(Q30881695)

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A molecular dynamics simulation study of oriented DNA with polyamine and sodium counterions: diffusion and averaged binding of water and cations.

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scholarly article

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Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:14530445%20AND%20SRC:MED&resulttype=core&format=json

19 December 2019

A molecular dynamics simulation study of oriented DNA with polyamine and sodium counterions: diffusion and averaged binding of water and cations (English)

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:14530445%20AND%20SRC:MED&resulttype=core&format=json

19 December 2019

molecular dynamics simulation

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Alexander P Lyubartsev

2

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Europe PubMed Central

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19 December 2019

Aatto Laaksonen

3

1 reference

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19 December 2019

author name string

Nikolay Korolev

1

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19 December 2019

Lars Nordenskiöld

4

1 reference

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19 December 2019

language of work or name

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publication date

1 October 2003

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19 December 2019

Nucleic Acids Research

1 reference

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19 December 2019

31

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19 December 2019

20

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19 December 2019

5971-5981

1 reference

Europe PubMed Central

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19 December 2019

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=219480

21 June 2018

DNA polymorphism: a comparison of force fields for nucleic acids

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=219480

21 June 2018

Charge transport in DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=219480

21 June 2018

Molecular dynamics applied to nucleic acids

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=219480

21 June 2018

Solvation and hydration of proteins and nucleic acids: a theoretical view of simulation and experiment

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=219480

21 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=219480

21 June 2018

Polyamine-nucleic acid interactions and the effects on structure in oriented DNA fibers

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=219480

21 June 2018

DNA condensation by polyamines: a laser light scattering study of structural effects

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=219480

21 June 2018

X-ray crystallographic observation of "in-line" and "adjacent" conformations in a bulged self-cleaving RNA/DNA hybrid

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=219480

21 June 2018

Polyamines in cell growth and cell death: molecular mechanisms and therapeutic applications

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=219480

21 June 2018

Fourier transform Raman study of the structural specificities on the interaction between DNA and biogenic polyamines

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=219480

21 June 2018

Molecular dynamics simulation of nucleic acids

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=219480

21 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=219480

21 June 2018

Polyamines: mysterious modulators of cellular functions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=219480

21 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=219480

21 June 2018

Molecular dynamics simulations of the d(CCAACGTTGG)(2) decamer: influence of the crystal environment.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=219480

21 June 2018

Sodium and chlorine ions as part of the DNA solvation shell

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=219480

21 June 2018

Ionic and structural specificity effects of natural and synthetic polyamines on the aggregation and resolubilization of single-, double-, and triple-stranded DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=219480

21 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=219480

21 June 2018

Hydration of the phosphate group in double-helical DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=219480

21 June 2018

DNA bending by small, mobile multivalent cations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=219480

21 June 2018

DNA condensation by multivalent cations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=219480

21 June 2018

Precipitation of DNA by polyamines: a polyelectrolyte behavior

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=219480

21 June 2018

Evidence for a hydroxide ion bridging two magnesium ions at the active site of the hammerhead ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=219480

21 June 2018

Hydration of the DNA bases is local

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=219480

21 June 2018

Salt-nucleic acid interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=219480

21 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=219480

21 June 2018

Relative affinities of divalent polyamines and of their N-methylated analogs for helical DNA determined by sodium-23 NMR

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=219480

21 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=219480

21 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=219480

21 June 2018

Application of the Poisson Boltzmann polyelectrolyte model for analysis of thermal denaturation of DNA in the presence of Na+ and polyamine cations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=219480

25 November 2018

Long-range oxidative damage to DNA: protection of guanines by a nonspecifically bound disulfide.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=219480

25 November 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=219480

25 November 2018

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/14530445

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Ionic and structural effects on the thermal helix-coil transition of DNA complexed with natural and synthetic polyamines

1 reference

https://pubmed.ncbi.nlm.nih.gov/14530445

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Thermodynamics of DNA binding and condensation: isothermal titration calorimetry and electrostatic mechanism

1 reference

https://pubmed.ncbi.nlm.nih.gov/14530445

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Molecular-dynamics study of atomic motions in water

1 reference

https://pubmed.ncbi.nlm.nih.gov/14530445

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Equilibrium dialysis studies of polyamine binding to DNA

1 reference

https://pubmed.ncbi.nlm.nih.gov/14530445

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Radioprotection of DNA by spermine: a molecular modelling approach

1 reference

https://pubmed.ncbi.nlm.nih.gov/14530445

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/14530445

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1093/NAR/GKG802

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:14530445%20AND%20SRC:MED&resulttype=core&format=json

19 December 2019

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:14530445%20AND%20SRC:MED&resulttype=core&format=json

19 December 2019

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:14530445%20AND%20SRC:MED&resulttype=core&format=json

19 December 2019

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