(Q40293143)

19 September 2017

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

1 reference

19 September 2017

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4

Modesto Orozco

1 reference

19 September 2017

Manuel Rueda

1

1 reference

19 September 2017

Elena Cubero

series ordinal

2

1 reference

19 September 2017

Charles A Laughton

series ordinal

3

1 reference

19 September 2017

language of work or name

English

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publication date

1 August 2004

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19 September 2017

12

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inferred from page(s)

published in

Biophysical Journal

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19 September 2017

87

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19 September 2017

2

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19 September 2017

800-811

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Theoretical methods for the simulation of nucleic acids.

19 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304490

Molecular dynamics simulations of RNA kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304490

Sodium-ion binding to DNA: detection by ultrafast time-resolved stokes-shift spectroscopy

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304490

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304490

Non-Watson-Crick basepairing and hydration in RNA motifs: molecular dynamics of 5S rRNA loop E.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304490

A crystallographic study of the binding of 13 metal ions to two related RNA duplexes

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304490

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304490

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304490

On the competition between water, sodium ions, and spermine in binding to DNA: a molecular dynamics computer simulation study

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304490

Critical effect of the N2 amino group on structure, dynamics, and elasticity of DNA polypurine tracts

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304490

DNA-cation interactions: quo vadis?

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304490

Molecular dynamics simulation of nucleic acids: successes, limitations, and promise

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304490

Cooperativity in drug-DNA recognition: a molecular dynamics study

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304490

Locating monovalent cations in the grooves of B-DNA

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304490

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304490

Detection of alkali metal ions in DNA crystals using state-of-the-art X-ray diffraction experiments

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304490

Preferential counterion binding to A-tract DNA oligomers

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304490

DNA structure: what's in charge?

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304490

Molecular dynamics simulation of nucleic acids

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304490

Electrostatic mechanisms of DNA deformation

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304490

Nucleic acids: theory and computer simulation, Y2K.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304490

Sequence-specific binding of counterions to B-DNA.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304490

Sodium and chlorine ions as part of the DNA solvation shell

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304490

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304490

DNA structure: cations in charge?

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304490

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304490

Structure of the potassium form of CGCGAATTCGCG: DNA deformation by electrostatic collapse around inorganic cations

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304490

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304490

Modeling DNA in aqueous solutions: theoretical and computer simulation studies on the ion atmosphere of DNA.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304490

Structure of a B-DNA dodecamer: conformation and dynamics

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304490

Molecular dynamics simulation of the hydration shell of a B-DNA decamer reveals two main types of minor-groove hydration depending on groove width

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304490

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304490

Simulations of the molecular dynamics of nucleic acids

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304490

Sodium ions and water molecules in the structure of poly(dA).poly(dT).

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304490

Classical molecular interaction potentials: improved setup procedure in molecular dynamics simulations of proteins.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304490

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

20 August 2018

1 reference

12 December 2020

Influence of the dynamic positions of cations on the structure of the DNA minor groove: sequence-dependent effects

1 reference

12 December 2020

The Structure and Dynamics of DNA in the Gas Phase

1 reference

12 December 2020

Water and Ions in a High Resolution Structure of B-DNA

1 reference

12 December 2020

Monte Carlo calculations of ion distributions surrounding the oligonucleotide d(ATATATATAT)2 in the B, A, and wrinkled D conformations

1 reference

12 December 2020

The Mg2+ binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations

1 reference

12 December 2020

Theoretical Studies of d(A:T)-Based Parallel-Stranded DNA Duplexes

1 reference

12 December 2020

10.1529/BIOPHYSJ.104.040451

Identifiers

DOI

1 reference

19 September 2017

1 reference

19 September 2017

PubMed publication ID

15298889

1 reference