DNA information: from digital code to analogue structure (Q38012106)

27 August 2017

title

DNA information: from digital code to analogue structure (English)

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27 August 2017

A A Travers

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27 August 2017

G Muskhelishvili

series ordinal

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27 August 2017

J M T Thompson

series ordinal

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27 August 2017

language of work or name

English

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publication date

1 June 2012

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Philosophical Transactions of the Royal Society A

27 August 2017

published in

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27 August 2017

volume

370

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27 August 2017

issue

1969

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27 August 2017

page(s)

2960-2986

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27 August 2017

cites work

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

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DNA stretching and extreme kinking in the nucleosome core

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Structure of RCC1 chromatin factor bound to the nucleosome core particle

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Nucleosome structural studies

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Rapid spontaneous accessibility of nucleosomal DNA.

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spFRET using alternating excitation and FCS reveals progressive DNA unwrapping in nucleosomes

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Nucleosome disassembly intermediates characterized by single-molecule FRET.

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Nucleosome accessibility governed by the dimer/tetramer interface

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The role of DNA shape in protein-DNA recognition

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Nonsequence-specific DNA recognition: a structural perspective

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The exocyclic groups of DNA modulate the affinity and positioning of the histone octamer

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Sequence periodicities in chicken nucleosome core DNA.

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Role of DNA sequence in nucleosome stability and dynamics

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

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A translational signature for nucleosome positioning in vivo.

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The shape of the DNA minor groove directs binding by the DNA-bending protein Fis

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Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees

21 January 2018

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Dissection of the bacteriophage Mu strong gyrase site (SGS): significance of the SGS right arm in Mu biology and DNA gyrase mechanism

21 January 2018

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A systematic in vitro study of nucleoprotein complexes formed by bacterial nucleoid-associated proteins revealing novel types of DNA organization

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Spiral structure of Escherichia coli HU provides foundation for DNA supercoiling

21 January 2018

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The C-terminal domain of DNA gyrase A adopts a DNA-bending beta-pinwheel fold

21 January 2018

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The form and structure of kinetoplast DNA of Crithidia

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Bent helical structure in kinetoplast DNA.

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An introduction to the mechanics of DNA.

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DNA bending by asymmetric phosphate neutralization

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DNA bending by small, mobile multivalent cations

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A unified model for the origin of DNA sequence-directed curvature.

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

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HMG1 and 2, and related 'architectural' DNA-binding proteins

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IHF and HU: flexible architects of bent DNA.

21 January 2018

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

21 January 2018

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Working the kinks out of nucleosomal DNA

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Intrinsic flexibility of B-DNA: the experimental TRX scale

21 January 2018

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The structure of DNA in the nucleosome core

21 January 2018

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Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences.

21 January 2018

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Relative affinities of DNA sequences for the histone octamer depend strongly upon both the temperature and octamer concentration

21 January 2018

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

21 January 2018

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DNA flexibility studied by covalent closure of short fragments into circles

21 January 2018

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Understanding Apparent DNA Flexibility Enhancement by HU and HMGB Architectural Proteins

21 January 2018

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Bacterial repression loops require enhanced DNA flexibility.

21 January 2018

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Modeling the Lac repressor-operator assembly: the influence of DNA looping on Lac repressor conformation

21 January 2018

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Architectural elements in nucleoprotein complexes.

21 January 2018

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DNA chaperones: a solution to a persistence problem?

21 January 2018

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Temperature and salt dependence of the gel migration anomaly of curved DNA fragments

21 January 2018

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The influence of DNA stiffness upon nucleosome formation

21 January 2018

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DNA Gyrase and DNA Supercoiling

21 January 2018

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The inverted repeat as a recognizable structural feature in supercoiled DNA molecules

21 January 2018

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Association of an S1 nuclease-sensitive structure with short direct repeats 5' of Drosophila heat shock genes

21 January 2018

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Coordination of genomic structure and transcription by the main bacterial nucleoid-associated protein HU.

21 January 2018

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FIS modulates the kinetics of successive interactions of RNA polymerase with the core and upstream regions of the tyrT promoter

21 January 2018

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https://api.crossref.org/works/10.1098%2FRSTA.2011.0231

DNA bending and its relation to nucleosome positioning.

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTA.2011.0231

Dissecting the logical types of network control in gene expression profiles

21 January 2018

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Analog regulation of metabolic demand

21 January 2018

1 reference

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The structure of an oligo(dA).oligo(dT) tract and its biological implications

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTA.2011.0231

Crystal lattice packing is important in determining the bend of a DNA dodecamer containing an adenine tract

21 January 2018

1 reference

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Stacked-unstacked equilibrium at the nick site of DNA

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTA.2011.0231

High-resolution mapping of sequence-directed nucleosome positioning on genomic DNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTA.2011.0231

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTA.2011.0231

Sequence-dependent DNA structure: tetranucleotide conformational maps

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTA.2011.0231

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTA.2011.0231

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTA.2011.0231

Time-resolved fluorescence resonance energy transfer studies of DNA bending in double-stranded oligonucleotides and in DNA-protein complexes

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTA.2011.0231

Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTA.2011.0231

Single-molecule studies of DNA mechanics

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTA.2011.0231

Estimating the persistence length of a worm-like chain molecule from force-extension measurements

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTA.2011.0231

Structural transitions and elasticity from torque measurements on DNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTA.2011.0231

Twisting and stretching single DNA molecules.

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTA.2011.0231

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTA.2011.0231

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTA.2011.0231

Implications of the dependence of the elastic properties of DNA on nucleotide sequence

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTA.2011.0231

DNA overwinds when stretched

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTA.2011.0231

Twist-stretch coupling and phase transition during DNA supercoiling

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTA.2011.0231

Catabolite activator protein: DNA binding and transcription activation

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTA.2011.0231

Exact theory of kinkable elastic polymers.

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTA.2011.0231

Kinking occurs during molecular dynamics simulations of small DNA minicircles

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTA.2011.0231

Kinking the double helix by bending deformation

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTA.2011.0231

Spontaneous sharp bending of double-stranded DNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTA.2011.0231

DNA twisting flexibility and the formation of sharply looped protein-DNA complexes

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTA.2011.0231

Cyclization of short DNA fragments and bending fluctuations of the double helix

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTA.2011.0231

Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTA.2011.0231

Chemically accurate coarse graining of double-stranded DNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTA.2011.0231

Mesoscale modeling of multi-protein-DNA assemblies: the role of the catabolic activator protein in Lac-repressor-mediated looping

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTA.2011.0231

Effects of the nucleoid protein HU on the structure, flexibility, and ring-closure properties of DNA deduced from Monte Carlo simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTA.2011.0231

Two perspectives on the twist of DNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTA.2011.0231

Sequence-Dependent Effects in the Cyclization of Short DNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1098%2FRSTA.2011.0231

Crystal structure of the nucleosome core particle at 2.8 Å resolution

21 January 2018

1 reference

4 November 2023

https://opencitations.net/index/coci/api/v1/citations/10.1038/38444

Identifiers

DOI

10.1098/RSTA.2011.0231

1 reference

27 August 2017

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