(Q34312985)

25223784

1 August 2017

title

Unraveling the sequence-dependent polymorphic behavior of d(CpG) steps in B-DNA (English)

1 reference

1 August 2017

1

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2 June 2020

Ignacio Faustino

2

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2 June 2020

Richard Lavery

5

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2 June 2020

6

Modesto Orozco

1 reference

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2 June 2020

author name string

Federica Battistini

3

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2 June 2020

Krystyna Zakrzewska

4

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2 June 2020

language of work or name

English

0 references

publication date

15 September 2014

1 reference

25223784

1 August 2017

published in

Nucleic Acids Research

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2 June 2020

volume

42

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2 June 2020

issue

18

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2 June 2020

page(s)

11304-11320

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Creative Commons Attribution 4.0 International

2 June 2020

copyright license

start time

11 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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Understanding the connection between epigenetic DNA methylation and nucleosome positioning from computer simulations

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Backbone FC-H···O hydrogen bonds in 2'F-substituted nucleic acids

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B-DNA structure is intrinsically polymorphic: even at the level of base pair positions

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Structural diversity and specific recognition of four stranded G-quadruplex DNA.

6 July 2018

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Functional relevance of CpG island length for regulation of gene expression

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G+C content dominates intrinsic nucleosome occupancy

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

6 July 2018

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Conformational analysis of nucleic acids revisited: Curves+

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Circular dichroism and conformational polymorphism of DNA.

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DNA-binding drugs caught in action: the latest 3D pictures of drug-DNA complexes.

6 July 2018

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Polymorphism of human telomeric quadruplex structures

6 July 2018

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Towards a molecular dynamics consensus view of B-DNA flexibility

6 July 2018

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A high-resolution atlas of nucleosome occupancy in yeast

6 July 2018

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

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A genomic code for nucleosome positioning

6 July 2018

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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

6 July 2018

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Sequence-selective DNA recognition: natural products and nature's lessons

6 July 2018

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Bioconductor: open software development for computational biology and bioinformatics

6 July 2018

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

6 July 2018

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Water-DNA interactions as studied by X-ray and neutron fibre diffraction

6 July 2018

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Exploring the counterion atmosphere around DNA: what can be learned from molecular dynamics simulations?

6 July 2018

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6 July 2018

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DNA Basepair Step Deformability Inferred from Molecular Dynamics Simulations

6 July 2018

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Molecular dynamics simulations of A. T-rich oligomers: sequence-specific binding of Na+ in the minor groove of B-DNA.

6 July 2018

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The role of the phosphorus BI-BII transition in protein-DNA recognition: the NF-kappaB complex

6 July 2018

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Plasticity in protein-DNA recognition: lac repressor interacts with its natural operator 01 through alternative conformations of its DNA-binding domain

6 July 2018

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Role of mitogen-activated protein kinases in CpG DNA-mediated IL-10 and IL-12 production: central role of extracellular signal-regulated kinase in the negative feedback loop of the CpG DNA-mediated Th1 response

6 July 2018

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Quadruplex structures in nucleic acids

6 July 2018

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

6 July 2018

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Unexpected BII conformer substate population in unoriented hydrated films of the d(CGCGAATTCGCG)2 dodecamer and of native B-DNA from salmon testes

6 July 2018

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

6 July 2018

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The B-DNA dodecamer at high resolution reveals a spine of water on sodium

6 July 2018

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6 July 2018

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6 July 2018

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Asymmetrical distribution of CpG in an 'average' mammalian gene

6 July 2018

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CpG-rich islands and the function of DNA methylation

6 July 2018

1 reference

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Structural comparison of anticancer drug-DNA complexes: adriamycin and daunomycin

6 July 2018

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6 July 2018

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The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides

6 July 2018

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Sequence-dependent elastic properties of DNA.

6 July 2018

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Regulation of murine airway eosinophilia and Th2 cells by antigen-conjugated CpG oligodeoxynucleotides as a novel antigen-specific immunomodulator.

21 January 2018

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Comparison of simple potential functions for simulating liquid water

21 January 2018

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Dynamics of B-DNA on the microsecond time scale

21 January 2018

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21 January 2018

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Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

21 January 2018

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

21 January 2018

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THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method

21 January 2018

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Analyzing ion distributions around DNA.

21 January 2018

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DNAlive: a tool for the physical analysis of DNA at the genomic scale

21 January 2018

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21 January 2018

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21 January 2018

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Estimating the Dimension of a Model

21 January 2018

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Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations

21 January 2018

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Docking studies on DNA intercalators

21 January 2018

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Molecular configuration in sodium thymonucleate. 1953.

21 January 2018

1 reference

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Molecular dynamics with coupling to an external bath

28 October 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU809

Parametrized Models of Aqueous Free Energies of Solvation Based on Pairwise Descreening of Solute Atomic Charges from a Dielectric Medium

21 January 2018

1 reference

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Hydrogen Bond versus Anti-Hydrogen Bond: A Comparative Analysis Based on the Electron Density Topology

21 January 2018

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C−H···O Contacts in the Adenine···Uracil Watson−Crick and Uracil···Uracil Nucleic Acid Base Pairs: Nonempirical ab Initio Study with Inclusion of Electron Correlation Effects

21 January 2018

1 reference

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CpG islands in chromatin organization and gene expression

21 January 2018

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12 December 2020

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12 December 2020

Limiting laws and counterion condensation in polyelectrolyte solutions. IV. The approach to the limit and the extraordinary stability of the charge fraction

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12 December 2020

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

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12 December 2020

Optimised parameters for A-DNA and B-DNA

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12 December 2020

Identifiers

DOI

10.1093/NAR/GKU809

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25223784%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25223784%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

25223784

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25223784%20AND%20SRC:MED&resulttype=core&format=json