Published in Nat New Biol on November 14, 1973
Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res (2003) 77.89
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res (1981) 61.59
A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci U S A (1998) 24.28
Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids. Microbiol Rev (1983) 23.08
Predicting DNA duplex stability from the base sequence. Proc Natl Acad Sci U S A (1986) 21.73
Improved free-energy parameters for predictions of RNA duplex stability. Proc Natl Acad Sci U S A (1986) 19.52
SR alpha promoter: an efficient and versatile mammalian cDNA expression system composed of the simian virus 40 early promoter and the R-U5 segment of human T-cell leukemia virus type 1 long terminal repeat. Mol Cell Biol (1988) 12.84
Characterization of translational initiation sites in E. coli. Nucleic Acids Res (1982) 11.91
Improved predictions of secondary structures for RNA. Proc Natl Acad Sci U S A (1989) 11.52
How ribosomes select initiator regions in mRNA: base pair formation between the 3' terminus of 16S rRNA and the mRNA during initiation of protein synthesis in Escherichia coli. Proc Natl Acad Sci U S A (1975) 10.60
Fast algorithm for predicting the secondary structure of single-stranded RNA. Proc Natl Acad Sci U S A (1980) 10.48
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
A combined computational-experimental approach predicts human microRNA targets. Genes Dev (2004) 9.82
ViennaRNA Package 2.0. Algorithms Mol Biol (2011) 9.43
Structure of a split yeast gene: complete nucleotide sequence of the actin gene in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A (1980) 8.88
Nucleotide sequence of the E coli gene coding for dihydrofolate reductase. Nucleic Acids Res (1980) 8.75
Nucleotide sequence of an Escherichia coli chromosomal hemolysin. J Bacteriol (1985) 8.53
Influences of mRNA secondary structure on initiation by eukaryotic ribosomes. Proc Natl Acad Sci U S A (1986) 8.00
Computer method for predicting the secondary structure of single-stranded RNA. Nucleic Acids Res (1978) 7.55
Base-base mismatches. Thermodynamics of double helix formation for dCA3XA3G + dCT3YT3G (X, Y = A,C,G,T). Nucleic Acids Res (1985) 7.19
Complete nucleotide sequence of macrolide-lincosamide-streptogramin B-resistance transposon Tn917 in Streptococcus faecalis. J Bacteriol (1985) 7.00
The structure of the gene for the large subunit of ribulose 1,5-bisphosphate carboxylase from spinach chloroplast DNA. Nucleic Acids Res (1981) 6.69
A comprehensive sequence analysis program for the IBM personal computer. Nucleic Acids Res (1984) 6.58
Complete nucleotide sequence of the attenuated poliovirus Sabin 1 strain genome. Proc Natl Acad Sci U S A (1982) 6.09
Transcription termination at the trp operon attenuators of Escherichia coli and Salmonella typhimurium: RNA secondary structure and regulation of termination. Proc Natl Acad Sci U S A (1977) 6.08
Characterization, sequence determination, and immunogenicity of a 64-kilodalton protein of Mycobacterium bovis BCG expressed in escherichia coli K-12. Infect Immun (1987) 6.00
Nucleotide sequence of the gene for the M(r) 32,000 thylakoid membrane protein from Spinacia oleracea and Nicotiana debneyi predicts a totally conserved primary translation product of M(r) 38,950. Proc Natl Acad Sci U S A (1982) 5.57
Circumstances and mechanisms of inhibition of translation by secondary structure in eucaryotic mRNAs. Mol Cell Biol (1989) 5.52
A new principle of RNA folding based on pseudoknotting. Nucleic Acids Res (1985) 5.48
Los Alamos sequence analysis package for nucleic acids and proteins. Nucleic Acids Res (1982) 5.48
Chromogenic identification of genetic regulatory signals in Bacillus subtilis based on expression of a cloned Pseudomonas gene. Proc Natl Acad Sci U S A (1983) 5.33
