initiation. J Mol Biol (1991) 1.43
DNA bending by the bulge defect. Biochemistry (1989) 1.43
Comparative gel electrophoresis measurement of the DNA bend angle induced by the catabolite activator protein. Biopolymers (1990) 1.39
Isolation and characterization of a spacerless dinucleosome from H1-deleted chromatin. Nucleic Acids Res (1977) 1.37
NMR of enzymatically synthesized uniformly 13C15N-labeled DNA oligonucleotides. Proc Natl Acad Sci U S A (1995) 1.37
DNA bending in protein-DNA complexes. Methods Enzymol (1991) 1.36
Determinants of RNA hairpin loop-loop complex stability. J Mol Biol (1995) 1.35
Sequence elements responsible for DNA curvature. J Mol Biol (1994) 1.35
Fos and Jun do not bend the AP-1 recognition site. Proc Natl Acad Sci U S A (1996) 1.35
The solution structure of an RNA loop-loop complex: the ColE1 inverted loop sequence. Structure (1998) 1.35
A non-intercalating proflavine derivative. Eur J Biochem (1973) 1.34
Characterization of the solution conformations of unbound and Tat peptide-bound forms of HIV-1 TAR RNA. Biochemistry (1999) 1.34
Specific binding and protection of form II SV40 deoxyribonucleic acid by ribonucleic acid polymerase II from wheat germ. Biochemistry (1980) 1.34
Structural model for an oligonucleotide containing a bulged guanosine by NMR and energy minimization. Biochemistry (1988) 1.33
Helical repeat and chirality effects on DNA gel electrophoretic mobility. Proc Natl Acad Sci U S A (1991) 1.32
Transcription reinitiation rate: a special role for the TATA box. Mol Cell Biol (1997) 1.31
Interaction of human immunodeficiency virus type 1 Tat-derived peptides with TAR RNA. Biochemistry (1995) 1.30
Interaction of netropsin and distamycin with deoxyribonucleic acid: electric dichroism study. Biochemistry (1980) 1.30
Transient electric dichroism studies of the structure of the DNA complex with intercalated drugs. Biochemistry (1979) 1.29
Topological distributions and the torsional rigidity of DNA. A Monte Carlo study of DNA circles. J Mol Biol (1986) 1.29
A proton-coupled conformational switch of Escherichia coli 5S ribosomal RNA. Proc Natl Acad Sci U S A (1980) 1.29
Measurement of the DNA bend angle induced by the catabolite activator protein using Monte Carlo simulation of cyclization kinetics. J Mol Biol (1998) 1.29
The carbohydrate domain of calicheamicin gamma I1 determines its sequence specificity for DNA cleavage. Proc Natl Acad Sci U S A (1991) 1.28
Pathway-dependent refolding of E. coli 5S RNA. Nucleic Acids Res (1977) 1.26
Measurement of diffusion constants for nucleic acids by NMR. J Biomol NMR (1997) 1.25