DNA flexibility studied by covalent closure of short fragments into circles.

PubWeight™: 5.44‹?› | Rank: Top 1%

🔗 View Article (PMC 320266)

Published in Proc Natl Acad Sci U S A on August 01, 1981

Authors

D Shore, J Langowski, R L Baldwin

Articles citing this

(truncated to the top 100)

Evidence that the MIF2 gene of Saccharomyces cerevisiae encodes a centromere protein with homology to the mammalian centromere protein CENP-C. Mol Biol Cell (1995) 4.23

lac repressor forms loops with linear DNA carrying two suitably spaced lac operators. EMBO J (1987) 4.02

Curved DNA: design, synthesis, and circularization. Proc Natl Acad Sci U S A (1986) 3.72

T-loop assembly in vitro involves binding of TRF2 near the 3' telomeric overhang. EMBO J (2001) 3.28

Novel use of polymerase chain reaction to amplify cellular DNA adjacent to an integrated provirus. J Virol (1989) 2.92

Evidence for the existence of stable curvature of DNA in solution. Proc Natl Acad Sci U S A (1984) 2.67

Cooperativity in long-range gene regulation by the lambda CI repressor. Genes Dev (2004) 2.65

DNA looping. Microbiol Rev (1992) 2.63

CAP and RNA polymerase interactions with the lac promoter: binding stoichiometry and long range effects. Nucleic Acids Res (1983) 2.60

Extreme bendability of DNA less than 100 base pairs long revealed by single-molecule cyclization. Science (2012) 2.42

Cyclization of short DNA fragments and bending fluctuations of the double helix. Proc Natl Acad Sci U S A (2005) 2.29

Involvement of outside DNA sequences in the major kinetic path by which EcoRI endonuclease locates and leaves its recognition sequence. Proc Natl Acad Sci U S A (1982) 2.29

Protein-induced bending and DNA cyclization. Proc Natl Acad Sci U S A (1992) 2.12

High-mobility-group 1 protein mediates DNA bending as determined by ring closures. Proc Natl Acad Sci U S A (1993) 2.03

DNA twisting flexibility and the formation of sharply looped protein-DNA complexes. Proc Natl Acad Sci U S A (2005) 2.00

Exact theory of kinkable elastic polymers. Phys Rev E Stat Nonlin Soft Matter Phys (2005) 1.90

Thymine dimers bend DNA. Proc Natl Acad Sci U S A (1988) 1.86

A constant radius of curvature model for the organization of DNA in toroidal condensates. Proc Natl Acad Sci U S A (1995) 1.73

Single-molecule measurements of the persistence length of double-stranded RNA. Biophys J (2005) 1.67

DNA curvature and flexibility in vitro and in vivo. Q Rev Biophys (2010) 1.63

Efficient concerted integration of retrovirus-like DNA in vitro by avian myeloblastosis virus integrase. Nucleic Acids Res (1994) 1.58

Cutting and closing without recombination in V(D)J joining. EMBO J (1991) 1.57

p53 oligomerization and DNA looping are linked with transcriptional activation. EMBO J (1994) 1.57

Statistical mechanics of sequence-dependent circular DNA and its application for DNA cyclization. Biophys J (2003) 1.55

A semiflexible polymer model applied to loop formation in DNA hairpins. Biophys J (2001) 1.54

Lac repressor hinge flexibility and DNA looping: single molecule kinetics by tethered particle motion. Nucleic Acids Res (2006) 1.48

Sequence dependence of DNA bending rigidity. Proc Natl Acad Sci U S A (2010) 1.44

A computational study of nucleosomal DNA flexibility. Biophys J (2006) 1.42

Three-arm nucleic acid junctions are flexible. Nucleic Acids Res (1986) 1.41

Normalization of a chromosomal contact map. BMC Genomics (2012) 1.41

Protein roadblocks and helix discontinuities are barriers to the initiation of mismatch repair. Proc Natl Acad Sci U S A (2007) 1.38

Multimerization-cyclization of DNA fragments as a method of conformational analysis. Biophys J (2000) 1.35

Quantitative study of polymer conformation and dynamics by single-particle tracking. Biophys J (1999) 1.34

