Intrinsic flexibility of B-DNA: the experimental TRX scale (Q30493018)

14 October 2017

Intrinsic flexibility of B-DNA: the experimental TRX scale (English)

1 reference

14 October 2017

4

Nicolas Foloppe

1 reference

14 October 2017

Brahim Heddi

1

1 reference

14 October 2017

Christophe Oguey

series ordinal

2

1 reference

14 October 2017

Christophe Lavelle

series ordinal

3

1 reference

14 October 2017

Brigitte Hartmann

series ordinal

5

1 reference

14 October 2017

language of work or name

English

0 references

publication date

17 November 2009

1 reference

14 October 2017

Nucleic Acids Research

1 reference

14 October 2017

38

1 reference

14 October 2017

3

1 reference

14 October 2017

1034-1047

1 reference

Nuance in the double-helix and its role in protein-DNA recognition.

14 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

DNA sequence-directed organization of chromatin: structure-based computational analysis of nucleosome-binding 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=2817485

Poly(dA:dT) tracts: major determinants of nucleosome organization

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

The DNA-encoded nucleosome organization of a eukaryotic genome

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

Distinct modes of regulation by chromatin encoded through nucleosome positioning signals

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

DNA physical properties determine nucleosome occupancy from yeast to fly.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

Characteristics of nucleosome core DNA and their applications in predicting nucleosome positions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

Towards a molecular dynamics consensus view of B-DNA flexibility

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

Sequence-dependent DNA deformability studied using molecular dynamics 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=2817485

Nucleosome positioning signals in genomic 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=2817485

NMR studies of RNA dynamics and structural plasticity using NMR residual dipolar couplings.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

A novel roll-and-slide mechanism of DNA folding in chromatin: implications for nucleosome positioning

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

The DNA structure responds differently to physiological concentrations of K(+) or Na(+).

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

A physical picture of atomic motions within the Dickerson DNA dodecamer in solution derived from joint ensemble refinement against NMR and large-angle X-ray scattering 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=2817485

A genomic code for nucleosome positioning

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

B-DNA under stress: over- and untwisting of DNA during molecular dynamics 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=2817485

X-ray diffraction "fingerprinting" of DNA structure in solution for quantitative evaluation of molecular dynamics 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=2817485

Principal component analysis of DNA oligonucleotide structural 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=2817485

Improved alignment of nucleosome DNA sequences using a mixture model

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: sequence context effects on the dynamical structures of the 10 unique dinucleotide steps

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

Alteration of the nucleosomal DNA path in the crystal structure of a human nucleosome core particle

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

How sequence defines structure: a crystallographic map of DNA structure and conformation.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

Protein-DNA recognition patterns and predictions.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

The structural basis of DNA flexibility

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

Residual dipolar couplings in NMR structure 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=2817485

DNA sequence-dependent deformability--insights from computer 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=2817485

DNA Basepair Step Deformability Inferred from Molecular Dynamics 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=2817485

Overall structure and sugar dynamics of a DNA dodecamer from homo- and heteronuclear dipolar couplings and 31P chemical shift anisotropy

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

Conformational Characteristics and Correlations in Crystal Structures of Nucleic Acid Oligonucleotides: Evidence for Sub-states

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

The structure of DNA in the nucleosome core

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

Crystal structures of nucleosome core particles in complex with minor groove DNA-binding ligands

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

Alpha/gamma transitions in the B-DNA backbone

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

Residual dipolar couplings in nucleic acid structure determination

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a 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=2817485

The papillomavirus E2 proteins: structure, function, and biology

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

Role of DNA sequence in nucleosome stability and dynamics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

Improving the accuracy of NMR structures of DNA by means of a database potential of mean force describing base-base positional 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=2817485

An overview of the structures of protein-DNA 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=2817485

BII nucleotides in the B and C forms of natural-sequence polymeric DNA: A new model for the C form 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=2817485

Asymmetries in the nucleosome core particle at 2.5 A 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=2817485

Poly(dA.dT) sequences exist as rigid DNA structures in nucleosome-free yeast promoters in vivo

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

A theoretical model for the prediction of sequence-dependent nucleosome thermodynamic stability

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

CAF-1 and the inheritance of chromatin states: at the crossroads of DNA replication and repair

