Sequence-dependent motions of DNA: a normal mode analysis at the base-pair level (Q30476422)

18 September 2017

Sequence-dependent motions of DNA: a normal mode analysis at the base-pair level (English)

1 reference

18 September 2017

Atsushi Matsumoto

1

1 reference

PMCID

1302125

18 September 2017

Wilma K Olson

series ordinal

2

1 reference

PMCID

1302125

18 September 2017

language of work or name

English

0 references

publication date

1 July 2002

1 reference

18 September 2017

20

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based on heuristic

inferred from page(s)

published in

Biophysical Journal

1 reference

18 September 2017

83

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18 September 2017

22-41

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18 September 2017

1

1 reference

A standard reference frame for the description of nucleic acid base-pair geometry.

18 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

A refined prediction method for gel retardation of DNA oligonucleotides from dinucleotide step parameters: reconciliation of DNA bending models with crystal structure data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Conformational deformability of RNA: a harmonic mode analysis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Collective protein dynamics in relation to function

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Quantitative comparison of DNA looping in vitro and in vivo: chromatin increases effective DNA flexibility at short distances

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Investigating protein dynamics in collective coordinate space

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Resolving the discrepancies among nucleic acid conformational analyses

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

The SWI/SNF complex creates loop domains in DNA and polynucleosome arrays and can disrupt DNA-histone contacts within these domains

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

DNA sequence-dependent deformability deduced from protein-DNA crystal complexes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

The effect of distance on long-range chromatin interactions.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Sequence specificity of bacteriophage 434 repressor-operator complexation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Measurement of the DNA bend angle induced by the catabolite activator protein using Monte Carlo simulation of cyclization kinetics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Scanning force microscopy under aqueous solutions.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Ionic effects on the elasticity of single DNA molecules

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Stretching DNA with optical tweezers

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Simulating DNA at low resolution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

The effects of sequence context on DNA curvature.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Trinucleotide models for DNA bending propensity: comparison of models based on DNaseI digestion and nucleosome packaging data.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Nucleic acid structure analysis. Mathematics for local Cartesian and helical structure parameters that are truly comparable between structures.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Entropic elasticity of lambda-phage DNA

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Normal mode calculation of a netropsin-DNA complex: effect of structural deformation on vibrational spectrum.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Modeling of long-range electrostatic interactions in DNA.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Atomic force microscopy of nucleoprotein complexes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Torison dynamics and depolarization of fluorescence of linear macromolecules. II. Fluorescence polarization anisotropy measurements on a clean viral phi 29 DNA.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Chain flexibility and hydrodynamics of the B and Z forms of poly(dG-dC).poly(dG-dC).

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Fluorescence depolarization and temperature dependence of the torsion elastic constant of linear phi 29 deoxyribonucleic acid

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Electron microscopic measurement of chain flexibility of poly(dG-dC).poly(dG-dC) modified by cis-diamminedichloroplatinum(II).

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Torsional motion and elasticity of the deoxyribonucleic acid double helix and its nucleosomal complexes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Torsional dynamics and rigidity of fractionated poly(dGdC).

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Dependence of oxygen quenching of intercalated methylene blue triplet lifetime on DNA base-pair composition.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

The flexibility of alternating dA-dT sequences

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Ring closure probabilities for DNA fragments by Monte Carlo simulation.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Importance of DNA stiffness in protein-DNA binding specificity

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Harmonic vibrations and thermodynamic stability of a DNA oligomer in monovalent salt solution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Structural basis for DNA bending

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Langevin modes of macromolecules: applications to crambin and DNA hexamers

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Electron microscopy mapping of pBR322 DNA curvature. Comparison with theoretical models

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Dynamic bending rigidity of DNA.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Static and statistical bending of DNA evaluated by Monte Carlo simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Conformational sub-states in B-DNA.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Electron microscopic visualization of DNA and DNA-protein complexes as adjunct to biochemical studies

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

On conformations of the superhelix structure.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Anisotropic flexibility of DNA and the nucleosomal structure

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

The flexible DNA double helix. II. Superhelix formation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Gene duplications in the structural evolution of chymotrypsin

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

How many base-pairs per turn does DNA have in solution and in chromatin? Some theoretical calculations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Possibility of nonkinked packing of DNA in chromatin

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Configurational statistics of the DNA duplex: extended generator matrices to treat the rotations and translations of adjacent residues.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

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

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Dependence of DNA helix flexibility on base composition.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Orientation relaxation of DNA restriction fragments and the internal mobility of the double helix

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Physical properties of DNA in vivo as probed by the length dependence of the lac operator looping process

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302125

Theory of twisting and bending of chain macromolecules; analysis of the fluorescence depolarization of DNA

26 November 2018

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975147-3

Some Studies Concerning Rotating Axes and Polyatomic Molecules

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975147-3

Electrostatic effects in short superhelical DNA

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975147-3

B-DNA twisting correlates with base-pair morphology.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975147-3

Influence of drug binding on DNA flexibility: a normal mode analysis

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975147-3

Investigation of the flexibility of DNA using transient electric birefringence

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975147-3

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975147-3

Sequence-directed curvature of DNA

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975147-3

Torsional rigidity of DNA and length dependence of the free energy of DNA supercoiling

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975147-3

Normal-Mode calculation for methylated Z-DNA poly(dG-m5dC) · (dG-m5dC)

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975147-3

Transition from B to Z DNA: contribution of internal fluctuations to the configurational entropy difference

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975147-3

DNA conformational studies from electron microscopy. I. Excluded volume effect and structure dimensionality

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975147-3

DNA stretching and compression: large-scale simulations of double helical structures

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975147-3

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975147-3

Modeling DNA deformations

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975147-3

Torsional constant of 27-mer DNA oligomers of different sequences

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975147-3

Structure and dynamics of double helices in solution: modes of DNA bending

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975147-3

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975147-3

Molecular dynamics studies of axis bending in d(G5-(GA4T4C)2-C5) and d(G5-(GT4A4C)2-C5): effects of sequence polarity on DNA curvature

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975147-3

Dynamics of DNA oligomers

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975147-3

10.1016/S0006-3495(02)75147-3

7 January 2021

Identifiers

DOI

1 reference

18 September 2017

1 reference

18 September 2017

1 reference

PMCID

1302125