Genetic rearrangement of DNA induces knots with a unique topology: implications for the mechanism of synapsis and crossing-over. Proc Natl Acad Sci U S A (1985) 1.32

Looping dynamics of linear DNA molecules and the effect of DNA curvature: a study by Brownian dynamics simulation. Biophys J (1998) 1.31

Tn7 transposition as a probe of cis interactions between widely separated (190 kilobases apart) DNA sites in the Escherichia coli chromosome. J Bacteriol (1996) 1.30

Analysis of in-vivo LacR-mediated gene repression based on the mechanics of DNA looping. PLoS One (2006) 1.30

DNA looping and translocation provide an optimal cleavage mechanism for the type III restriction enzymes. EMBO J (2007) 1.28

The RNA polymerase I transactivator upstream binding factor requires its dimerization domain and high-mobility-group (HMG) box 1 to bend, wrap, and positively supercoil enhancer DNA. Mol Cell Biol (1994) 1.27

V(D)J recombination: signal and coding joint resolution are uncoupled and depend on parallel synapsis of the sites. Mol Cell Biol (1993) 1.26

Statistical-mechanical theory of DNA looping. Biophys J (2005) 1.25

Variations of intramolecular ligation rates allow the detection of protein-induced bends in DNA. EMBO J (1986) 1.24

Electrostatic-undulatory theory of plectonemically supercoiled DNA. Biophys J (1999) 1.24

DNA supercoiling allows enhancer action over a large distance. Proc Natl Acad Sci U S A (2001) 1.24

Predicting indirect readout effects in protein-DNA interactions. Proc Natl Acad Sci U S A (2004) 1.23

First-principles calculation of DNA looping in tethered particle experiments. Phys Biol (2009) 1.20

Distortions induced in double-stranded oligonucleotides by the binding of cis- or trans-diammine-dichloroplatinum(II) to the d(GTG) sequence. Nucleic Acids Res (1990) 1.20

Strong bending of the DNA double helix. Nucleic Acids Res (2013) 1.19

Mutational analysis of all conserved basic amino acids in RAG-1 reveals catalytic, step arrest, and joining-deficient mutants in the V(D)J recombinase. Mol Cell Biol (2002) 1.19

Cloning and characterization of small circular DNA from Chinese hamster ovary cells. Mol Cell Biol (1984) 1.19

ATP-independent type II topoisomerase from trypanosomes. Proc Natl Acad Sci U S A (1986) 1.16

High-throughput approach for detection of DNA bending and flexibility based on cyclization. Proc Natl Acad Sci U S A (2003) 1.14

Loops in DNA: an overview of experimental and theoretical approaches. Eur Phys J E Soft Matter (2006) 1.13

Cloning exons of mapping of transcription: characterization of the Drosophila melanogaster alcohol dehydrogenase gene. Nucleic Acids Res (1983) 1.11

The activity of the scs and scs' insulator elements is not dependent on chromosomal context. Mol Cell Biol (1997) 1.10

Global structure and mechanical properties of a 10-bp nucleosome positioning motif. Proc Natl Acad Sci U S A (2000) 1.10

HMG proteins and DNA flexibility in transcription activation. Mol Cell Biol (2001) 1.10

Disruption of protein-mediated DNA looping by tension in the substrate DNA. Biophys J (2005) 1.09

Smooth DNA transport through a narrowed pore geometry. Biophys J (2014) 1.07

Electron microscopic studies of the interaction between a Bacillus subtilis alpha/beta-type small, acid-soluble spore protein with DNA: protein binding is cooperative, stiffens the DNA, and induces negative supercoiling. Proc Natl Acad Sci U S A (1994) 1.05

Sequence-dependent cooperative binding of p53 to DNA targets and its relationship to the structural properties of the DNA targets. Nucleic Acids Res (2010) 1.05

Phage Mu transposition immunity: protein pattern formation along DNA by a diffusion-ratchet mechanism. Mol Cell (2010) 1.05

Exploring writhe in supercoiled minicircle DNA. J Phys Condens Matter (2006) 1.03

3D reconstruction and comparison of shapes of DNA minicircles observed by cryo-electron microscopy. Nucleic Acids Res (2006) 1.02