Promoter-regulatory region of the major immediate early gene of human cytomegalovirus. Proc Natl Acad Sci U S A (1984) 5.04
Replacement of the Bacillus subtilis subtilisin structural gene with an In vitro-derived deletion mutation. J Bacteriol (1984) 5.03
Mry, a trans-acting positive regulator of the M protein gene of Streptococcus pyogenes with similarity to the receptor proteins of two-component regulatory systems. J Bacteriol (1991) 4.99
Compilation and analysis of DNA sequences associated with apparent streptomycete promoters. Nucleic Acids Res (1992) 4.95
5' and 3' terminal nucleotide sequences of the RNA genome segments of influenza virus. Nucleic Acids Res (1979) 4.90
Characterization of the spo0A locus and its deduced product. Proc Natl Acad Sci U S A (1985) 4.86
A computer algorithm for testing potential prokaryotic terminators. Nucleic Acids Res (1984) 4.73
Nucleotide sequence of the tetM tetracycline resistance determinant of the streptococcal conjugative shuttle transposon Tn1545. Nucleic Acids Res (1986) 4.47
Nucleotide sequence and expression of Escherichia coli trpR, the structural gene for the trp aporepressor. Proc Natl Acad Sci U S A (1980) 4.35
Nucleotide sequence of the amylase gene from Bacillus subtilis. Nucleic Acids Res (1983) 4.33
Isolation and characterization of Streptococcus cremoris Wg2-specific promoters. Appl Environ Microbiol (1987) 4.27
Human immunodeficiency virus type 1 LTR TATA and TAR region sequences required for transcriptional regulation. EMBO J (1989) 4.24
Inducible cephalosporinase production in clinical isolates of Enterobacter cloacae is controlled by a regulatory gene that has been deleted from Escherichia coli. EMBO J (1986) 4.15
A family of dispersed repetitive extragenic palindromic DNA sequences in E. coli. EMBO J (1984) 4.07
DNA sequence organization of IS10-right of Tn10 and comparison with IS10-left. Proc Natl Acad Sci U S A (1982) 4.05
Identification and arrangement of the DNA sequence recognized in specific transformation of Neisseria gonorrhoeae. Proc Natl Acad Sci U S A (1988) 4.04
Nucleotide sequence of the leader region of the phenylalanine operon of Escherichia coli. Proc Natl Acad Sci U S A (1978) 4.01
Cloning, nucleotide sequence, and characterization of genes encoding the secretion function of the Pasteurella haemolytica leukotoxin determinant. J Bacteriol (1989) 3.98
Novel form of transcription attenuation regulates expression the Bacillus subtilis tryptophan operon. J Bacteriol (1986) 3.90
Isolation of human glucose-6-phosphate dehydrogenase (G6PD) cDNA clones: primary structure of the protein and unusual 5' non-coding region. Nucleic Acids Res (1986) 3.86
Mutational analysis of the trans-activation-responsive region of the human immunodeficiency virus type I long terminal repeat. J Virol (1988) 3.69
Some simple computational methods to improve the folding of large RNAs. Nucleic Acids Res (1984) 3.69
Transposon Tn554: complete nucleotide sequence and isolation of transposition-defective and antibiotic-sensitive mutants. EMBO J (1985) 3.68
Lactococcin A, a new bacteriocin from Lactococcus lactis subsp. cremoris: isolation and characterization of the protein and its gene. J Bacteriol (1991) 3.68
Adenosine deaminase: characterization and expression of a gene with a remarkable promoter. EMBO J (1985) 3.68
Sequence of U1 RNA from Drosophila melanogaster: implications for U1 secondary structure and possible involvement in splicing. Nucleic Acids Res (1981) 3.65
The influenza virus panhandle is involved in the initiation of transcription. J Virol (1994) 3.56
The Ro small cytoplasmic ribonucleoproteins: identification of the antigenic protein and its binding site on the Ro RNAs. Proc Natl Acad Sci U S A (1984) 3.51
Structure of genes for virus-associated RNAI and RNAII of adenovirus type 2. Proc Natl Acad Sci U S A (1980) 3.45
Evidence for natural gene transfer from gram-positive cocci to Escherichia coli. J Bacteriol (1988) 3.43
