(Q40207477)

18 September 2017

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

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18 September 2017

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3

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author name string

Nikolay Korolev

series ordinal

1

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18 September 2017

Alexander P Lyubartsev

series ordinal

2

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18 September 2017

Lars Nordenskiöld

series ordinal

4

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18 September 2017

language of work or name

English

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publication date

1 June 2002

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18 September 2017

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18 September 2017

82

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18 September 2017

6

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18 September 2017

2860-2875

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Locating monovalent cations in the grooves of B-DNA

18 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302075

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=1302075

Water and ion binding around r(UpA)12 and d(TpA)12 oligomers--comparison with RNA and DNA (CpG)12 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=1302075

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=1302075

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302075

Structural basis of polyamine-DNA recognition: spermidine and spermine interactions with genomic B-DNAs of different GC content probed by Raman 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=1302075

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=1302075

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=1302075

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302075

X-ray crystallographic analysis of the hydration of A- and B-form DNA at atomic resolution

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302075

Water and monovalent ions in the minor groove of B-DNA oligonucleotides as seen by NMR.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302075

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=1302075

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=1302075

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=1302075

B-DNA at atomic resolution reveals extended hydration patterns

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302075

Spermine inhibition of the 2,5-diaziridinyl-1,4-benzoquinone (DZQ) crosslinking reaction with DNA duplexes containing poly(purine). poly(pyrimidine) 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=1302075

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=1302075

Molecular dynamics simulations of DNA in solutions with different counter-ions.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302075

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=1302075

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=1302075

Hydration of the phosphate group in double-helical 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=1302075

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=1302075

A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions, and solvation

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302075

Nine polymorphic crystal structures of d(CCGGGCCCGG), d(CCGGGCCm5CGG), d(Cm5CGGGCCm5CGG) and d(CCGGGCC(Br)5CGG) in three different conformations: effects of spermine binding and methylation on the bending and condensation of A-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=1302075

Hydration of the DNA bases is local

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302075

Spermine binding to GC-rich DNA: experimental and theoretical studies

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302075

The low-temperature crystal structure of the pure-spermine form of Z-DNA reveals binding of a spermine molecule in the minor groove

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302075

Spermine-DNA interactions: a theoretical 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=1302075

The origin of the A to B transition in DNA fibers and films

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302075

Molecular mechanics of the interactions of spermine with DNA: DNA bending as a result of ligand binding

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302075

Measuring the geometry of DNA grooves.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302075

A molecular dynamics simulation of a polyamine-induced conformational change of DNA. A possible mechanism for the B to Z transition

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302075

Spermine: an "invisible" component in the crystals of B-DNA. A grand canonical Monte Carlo and molecular dynamics simulation study

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302075

Localisation and dynamics of sodium counterions around DNA in solution from molecular dynamics simulation

20 August 2018

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975628-2

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975628-2

Structure of a B-DNA dodecamer. III. Geometry of hydration

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975628-2

Molecular dynamics simulation study of DNA dodecamer d(CGCGAATTCGCG) in solution: conformation and hydration

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975628-2

A molecular simulation picture of DNA hydration around A- and B-DNA

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975628-2

Modeling high-resolution hydration patterns in correlation with DNA sequence and conformation

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975628-2

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975628-2

A Brillouin scattering study of the hydration of Li- and Na-DNA films

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975628-2

M.DynaMix – a scalable portable parallel MD simulation package for arbitrary molecular mixtures

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975628-2

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975628-2

Radioprotection of DNA by spermine: a molecular modelling approach

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975628-2

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975628-2

A “Hydrat-Ion” Spine in a B-DNA Minor Groove

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975628-2

Molecular-dynamics study of atomic motions in water

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975628-2

Reversible multiple time scale molecular dynamics

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975628-2

Spermine-nucleic acid interactions: a theoretical study

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975628-2

10.1016/S0006-3495(02)75628-2

7 January 2021

Identifiers

DOI

1 reference

18 September 2017

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18 September 2017

1 reference