The antiparallel loops in gal DNA. Nucleic Acids Res (2008) 1.02

Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles. Nucleic Acids Res (2009) 1.02

Spontaneous sharp bending of DNA: role of melting bubbles. Nucleic Acids Res (2006) 1.02

Probing the elasticity of DNA on short length scales by modeling supercoiling under tension. Biophys J (2012) 1.01

Temperature dependence of DNA persistence length. Nucleic Acids Res (2010) 1.00

Chromatin structure can strongly facilitate enhancer action over a distance. Proc Natl Acad Sci U S A (2006) 1.00

Strained DNA is kinked by low concentrations of Zn2+. Proc Natl Acad Sci U S A (1997) 0.99

Tetramer opening in LacI-mediated DNA looping. Proc Natl Acad Sci U S A (2009) 0.99

Gapped DNA and cyclization of short DNA fragments. Biophys J (2005) 0.98

Supercoiled Minivector DNA resists shear forces associated with gene therapy delivery. Gene Ther (2011) 0.98

Circle ligation of in vitro assembled chromatin indicates a highly flexible structure. Nucleic Acids Res (2002) 0.97

Dynamic strategies for target-site search by DNA-binding proteins. Biophys J (2010) 0.97

Helical-repeat dependence of integrative recombination of bacteriophage lambda: role of the P1 and H1 protein binding sites. Proc Natl Acad Sci U S A (1988) 0.97

Quantitative methods for measuring DNA flexibility in vitro and in vivo. Methods Enzymol (2011) 0.97

Do basic region-leucine zipper proteins bend their DNA targets ... does it matter? Proc Natl Acad Sci U S A (1996) 0.96

End-to-end attraction of duplex DNA. Nucleic Acids Res (2012) 0.96

T4 DNA ligase is more than an effective trap of cyclized dsDNA. Nucleic Acids Res (2007) 0.95

Branch capture reactions: effect of recipient structure. Nucleic Acids Res (1990) 0.94

Characterization of the ATF/CREB site and its complex with GCN4. Proc Natl Acad Sci U S A (1998) 0.93

Molecular screening for P-element insertions in a large genomic region of Drosophila melanogaster using polymerase chain reaction mediated by the vectorette. Genetics (1998) 0.92

Probing the elastic limit of DNA bending. Nucleic Acids Res (2014) 0.92

Stereochemistry-dependent bending in oligonucleotide duplexes induced by site-specific covalent benzo[a]pyrene diol epoxide-guanine lesions. Nucleic Acids Res (1995) 0.90

Quantitation of the DNA tethering effect in long-range DNA looping in vivo and in vitro using the Lac and λ repressors. Proc Natl Acad Sci U S A (2013) 0.89

The statistical-mechanics of chromosome conformation capture. Nucleus (2013) 0.88

Poly(dA:dT)-rich DNAs are highly flexible in the context of DNA looping. PLoS One (2013) 0.88

Electrostatics of DNA-DNA juxtapositions: consequences for type II topoisomerase function. J Phys Condens Matter (2006) 0.88

Plug and play modular strategies for synthetic retrotransposons. Methods (2009) 0.88

IHF-binding sites inhibit DNA loop formation and transcription initiation. Nucleic Acids Res (2009) 0.87

Analysis of kinetics in noisy systems: application to single molecule tethered particle motion. Biophys J (2007) 0.87

Measurements of DNA-loop formation via Cre-mediated recombination. Nucleic Acids Res (2012) 0.86

New peptide inhibitors of type IB topoisomerases: similarities and differences vis-a-vis inhibitors of tyrosine recombinases. J Mol Biol (2006) 0.86

The chromosomal protein MC1 from the archaebacterium Methanosarcina sp. CHTI 55 induces DNA bending and supercoiling. Nucleic Acids Res (1991) 0.86

The role of an upstream promoter interaction in initiation of bacterial transcription. EMBO J (2006) 0.86

Cooperativity in nucleosomes assembly on supercoiled pBR322 DNA. Nucleic Acids Res (1989) 0.86