Activation of the c-myc gene by translocation: a model for translational control. Proc Natl Acad Sci U S A (1983) 3.36
The cDNA sequences of the sea urchin U7 small nuclear RNA suggest specific contacts between histone mRNA precursor and U7 RNA during RNA processing. EMBO J (1984) 3.36
Multivalent translational control of transcription termination at attenuator of ilvGEDA operon of Escherichia coli K-12. Proc Natl Acad Sci U S A (1980) 3.30
DNA sequence of mip, a Legionella pneumophila gene associated with macrophage infectivity. Infect Immun (1989) 3.29
Attenuation in the Escherichia coli tryptophan operon: role of RNA secondary structure involving the tryptophan codon region. Proc Natl Acad Sci U S A (1979) 3.28
Use of the Escherichia coli beta-glucuronidase (gusA) gene as a reporter gene for analyzing promoters in lactic acid bacteria. Appl Environ Microbiol (1994) 3.25
Satellite tobacco ringspot virus RNA: A subset of the RNA sequence is sufficient for autolytic processing. Proc Natl Acad Sci U S A (1986) 3.24
Gonococcal transferrin-binding protein 1 is required for transferrin utilization and is homologous to TonB-dependent outer membrane receptors. J Bacteriol (1992) 3.21
Architecture and anatomy of the chromosomal locus in human chromosome 21 encoding the Cu/Zn superoxide dismutase. EMBO J (1985) 3.18
Features of the formate dehydrogenase mRNA necessary for decoding of the UGA codon as selenocysteine. Proc Natl Acad Sci U S A (1990) 3.17
A "bulged" double helix in a RNA-protein contact site. Proc Natl Acad Sci U S A (1981) 3.16
Molecular cloning and the nucleotide sequence of the Mr 28 000 crystal protein gene of Bacillus thuringiensis subsp. israelensis. Nucleic Acids Res (1985) 3.16
Sequence and secondary structure of Drosophila melanogaster 5.8S and 2S rRNAs and of the processing site between them. Nucleic Acids Res (1979) 3.15
Prediction of RNA secondary structure, including pseudoknotting, by computer simulation. Nucleic Acids Res (1990) 3.15
Nucleotide sequence of the cell wall proteinase gene of Streptococcus cremoris Wg2. Appl Environ Microbiol (1988) 3.11
Feedback regulation of ribosomal protein gene expression in Escherichia coli: structural homology of ribosomal RNA and ribosomal protein MRNA. Proc Natl Acad Sci U S A (1980) 3.11
A dynamic programming algorithm for finding alternative RNA secondary structures. Nucleic Acids Res (1986) 3.09
Determination of the optimal aligned spacing between the Shine-Dalgarno sequence and the translation initiation codon of Escherichia coli mRNAs. Nucleic Acids Res (1994) 3.08
Quantitative analysis of the relationship between nucleotide sequence and functional activity. Nucleic Acids Res (1986) 3.02
Chrysanthemum stunt viroid: primary sequence and secondary structure. Nucleic Acids Res (1981) 3.00
T-DNA integration: a mode of illegitimate recombination in plants. EMBO J (1991) 3.00
Nucleotide sequence of the human N-myc gene. Proc Natl Acad Sci U S A (1986) 2.99
Nucleotide sequence of ermA, a macrolide-lincosamide-streptogramin B determinant in Staphylococcus aureus. J Bacteriol (1985) 2.98
Molecular cloning and nucleotide sequence of the gene encoding the major peptidoglycan hydrolase of Lactococcus lactis, a muramidase needed for cell separation. J Bacteriol (1995) 2.97
DNA cloning and organization of the Staphylococcus aureus gyrA and gyrB genes: close homology among gyrase proteins and implications for 4-quinolone action and resistance. J Bacteriol (1990) 2.96
Gene for an immunoglobulin-binding protein from a group G streptococcus. J Bacteriol (1986) 2.95
Analysis of the gene coding for the murine cellular tumour antigen p53. EMBO J (1984) 2.94
leu operon of Salmonella typhimurium is controlled by an attenuation mechanism. Proc Natl Acad Sci U S A (1979) 2.91
