(Q35769969)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22385853%20AND%20SRC:MED&resulttype=core&format=json

24 January 2020

title

RNA and its ionic cloud: solution scattering experiments and atomically detailed simulations (English)

1 reference

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24 January 2020

3

1 reference

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24 January 2020

author name string

Serdal Kirmizialtin

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22385853%20AND%20SRC:MED&resulttype=core&format=json

24 January 2020

Suzette A Pabit

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22385853%20AND%20SRC:MED&resulttype=core&format=json

24 January 2020

Lois Pollack

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22385853%20AND%20SRC:MED&resulttype=core&format=json

24 January 2020

Ron Elber

5

1 reference

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24 January 2020

language of work or name

English

0 references

publication date

21 February 2012

1 reference

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24 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22385853%20AND%20SRC:MED&resulttype=core&format=json

24 January 2020

volume

102

1 reference

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24 January 2020

issue

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22385853%20AND%20SRC:MED&resulttype=core&format=json

24 January 2020

page(s)

819-828

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22385853%20AND%20SRC:MED&resulttype=core&format=json

The ionic atmosphere around A-RNA: Poisson-Boltzmann and molecular dynamics simulations.

24 January 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283807

Interpreting protein/DNA interactions: distinguishing specific from non-specific and electrostatic from non-electrostatic components

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283807

Counting ions around DNA with anomalous small-angle X-ray scattering.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283807

Ion-RNA interactions thermodynamic analysis of the effects of mono- and divalent ions on RNA conformational equilibria

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283807

Computational exploration of mobile ion distributions around RNA duplex

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283807

Both helix topology and counterion distribution contribute to the more effective charge screening in dsRNA compared with dsDNA.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283807

Direct quantitation of Mg2+-RNA interactions by use of a fluorescent dye.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283807

Critical assessment of nucleic acid electrostatics via experimental and computational investigation of an unfolded state ensemble

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283807

Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283807

Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283807

RNA helix stability in mixed Na+/Mg2+ solution

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283807

Charge density of divalent metal cations determines RNA stability

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283807

Mg2+-RNA interaction free energies and their relationship to the folding of RNA tertiary structures

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283807

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283807

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283807

Simulation and modeling of nucleic acid structure, dynamics and interactions

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283807

A guide to ions and RNA structure

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283807

Non–coding RNA genes and the modern RNA world

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283807

A thermodynamic framework for Mg2+ binding to RNA.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283807

Electrostatics of nanosystems: application to microtubules and the ribosome

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283807

Molecular dynamics simulation of nucleic acids

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283807

On the role of magnesium ions in RNA stability

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283807

Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283807

Effects of polyvalent cations on the folding of an rRNA three-way junction and binding of ribosomal protein S15

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283807

Salt effects on nucleic acids

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283807

Electrostatic interactions in macromolecules: theory and applications

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283807

Theory of the delocalized binding of Mg(II) to DNA: preliminary analysis for low binding levels

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283807

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283807

Biophysical, chemical, and functional probes of RNA structure, interactions and folding: Part A. Preface.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283807

Importance of partially unfolded conformations for Mg(2+)-induced folding of RNA tertiary structure: structural models and free energies of Mg2+ interactions.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283807

Inter-DNA attraction mediated by divalent counterions.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283807

Tertiary structure of an RNA pseudoknot is stabilized by "diffuse" Mg2+ ions.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283807

The crystal and solution structures of glyceraldehyde-3-phosphate dehydrogenase reveal different quaternary structures.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283807

Systematic comparison of force fields for microscopic simulations of NaCl in aqueous solutions: diffusion, free energy of hydration, and structural properties.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283807

Mg(2+) binding to tRNA revisited: the nonlinear Poisson-Boltzmann model.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283807

Calculating the electrostatic properties of RNA provides new insights into molecular interactions and function

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283807

Counterion Charge Density Determines the Position and Plasticity of RNA Folding Transition States

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283807

CrystalVersusSolution Structures of Thiamine Diphosphate-dependent Enzymes

15 November 2018

1 reference

12 December 2020

Stabilization of RNA tertiary structure by monovalent cations

1 reference

12 December 2020

Ion atmosphere of three-way junction nucleic acid

1 reference

12 December 2020

Parameters of monovalent ions in the AMBER-99 forcefield: assessment of inaccuracies and proposed improvements

1 reference

12 December 2020

Using anomalous small angle X-ray scattering to probe the ion atmosphere around nucleic acids

1 reference

12 December 2020

A magnesium ion core at the heart of a ribozyme domain

1 reference

12 December 2020

Counterion condensation revisited

1 reference

12 December 2020

10.1016/J.BPJ.2012.01.013

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22385853%20AND%20SRC:MED&resulttype=core&format=json

24 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22385853%20AND%20SRC:MED&resulttype=core&format=json

24 January 2020

PubMed publication ID

22385853

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22385853%20AND%20SRC:MED&resulttype=core&format=json