Failure of hairpin-ended and nicked DNA To activate DNA-dependent protein kinase: implications for V(D)J recombination. Mol Cell Biol (1998) 0.85

Action at a distance in supercoiled DNA: effects of sequence on slither, branching, and intramolecular concentration. Biophys J (1996) 0.85

Articles by these authors

Intermediates in the folding reactions of small proteins. Annu Rev Biochem (1990) 6.42

Unusually stable helix formation in short alanine-based peptides. Proc Natl Acad Sci U S A (1989) 5.80

Helix stabilization by Glu-...Lys+ salt bridges in short peptides of de novo design. Proc Natl Acad Sci U S A (1987) 5.73

Specific intermediates in the folding reactions of small proteins and the mechanism of protein folding. Annu Rev Biochem (1982) 5.45

Temperature dependence of the hydrophobic interaction in protein folding. Proc Natl Acad Sci U S A (1986) 5.42

Evidence that a complex of SIR proteins interacts with the silencer and telomere-binding protein RAP1. Genes Dev (1994) 5.21

Cation-induced toroidal condensation of DNA studies with Co3+(NH3)6. J Mol Biol (1980) 4.88

A protein-counting mechanism for telomere length regulation in yeast. Science (1997) 4.79

Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast. Nature (1999) 4.71

A RAP1-interacting protein involved in transcriptional silencing and telomere length regulation. Genes Dev (1992) 4.53

A novel Rap1p-interacting factor, Rif2p, cooperates with Rif1p to regulate telomere length in Saccharomyces cerevisiae. Genes Dev (1997) 4.05

Energetics of DNA twisting. I. Relation between twist and cyclization probability. J Mol Biol (1983) 4.05

Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions. Protein Sci (1994) 3.94

Substrate preferences in rumen bacteria: evidence of catabolite regulatory mechanisms. Appl Environ Microbiol (1978) 3.90

Anomalous diffusion of fluorescent probes inside living cell nuclei investigated by spatially-resolved fluorescence correlation spectroscopy. J Mol Biol (2000) 3.65

Structural characterization of a partly folded apomyoglobin intermediate. Science (1990) 3.53

Mechanism of helix induction by trifluoroethanol: a framework for extrapolating the helix-forming properties of peptides from trifluoroethanol/water mixtures back to water. Biochemistry (1997) 3.52

Involvement of the silencer and UAS binding protein RAP1 in regulation of telomere length. Science (1990) 3.52

Parameters of helix-coil transition theory for alanine-based peptides of varying chain lengths in water. Biopolymers (1991) 3.51

Stability of alpha-helices. Adv Protein Chem (1995) 3.36

Characterization of two genes required for the position-effect control of yeast mating-type genes. EMBO J (1984) 3.30

The mechanism of alpha-helix formation by peptides. Annu Rev Biophys Biomol Struct (1992) 3.22

Tests of the helix dipole model for stabilization of alpha-helices. Nature (1987) 3.19

NMR evidence for an early framework intermediate on the folding pathway of ribonuclease A. Nature (1988) 3.09

Relative helix-forming tendencies of nonpolar amino acids. Nature (1990) 3.02

Helix formation by dAT oligomers. I. Hairpin and straight-chain helices. J Mol Biol (1968) 2.99

Helix propagation and N-cap propensities of the amino acids measured in alanine-based peptides in 40 volume percent trifluoroethanol. Protein Sci (1996) 2.93

Targeting of SIR1 protein establishes transcriptional silencing at HM loci and telomeres in yeast. Cell (1993) 2.91

Calorimetric determination of the enthalpy change for the alpha-helix to coil transition of an alanine peptide in water. Proc Natl Acad Sci U S A (1991) 2.84

Separation of transcriptional activation and silencing functions of the RAP1-encoded repressor/activator protein 1: isolation of viable mutants affecting both silencing and telomere length. Proc Natl Acad Sci U S A (1991) 2.80

Cohesive sites on the deoxyribonucleic acids from several temperate coliphages. J Mol Biol (1966) 2.75

A salt bridge stabilizes the helix formed by isolated C-peptide of RNase A. Proc Natl Acad Sci U S A (1982) 2.71