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

Intrinsic conformational properties of deoxyribonucleosides: implicated role for cytosine in the equilibrium among the A, B, and Z forms 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=2817485

Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA 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=2817485

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=2817485

A topological approach to nucleosome structure and dynamics: the linking number paradox and other issues

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

Flexibility of the B-DNA backbone: effects of local and neighbouring sequences on pyrimidine-purine steps

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

Sensitivity of NMR internucleotide distances to B-DNA conformation: underlying mechanics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

Influence of sequence on the conformation of the B-DNA helix

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

Solution structure of the CpG containing d(CTTCGAAG)2 oligonucleotide: NMR data and energy calculations are compatible with a BI/BII equilibrium at CpG.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

Towards an understanding of protein-DNA recognition

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

BI-BII transitions 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=2817485

The non-B-DNA structure of d(CA/TG)n does not differ from that of Z-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=2817485

Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

Chemical probes of DNA conformation: detection of Z-DNA at nucleotide 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=2817485

DNA bending and its relation to nucleosome positioning.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

Sequence periodicities in chicken nucleosome core 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=2817485

Some rules for predicting the base-sequence dependence of DNA conformation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

The definition of generalized helicoidal parameters and of axis curvature for irregular 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=2817485

Analysis of local helix geometry in three B-DNA decamers and eight dodecamers

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

Free-energy component analysis of 40 protein-DNA complexes: a consensus view on the thermodynamics of binding at the molecular level.

20 June 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP962

DNA deformation energetics and protein binding

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP962

DNA variability in five crystal structures of d(CGCAATTGCG).

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP962

Importance of accurate DNA structures in solution: the Jun-Fos model

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP962

DNA deformability at the base pair level.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP962

Insight into G[bond]T mismatch recognition using molecular dynamics with time-averaged restraints derived from NMR spectroscopy

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP962

NMR evidence for mechanical coupling of phosphate B(I)-B(II) transitions with deoxyribose conformational exchange in DNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP962

Conformations of the sugar-phosphate backbone in helical DNA crystal structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP962

DNA fine structure and dynamics in crystals and in solution: the impact of BI/BII backbone conformations

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP962

Nucleosomal locations of dominant DNA sequence motifs for histone-DNA interactions and nucleosome positioning

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP962

How NF-κB can be attracted by its cognate DNA

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP962

Sequence-dependent DNA structure: a database of octamer structural parameters

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP962

Sequence-dependent nucleosome positioning

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP962

The influence of DNA stiffness upon nucleosome formation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP962

Fine mapping of inherent flexibility variation along DNA molecules: validation by atomic force microscopy (AFM) in buffer

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP962

Sequence-Dependent Conformational Energy of DNA Derived from Molecular Dynamics Simulations: Toward Understanding the Indirect Readout Mechanism in Protein−DNA Recognition

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP962

Crystallographic studies of DNA helix structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP962

Toward a Full Characterization of Nucleic Acid Components in Aqueous Solution: Simulations of Nucleosides

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP962

DNA helix structure and refinement algorithm: comparison of models for d(CCAGGCm5CTGG) derived from NUCLSQ, TNT and X-PLOR.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2817485

Nucleosome positions predicted through comparative genomics

26 November 2018

1 reference

12 December 2020

Helix morphology changes in B-DNA induced by spontaneous B(I)<==>B(II) substrate interconversion

1 reference

12 December 2020

Structural behavior of the CpG step in two related oligonucleotides reflects its malleability in solution

1 reference

12 December 2020

Quantification of DNA BI/BII backbone states in solution. Implications for DNA overall structure and recognition

1 reference

12 December 2020

Nucleic acid model building: the multiple backbone solutions associated with a given base morphology

1 reference

12 December 2020

DNA sequence-dependent contributions of core histone tails to nucleosome stability: differential effects of acetylation and proteolytic tail removal

1 reference

12 December 2020

DNA recognition by structure-selective nucleases

1 reference

12 December 2020

New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning

1 reference

12 December 2020

1 reference

12 December 2020

Stochastic distribution of a short region of Z-DNA within a long repeated sequence in negatively supercoiled plasmids

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKP962

1 reference

14 October 2017

1 reference

14 October 2017

PubMed publication ID

19920127

1 reference