(Q36109636)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22844516%20AND%20SRC:MED&resulttype=core&format=json

9 February 2020

title

Mg2+ in the major groove modulates B-DNA structure and dynamics (English)

1 reference

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9 February 2020

1

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9 February 2020

Catherine Etchebest

4

1 reference

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9 February 2020

author name string

Olivier Boittin

2

1 reference

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9 February 2020

Oliver Mauffret

3

1 reference

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9 February 2020

Brigitte Hartmann

5

1 reference

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9 February 2020

language of work or name

English

0 references

publication date

23 July 2012

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9 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22844516%20AND%20SRC:MED&resulttype=core&format=json

9 February 2020

volume

7

1 reference

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9 February 2020

issue

7

1 reference

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9 February 2020

page(s)

e41704

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Creative Commons Attribution 4.0 International

9 February 2020

copyright license

start time

23 July 2012

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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1 reference

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Properties of the Nucleic-acid Bases in Free and Watson-Crick Hydrogen-bonded States: Computational Insights into the Sequence-dependent Features of Double-helical DNA

2 October 2017

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Understanding the sequence-dependence of DNA groove dimensions: implications for DNA interactions

2 October 2017

1 reference

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Using soft X-rays for a detailed picture of divalent metal binding in the nucleosome

2 October 2017

1 reference

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Differential stability of DNA crossovers in solution mediated by divalent cations

2 October 2017

1 reference

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A measure of bending in nucleic acids structures applied to A-tract DNA.

2 October 2017

1 reference

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DNA structures from phosphate chemical shifts

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

Intrinsic flexibility of B-DNA: the experimental TRX scale

2 October 2017

1 reference

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Conformational analysis of nucleic acids revisited: Curves+

2 October 2017

1 reference

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The interaction of manganese ions with DNA

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

Solution structure of a purine rich hexaloop hairpin belonging to PGY/MDR1 mRNA and targeted by antisense oligonucleotides

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

The Amber biomolecular simulation programs

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

Ion motions in molecular dynamics simulations on DNA.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

DNA and its counterions: a molecular dynamics study

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

The structure of DNA in the nucleosome core

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

A comparative study of DNA complexation with Mg(II) and Ca(II) in aqueous solution: major and minor grooves bindings

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

Cations as hydrogen bond donors: a view of electrostatic interactions in DNA.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

DNA-dependent divalent cation binding in the nucleosome core particle

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

DNA-cation interactions: quo vadis?

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

Intrinsic bending and deformability at the T-A step of CCTTTAAAGG: a comparative analysis of T-A and A-T steps within A-tracts

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

Electrostatics of nanosystems: application to microtubules and the ribosome

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

Magnesium increases the curvature of duplex DNA that contains dA tracts

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

DNA-cation interactions: The major and minor grooves are flexible ionophores.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

1 A crystal structures of B-DNA reveal sequence-specific binding and groove-specific bending of DNA by magnesium and calcium

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

Water and ion binding around RNA and DNA (C,G) oligomers

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

Solvent organization in an oligonucleotide crystal. The structure of d(GCGAATTCG)2 at atomic resolution

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

Conformational flexibility of B-DNA at 0.74 A resolution: d(CCAGTACTGG)(2)

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

Absence of minor groove monovalent cations in the crosslinked dodecamer C-G-C-G-A-A-T-T-C-G-C-G

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

Structure of d(CGCGAATTCGCG) in the presence of Ca(2+) ions

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

Atomic-resolution crystal structures of B-DNA reveal specific influences of divalent metal ions on conformation and packing

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

Structure of the oligonucleotide d(CGTATATACG) as a site-specific complex with nickel ions

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

Binding sites and dynamics of ammonium ions in a telomere repeat DNA quadruplex.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

Strained DNA is kinked by low concentrations of Zn2+

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

BI-BII transitions in B-DNA.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

Crystallographic analysis of C-C-A-A-G-C-T-T-G-G and its implications for bending in B-DNA

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

Sequence-selective metal ion binding to DNA oligonucleotides.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

Sequence-selective metal ion binding to DNA hexamers.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

Molecular electrostatic potential of the nucleic acids

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

The binding of manganese(II) and zinc(II) to the synthetic oligonucleotide d(C-G-C-G-A-A-T-T-C-G-C-G)2. A 1H NMR study

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

The structure of B-helical C-G-A-T-C-G-A-T-C-G and comparison with C-C-A-A-C-G-T-T-G-G. The effect of base pair reversals

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

Molecular dynamics simulations of an oligonucleotide duplex with adenine tracts phased by a full helix turn.

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

Structure of a B-DNA decamer with a central T-A step: C-G-A-T-T-A-A-T-C-G

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3402463

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

2 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0041704

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/10.1371%2FJOURNAL.PONE.0041704

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0041704

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0041704

The Dickerson-Drew B-DNA Dodecamer Revisited at Atomic Resolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0041704

Molecular dynamics with coupling to an external bath

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0041704

A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat

21 January 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

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

1 reference

12 December 2020

Physiological concentration of magnesium ions induces a strong macroscopic curvature in GGGCCC-containing DNA

1 reference

12 December 2020

10.1371/JOURNAL.PONE.0041704

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22844516%20AND%20SRC:MED&resulttype=core&format=json

9 February 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22844516%20AND%20SRC:MED&resulttype=core&format=json

9 February 2020

PubMed publication ID

22844516

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22844516%20AND%20SRC:MED&resulttype=core&format=json