RNA and its ionic cloud: solution scattering experiments and atomically detailed simulations. (Q35769969)

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24 January 2020

title

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

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24 January 2020

3

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24 January 2020

author name string

Serdal Kirmizialtin

1

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24 January 2020

Suzette A Pabit

2

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24 January 2020

Lois Pollack

4

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24 January 2020

Ron Elber

5

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24 January 2020

publication date

21 February 2012

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24 January 2020

language of work or name

0 references

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24 January 2020

volume

102

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24 January 2020

issue

4

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24 January 2020

page(s)

819-828

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

24 January 2020

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

12 July 2018

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

12 July 2018

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

12 July 2018

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Computational exploration of mobile ion distributions around RNA duplex

12 July 2018

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

12 July 2018

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

12 July 2018

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

12 July 2018

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

12 July 2018

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Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids

12 July 2018

1 reference

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RNA helix stability in mixed Na+/Mg2+ solution

12 July 2018

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Charge density of divalent metal cations determines RNA stability

12 July 2018

1 reference

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

12 July 2018

1 reference

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12 July 2018

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12 July 2018

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Simulation and modeling of nucleic acid structure, dynamics and interactions

12 July 2018

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A guide to ions and RNA structure

12 July 2018

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Non–coding RNA genes and the modern RNA world

12 July 2018

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A thermodynamic framework for Mg 2+ binding to RNA

12 July 2018

1 reference

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Electrostatics of nanosystems: application to microtubules and the ribosome

12 July 2018

1 reference

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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

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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

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Electrostatic interactions in macromolecules: theory and applications

12 July 2018

1 reference

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

12 July 2018

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

12 July 2018

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

12 July 2018

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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

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Inter-DNA attraction mediated by divalent counterions

25 September 2018

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

25 September 2018

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

25 September 2018

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

25 September 2018

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

25 September 2018

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

25 September 2018

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

25 September 2018

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CrystalVersusSolution Structures of Thiamine Diphosphate-dependent Enzymes

15 November 2018

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12 December 2020

Stabilization of RNA tertiary structure by monovalent cations

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12 December 2020

Ion atmosphere of three-way junction nucleic acid

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12 December 2020

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

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12 December 2020

Using Anomalous Small Angle X-Ray Scattering to Probe the Ion Atmosphere Around Nucleic Acids

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12 December 2020

A magnesium ion core at the heart of a ribozyme domain

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12 December 2020

Counterion condensation revisited

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12 December 2020

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Identifiers

DOI

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24 January 2020

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24 January 2020

PubMed publication ID

22385853

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