Energetics of DNA twisting. II. Topoisomer analysis. J Mol Biol (1983) 2.65

Action at a distance: DNA-looping and initiation of transcription. Trends Biochem Sci (1995) 2.64

Large differences in the helix propensities of alanine and glycine. Nature (1991) 2.61

Tandem genetic duplications in phage lambda. III. The frequency of duplication mutants in two derivatives of phage lambda is independent of known recombination systems. J Mol Biol (1975) 2.57

RAP1 is required for BAS1/BAS2- and GCN4-dependent transcription of the yeast HIS4 gene. Mol Cell Biol (1991) 2.55

RAP1 protein activates and silences transcription of mating-type genes in yeast. Genes Dev (1991) 2.51

Action of a RAP1 carboxy-terminal silencing domain reveals an underlying competition between HMR and telomeres in yeast. Genes Dev (1995) 2.50

Transcriptional regulation in the yeast life cycle. Science (1987) 2.46

Comparative hybridization of an array of 21,500 ovarian cDNAs for the discovery of genes overexpressed in ovarian carcinomas. Gene (1999) 2.45

Coagulation factor abnormalities after the Fontan procedure and its modifications. J Thorac Cardiovasc Surg (1997) 2.42

Enzymatic studies of pure cultures of rumen microorganisms. J Bacteriol (1966) 2.30

N- and C-capping preferences for all 20 amino acids in alpha-helical peptides. Protein Sci (1995) 2.27

Helix formation by d(TA) oligomers. II. Analysis of the helix-coli transitions of linear and circular oligomers. J Mol Biol (1970) 2.26

Guanidinium chloride induction of partial unfolding in amide proton exchange in RNase A. Science (1993) 2.24

Compartmentalization of interphase chromosomes observed in simulation and experiment. J Mol Biol (1999) 2.21

Energetics of the interaction between water and the helical peptide group and its role in determining helix propensities. Proc Natl Acad Sci U S A (2000) 2.17

NIMH Genetics Initiative Millenium Schizophrenia Consortium: linkage analysis of African-American pedigrees. Am J Med Genet (1998) 2.09

Nature of the charged-group effect on the stability of the C-peptide helix. Proc Natl Acad Sci U S A (1985) 2.09

Aromatic side-chain contribution to far-ultraviolet circular dichroism of helical peptides and its effect on measurement of helix propensities. Biochemistry (1993) 2.08

Enzymatic changes associated with the initiation and maintenance of lactation in the rat. J Biol Chem (1966) 2.07

Silencing of genes at nontelomeric sites in yeast is controlled by sequestration of silencing factors at telomeres by Rap 1 protein. Genes Dev (1996) 2.02

Urea unfolding of peptide helices as a model for interpreting protein unfolding. Proc Natl Acad Sci U S A (1995) 2.01

Determination of free energies of N-capping in alpha-helices by modification of the Lifson-Roig helix-coil therapy to include N- and C-capping. Biochemistry (1994) 1.99

Comparison of substrate affinities among several rumen bacteria: a possible determinant of rumen bacterial competition. Appl Environ Microbiol (1979) 1.99

Kinetics of amide proton exchange in helical peptides of varying chain lengths. Interpretation by the Lifson-Roig equation. Biochemistry (1992) 1.97

Three-state analysis of sperm whale apomyoglobin folding. Biochemistry (1993) 1.96

The energetics of ion-pair and hydrogen-bonding interactions in a helical peptide. Biochemistry (1993) 1.94

Hydrogen exchange in thermally denatured ribonuclease A. Biochemistry (1991) 1.92

Monomolecular condensation of lambda-DNA induced by cobalt hexamine. Biopolymers (1983) 1.91

Comparison of maintenance energy expenditures and growth yields among several rumen bacteria grown on continuous culture. Appl Environ Microbiol (1979) 1.88

Comparison of NH exchange and circular dichroism as techniques for measuring the parameters of the helix-coil transition in peptides. Biochemistry (1997) 1.85

A quantitative treatment of the kinetics of the folding transition of ribonuclease A. Biochemistry (1976) 1.83

Helix capping propensities in peptides parallel those in proteins. Proc Natl Acad Sci U S A (1993) 1.83

