An ensemble of B-DNA dinucleotide geometries lead to characteristic nucleosomal DNA structure and provide plasticity required for gene expression (Q33786176)

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scientific article published on January 5, 2011

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English	An ensemble of B-DNA dinucleotide geometries lead to characteristic nucleosomal DNA structure and provide plasticity required for gene expression	scientific article published on January 5, 2011

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scholarly article

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Europe PubMed Central

PubMed publication ID

29 July 2017

An ensemble of B-DNA dinucleotide geometries lead to characteristic nucleosomal DNA structure and provide plasticity required for gene expression (English)

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Europe PubMed Central

PubMed publication ID

29 July 2017

gene expression

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Europe PubMed Central

PubMed publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A21208404

21 November 2024

author name string

Arvind Marathe

1

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29 July 2017

Manju Bansal

2

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29 July 2017

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National Center for Biotechnology Information

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=21208404

21 November 2024

publication date

5 January 2011

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29 July 2017

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https://bmcstructbiol.biomedcentral.com/counter/pdf/10.1186/1472-6807-11-1

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21 November 2024

http://www.biomedcentral.com/1472-6807/11/1

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A21208404

21 November 2024

http://www.biomedcentral.com/content/pdf/1472-6807-11-1.pdf

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A21208404

21 November 2024

http://www.biomedcentral.com/1472-6807/11/1/abstract

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A21208404

21 November 2024

https://europepmc.org/articles/PMC3031206

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A21208404

21 November 2024

https://europepmc.org/articles/PMC3031206?pdf=render

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Europe PubMed Central

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A21208404

21 November 2024

BMC Structural Biology

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Europe PubMed Central

PubMed publication ID

29 July 2017

11

1 reference

Europe PubMed Central

PubMed publication ID

29 July 2017

1

1 reference

Europe PubMed Central

PubMed publication ID

29 July 2017

Crystal structures of nucleosome core particles containing the '601' strong positioning sequence

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031206

4 July 2018

Sequence-dependent Kink-and-Slide deformations of nucleosomal DNA facilitated by histone arginines bound in the minor groove

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031206

4 July 2018

DNA architecture, deformability, and nucleosome positioning

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031206

4 July 2018

The role of DNA shape in protein-DNA recognition

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031206

4 July 2018

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031206

4 July 2018

What controls nucleosome positions?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031206

4 July 2018

Using DNA mechanics to predict in vitro nucleosome positions and formation energies.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031206

4 July 2018

Small local variations in B-form DNA lead to a large variety of global geometries which can accommodate most DNA-binding protein motifs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031206

4 July 2018

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

1 reference

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4 July 2018

Nucleosome positioning and gene regulation: advances through genomics

1 reference

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4 July 2018

The DNA-encoded nucleosome organization of a eukaryotic genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031206

4 July 2018

The effect of H3K79 dimethylation and H4K20 trimethylation on nucleosome and chromatin structure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031206

4 July 2018

A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031206

4 July 2018

A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031206

4 July 2018

Two strategies for gene regulation by promoter nucleosomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031206

4 July 2018

Geometry of the nucleosomal DNA superhelix

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031206

4 July 2018

Structure of the Drosophila nucleosome core particle highlights evolutionary constraints on the H2A-H2B histone dimer

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031206

4 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031206

4 July 2018

DNA stretching and extreme kinking in the nucleosome core

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031206

4 July 2018

A genomic code for nucleosome positioning

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031206

4 July 2018

The nucleosomal surface as a docking station for Kaposi's sarcoma herpesvirus LANA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031206

4 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031206

4 July 2018

Structural characterization of the histone variant macroH2A.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031206

4 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031206

4 July 2018

Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031206

4 July 2018

Molecular recognition of the nucleosomal "supergroove".

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031206

4 July 2018

Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions

1 reference

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4 July 2018

3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures

1 reference

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4 July 2018

The structure of DNA in the nucleosome core

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031206

4 July 2018

An assessment of three dinucleotide parameters to predict DNA curvature by quantitative comparison with experimental data

1 reference

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4 July 2018

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

1 reference

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4 July 2018

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

1 reference

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4 July 2018

Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: alteration of DNA binding specificity through alteration of DNA kinking

1 reference

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4 July 2018

Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: DNA binding specificity based on energetics of DNA kinking

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031206

4 July 2018

Crystal structure of a nucleosome core particle containing the variant histone H2A.Z

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031206

4 July 2018

Asymmetries in the nucleosome core particle at 2.5 A resolution

1 reference

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A-form conformational motifs in ligand-bound DNA structures

1 reference

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The Protein Data Bank

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Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome

1 reference

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4 July 2018

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

1 reference

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4 July 2018

Crystal structure of the nucleosome core particle at 2.8 Å resolution

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Sequence-dependent anisotropic flexibility of B-DNA. A conformational study

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Chromatin Structure: A Repeating Unit of Histones and DNA

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4 July 2018

Sequence-directed curvature of DNA.

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4 July 2018

Static and statistical bending of DNA evaluated by Monte Carlo simulations

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Sequence-dependent nucleosome positioning

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30 October 2018

Sequence structure of hidden 10.4-base repeat in the nucleosomes of C. elegans

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Kinking occurs during molecular dynamics simulations of small DNA minicircles.

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Three sequence rules for chromatin

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

1 reference

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Groove width and depth of B-DNA structures depend on local variation in slide

1 reference

https://pubmed.ncbi.nlm.nih.gov/21208404

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based on heuristic

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NUPARM and NUCGEN: software for analysis and generation of sequence dependent nucleic acid structures

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https://pubmed.ncbi.nlm.nih.gov/21208404

12 December 2020

based on heuristic

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A model for the cooperative binding of eukaryotic regulatory proteins to nucleosomal target sites

1 reference

https://pubmed.ncbi.nlm.nih.gov/21208404

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Sequence structure of human nucleosome DNA

1 reference

https://pubmed.ncbi.nlm.nih.gov/21208404

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Nucleosome positions predicted through comparative genomics

1 reference

https://pubmed.ncbi.nlm.nih.gov/21208404

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Nucleosome DNA bendability matrix (C. elegans)

1 reference

https://pubmed.ncbi.nlm.nih.gov/21208404

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Prediction of nucleosome positioning in genomes: limits and perspectives of physical and bioinformatic approaches

1 reference

https://pubmed.ncbi.nlm.nih.gov/21208404

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Evaluation of elastic rod models with long range interactions for predicting nucleosome stability

1 reference

https://pubmed.ncbi.nlm.nih.gov/21208404

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A self-consistent formulation for analysis and generation of non-uniform DNA structures

1 reference

https://pubmed.ncbi.nlm.nih.gov/21208404

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Mechanism of protein access to specific DNA sequences in chromatin: a dynamic equilibrium model for gene regulation

1 reference

https://pubmed.ncbi.nlm.nih.gov/21208404

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1186/1472-6807-11-1

1 reference

Europe PubMed Central

PubMed publication ID

29 July 2017

Dimensions Publication ID

0 references

PMC publication ID

1 reference

Europe PubMed Central

PubMed publication ID

29 July 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

29 July 2017

ResearchGate publication ID

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