The DNA sequence of the gene and genetic control sites for the excreted B. subtilis enzyme beta-glucanase. Nucleic Acids Res (1984) 2.90
Translational control of transcription termination at the attenuator of the Escherichia coli tryptophan operon. Proc Natl Acad Sci U S A (1978) 2.89
A regulatory sequence near the 3' end of sea urchin histone genes. Nucleic Acids Res (1979) 2.88
Nucleotide sequence of the Escherichia coli cad operon: a system for neutralization of low extracellular pH. J Bacteriol (1992) 2.88
A novel repeated DNA sequence located in the intergenic regions of bacterial chromosomes. Nucleic Acids Res (1990) 2.86
The tRNA-like structure at the 3' terminus of turnip yellow mosaic virus RNA. Differences and similarities with canonical tRNA. Nucleic Acids Res (1982) 2.83
Gene encoding the 37,000-dalton minor sigma factor of Bacillus subtilis RNA polymerase: isolation, nucleotide sequence, chromosomal locus, and cryptic function. J Bacteriol (1987) 2.81
Construction of a lactococcal expression vector: expression of hen egg white lysozyme in Lactococcus lactis subsp. lactis. Appl Environ Microbiol (1989) 2.78
Sequence studies of several alphavirus genomic RNAs in the region containing the start of the subgenomic RNA. Proc Natl Acad Sci U S A (1982) 2.77
The nucleotide sequences of the untranslated 5' regions of human alpha- and beta-globin mRNAs. Proc Natl Acad Sci U S A (1977) 2.75
Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis. Nucleic Acids Res (1981) 35.39
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
The locus of sequence-directed and protein-induced DNA bending. Nature (1984) 15.05
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
Free energy of imperfect nucleic acid helices. II. Small hairpin loops. J Mol Biol (1973) 10.07
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
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
Reversible unfolding of single RNA molecules by mechanical force. Science (2001) 8.14
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
Base-base mismatches. Thermodynamics of double helix formation for dCA3XA3G + dCT3YT3G (X, Y = A,C,G,T). Nucleic Acids Res (1985) 7.19
Absorbance melting curves of RNA. Methods Enzymol (1989) 6.64
Bent helical structure in kinetoplast DNA. Proc Natl Acad Sci U S A (1982) 6.43
Receptor clustering as a cellular mechanism to control sensitivity. Nature (1998) 6.30
Solution structure of an unusually stable RNA hairpin, 5'GGAC(UUCG)GUCC. Nature (1990) 6.23
Reactions at the termini of tRNA with T4 RNA ligase. Nucleic Acids Res (1978) 5.93
Prediction of RNA secondary structure. Proc Natl Acad Sci U S A (1971) 5.68
CUUCGG hairpins: extraordinarily stable RNA secondary structures associated with various biochemical processes. Proc Natl Acad Sci U S A (1988) 5.50
Telomeric DNA oligonucleotides form novel intramolecular structures containing guanine-guanine base pairs. Cell (1987) 4.85
Secondary structure of the Tetrahymena ribosomal RNA intervening sequence: structural homology with fungal mitochondrial intervening sequences. Proc Natl Acad Sci U S A (1983) 4.78
Relaxation kinetics of dimer formation by self complementary oligonucleotides. J Mol Biol (1971) 4.77
Self-complementary oligoribonucleotides: effects of helix defects and guanylic acid-cytidylic acid base pairs. J Mol Biol (1971) 4.54
Structure of the HIV-1 nucleocapsid protein bound to the SL3 psi-RNA recognition element. Science (1998) 4.52
Base pairing involving deoxyinosine: implications for probe design. Nucleic Acids Res (1985) 4.41
DNA-RNA hybrid duplexes containing oligo(dA:rU) sequences are exceptionally unstable and may facilitate termination of transcription. Nucleic Acids Res (1980) 4.37
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
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
Comparison between DNA melting thermodynamics and DNA polymerase fidelity. Proc Natl Acad Sci U S A (1988) 4.07