Acid catalysis of the formation of the slow-folding species of RNase A: evidence that the reaction is proline isomerization. Proc Natl Acad Sci U S A (1978) 1.78

Epigenetic switching of transcriptional states: cis- and trans-acting factors affecting establishment of silencing at the HMR locus in Saccharomyces cerevisiae. Mol Cell Biol (1993) 1.78

Catalysis of DNA reassociation by the Escherichia coli DNA binding protein: A polyamine-dependent reaction. J Mol Biol (1977) 1.73

Pathway of propionate formation in Bacteroides ruminicola. J Bacteriol (1967) 1.72

Interaction between water and polar groups of the helix backbone: an important determinant of helix propensities. Proc Natl Acad Sci U S A (1999) 1.70

A Brownian dynamics program for the simulation of linear and circular DNA and other wormlike chain polyelectrolytes. Biophys J (1998) 1.68

Yeast Ku protein plays a direct role in telomeric silencing and counteracts inhibition by rif proteins. Curr Biol (1999) 1.68

Characterization of right ventricular diastolic performance after complete repair of tetralogy of Fallot. Restrictive physiology predicts slow postoperative recovery. Circulation (1995) 1.67

Role of proline isomerization in folding of ribonuclease A at low temperatures. Proc Natl Acad Sci U S A (1979) 1.65

Early folding intermediate of ribonuclease A. Proc Natl Acad Sci U S A (1990) 1.65

Both the fast and slow refolding reactions of ribonuclease A yield native enzyme. Proc Natl Acad Sci U S A (1973) 1.64

Further studies of the helix dipole model: effects of a free alpha-NH3+ or alpha-COO- group on helix stability. Proteins (1989) 1.63

Second cytotoxic pathway of diphtheria toxin suggested by nuclease activity. Science (1989) 1.60

Cingulin contains globular and coiled-coil domains and interacts with ZO-1, ZO-2, ZO-3, and myosin. J Cell Biol (1999) 1.59

A helix stop signal in the isolated S-peptide of ribonuclease A. Nature (1984) 1.58

Effect of a single aspartate on helix stability at different positions in a neutral alanine-based peptide. Protein Sci (1993) 1.56

Detection of an early intermediate in the folding of ribonuclease A by protection of amide protons against exchange. J Mol Biol (1979) 1.55

Probing the stability of a partly folded apomyoglobin intermediate by site-directed mutagenesis. Biochemistry (1991) 1.55

Enhanced expression of the type II transforming growth factor beta receptor in human pancreatic cancer cells without alteration of type III receptor expression. Cancer Res (1993) 1.53

Assessing the flexibility of intermediate filaments by atomic force microscopy. J Mol Biol (2004) 1.49

Protein folding. Matching speed and stability. Nature (1994) 1.48

Multiple interactions in Sir protein recruitment by Rap1p at silencers and telomeres in yeast. Mol Cell Biol (2001) 1.48

Modulation of intramolecular interactions in superhelical DNA by curved sequences: a Monte Carlo simulation study. Biophys J (1995) 1.47

High-throughput plasmid mini preparations facilitated by micro-mixing. Nucleic Acids Res (1996) 1.46

Anatomical criteria for the diagnosis of sinus venosus defects. Heart (1997) 1.44

Helical peptides with three pairs of Asp-Arg and Glu-Arg residues in different orientations and spacings. Protein Sci (1993) 1.44

Sequence-dependent elastic properties of DNA. J Mol Biol (2000) 1.43

Brownian dynamics simulations of supercoiled DNA with bent sequences. Biophys J (1996) 1.42

Helix formation by d(TA) oligomers. 3. Electrostatic effects. J Mol Biol (1970) 1.41

An essential yeast gene encoding a TTAGGG repeat-binding protein. Mol Cell Biol (1993) 1.41

Exchange kinetics of individual amide protons in 15N-labeled helical peptides measured by isotope-edited NMR. Biochemistry (1994) 1.40

Test of the extended two-state model for the kinetic intermediates observed in the folding transition of ribonuclease A. J Mol Biol (1978) 1.39

Intermediates in protein folding reactions and the mechanism of protein folding. Annu Rev Biochem (1975) 1.39