Configurational transitions in Fourier series-represented DNA supercoils (Q33907501)

29 July 2017

title

Configurational transitions in Fourier series-represented DNA supercoils (English)

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ORCID Public Data File 2021

29 July 2017

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author name string

G Liu

1

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29 July 2017

T Schlick

2

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29 July 2017

A J Olson

3

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29 July 2017

W K Olson

4

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29 July 2017

language of work or name

English

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publication date

1 October 1997

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29 July 2017

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29 July 2017

volume

73

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29 July 2017

issue

4

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29 July 2017

page(s)

1742-1762

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Decomposition of the linking number of a closed ribbon: A problem from molecular biology

29 July 2017

cites work

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The effect of intrinsic curvature on conformational properties of circular DNA.

5 July 2018

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Visualization of supercoiled DNA with atomic force microscopy in situ

5 July 2018

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Force: a new structural control parameter?

5 July 2018

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Simulating DNA at low resolution

5 July 2018

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Effect of bending strain on the torsion elastic constant of DNA.

5 July 2018

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Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution

5 July 2018

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Crystal structure of the lactose operon repressor and its complexes with DNA and inducer

5 July 2018

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Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules

5 July 2018

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Atomic force microscopy of long and short double-stranded, single-stranded and triple-stranded nucleic acids

5 July 2018

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The elasticity of a single supercoiled DNA molecule

5 July 2018

1 reference

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The twist, writhe and overall shape of supercoiled DNA change during counterion-induced transition from a loosely to a tightly interwound superhelix. Possible implications for DNA structure in vivo

5 July 2018

1 reference

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DNA self-fitting: the double helix directs the geometry of its supramolecular assembly

5 July 2018

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Modulation of intramolecular interactions in superhelical DNA by curved sequences: a Monte Carlo simulation study

5 July 2018

1 reference

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Monte Carlo simulations of supercoiling free energies for unknotted and trefoil knotted DNAs

5 July 2018

1 reference

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The influence of salt on the structure and energetics of supercoiled DNA

5 July 2018

1 reference

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Self-fitting and Self-modifying Properties of theB-DNA Molecule

5 July 2018

1 reference

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Modeling superhelical DNA: recent analytical and dynamic approaches.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181075

Trapping of branched DNA in microfabricated structures

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181075

Effect of anisotropy of the bending rigidity on the supercoiling free energy of small circular DNAs

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181075

Alignment and Sensitive Detection of DNA by a Moving Interface

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181075

Monte Carlo computation of the supercoiling energy, the sedimentation constant, and the radius of gyration of unknotted and knotted circular DNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181075

A control element within a structural gene: The gal operon of Escherichia coli

5 July 2018

1 reference

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An operator at -280 base pairs that is required for repression of araBAD operon promoter: addition of DNA helical turns between the operator and promoter cyclically hinders repression

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181075

The writhing number of a space curve

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181075

Ring closure probabilities for DNA fragments by Monte Carlo simulation.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181075

DNA loops induced by cooperative binding of lambda repressor

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181075

5 July 2018

1 reference

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Gene regulation by proteins acting nearby and at a distance

5 July 2018

1 reference

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Chromatin reconstitution on small DNA rings. II. DNA supercoiling on the nucleosome

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181075

Modeling DNA supercoils and knots with B-spline functions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181075

DNA looping generated by DNA bending protein IHF and the two domains of lambda integrase

5 July 2018

1 reference

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Structure of plectonemically supercoiled DNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181075

The Hin invertasome: protein-mediated joining of distant recombination sites at the enhancer

5 July 2018

1 reference

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Processive recombination by the phage Mu Gin system: implications for the mechanisms of DNA strand exchange, DNA site alignment, and enhancer action

5 July 2018

1 reference

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Static and statistical bending of DNA evaluated by Monte Carlo simulations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181075

21 Computer simulation of DNA supercoiling

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181075

Supercoiled DNA energetics and dynamics by computer simulation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181075

DNA bending, flexibility, and helical repeat by cyclization kinetics.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181075

Langevin dynamics of peptides: the frictional dependence of isomerization rates of N-acetylalanyl-N'-methylamide

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181075

Trefoil knotting revealed by molecular dynamics simulations of supercoiled DNA

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181075

The flexible DNA double helix. II. Superhelix formation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181075

Structure and reactions of closed duplex DNA

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181075

Folding of the DNA double helix in chromatin-like structures from simian virus 40

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181075

Brownian dynamics simulations of supercoiled DNA with bent sequences

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181075

Action at a distance in supercoiled DNA: effects of sequence on slither, branching, and intramolecular concentration

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181075

DNA: an extensible molecule.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181075

Influence of fluctuations on DNA curvature. A comparison of flexible and static wedge models of intrinsically bent DNA.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181075

Direct observation of tube-like motion of a single polymer chain

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181075

On higher buckling transitions in supercoiled DNA.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181075

Static contributions to the persistence length of DNA and dynamic contributions to DNA curvature

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181075

Flexing and folding double helical DNA

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181075

Determination of DNA persistence length by cryo-electron microscopy. Separation of the static and dynamic contributions to the apparent persistence length of DNA.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181075

Polyelectrolyte effects in DNA condensation by polyamines.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181075

Twist and writhing in short circular DNAs according to first-order elasticity.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181075

Computer simulation of DNA supercoiling

29 October 2018

1 reference

12 December 2020

Watching molecules crowd: DNA double helices under osmotic stress

1 reference

12 December 2020

Electrostatic effects in short superhelical DNA

1 reference

12 December 2020

Transcription against an applied force

1 reference

12 December 2020

Analysis of the ring-closure probabilities of isotropic wormlike chains: application to duplex DNA

1 reference

12 December 2020

Base sequence effects in double-helical DNA. II. Configurational statistics of rodlike chains

1 reference

12 December 2020

Spatial translational motions of base pairs in DNA molecules: application of the extended matrix generator method

1 reference

12 December 2020

Conformational and thermodynamic properties of supercoiled DNA

1 reference

12 December 2020

Computer simulation of protein-induced structural changes in closed circular DNA

1 reference

12 December 2020

B-DNA twisting correlates with base-pair morphology.

1 reference

12 December 2020

Application of the method of phage T4 DNA ligase-catalyzed ring-closure to the study of DNA structure. II. NaCl-dependence of DNA flexibility and helical repeat

1 reference

12 December 2020

Molecular dynamics simulations of small DNA plasmids: effects of sequence and supercoiling on intramolecular motions

1 reference

12 December 2020

Evaluation of some basic positron-related characteristics of SiC

1 reference

12 December 2020

Solvent effects on supercoiled DNA dynamics explored by Langevin dynamics simulations

1 reference

12 December 2020

Molecular modeling of closed circular DNA thermodynamic ensembles

1 reference

12 December 2020

10.1016/S0006-3495(97)78205-5

Identifiers

DOI

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29 July 2017

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29 July 2017

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