Enzymatic oligoribonucleotide synthesis with T4 RNA ligase. Biochemistry (1978) 3.99
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
3'-Phosphatase activity in T4 polynucleotide kinase. Biochemistry (1977) 3.86
RNA recognition by Tat-derived peptides: interaction in the major groove? Cell (1991) 3.83
Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies. Nature (2005) 3.71
On the physical basis for ambiguity in genetic coding interactions. Proc Natl Acad Sci U S A (1978) 3.71
Sequence requirements of the hammerhead RNA self-cleavage reaction. Biochemistry (1990) 3.64
A thermodynamic study of unusually stable RNA and DNA hairpins. Nucleic Acids Res (1991) 3.59
Uniform binding of aminoacyl-tRNAs to elongation factor Tu by thermodynamic compensation. Science (2001) 3.54
Stability and properties of double and triple helices: dramatic effects of RNA or DNA backbone composition. Science (1992) 3.53
The conformation of loop E of eukaryotic 5S ribosomal RNA. Biochemistry (1993) 3.40
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
Role of divalent metal ions in the hammerhead RNA cleavage reaction. Biochemistry (1991) 3.31
Design of organic molecules with large two-photon absorption cross sections. Science (1998) 3.27
Molecular model of a lattice of signalling proteins involved in bacterial chemotaxis. Nat Cell Biol (2000) 3.27
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
Structure of an unusually stable RNA hairpin. Biochemistry (1991) 3.16
Characterization of RNA hairpin loop stability. Nucleic Acids Res (1988) 3.10
Calibration of DNA curvature and a unified description of sequence-directed bending. Proc Natl Acad Sci U S A (1988) 3.09
A dynamic programming algorithm for finding alternative RNA secondary structures. Nucleic Acids Res (1986) 3.09
DNA bend direction by phase sensitive detection. Nature (1987) 3.01
Evidence for the role of solvated metal hydroxide in the hammerhead cleavage mechanism. Biochemistry (1993) 2.91
Viscosity and sedimentation of the DNA from bacteriophages T2 and T7 and the relation to molecular weight. J Mol Biol (1965) 2.90
RNA structure and NMR spectroscopy. Q Rev Biophys (1991) 2.86
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
Calorimetric and spectroscopic investigation of the helix-to-coil transition of a ribo-oligonucleotide: rA7U7. J Mol Biol (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
Determination of the extent of DNA bending by an adenine-thymine tract. Biochemistry (1990) 2.72
Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops. Nucleic Acids Res (1992) 2.70
The influence of polyvalency on the binding properties of antibodies. Immunochemistry (1972) 2.67
Crystal structure of an RNA double helix incorporating a track of non-Watson-Crick base pairs. Nature (1991) 2.65
DNA and RNA oligomer thermodynamics: the effect of mismatched bases on double-helix stability. Biopolymers (1981) 2.62
In vitro selection of RNAs that undergo autolytic cleavage with Pb2+. Biochemistry (1992) 2.60
CAP and RNA polymerase interactions with the lac promoter: binding stoichiometry and long range effects. Nucleic Acids Res (1983) 2.60
Role of a bulged A residue in a specific RNA-protein interaction. Biochemistry (1987) 2.52
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
RNA folding causes secondary structure rearrangement. Proc Natl Acad Sci U S A (1998) 2.44
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
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
Circular differential scattering can be an important part of the circular dichroism of macromolecules. Proc Natl Acad Sci U S A (1983) 2.37
Is there a discriminator site in transfer RNA? Proc Natl Acad Sci U S A (1972) 2.37
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
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