(Q37008231)

17 August 2017

1 reference

title

RNA folding: thermodynamic and molecular descriptions of the roles of ions (English)

1 reference

17 August 2017

David E Draper

1

1 reference

PMCID

2599833

17 August 2017

language of work or name

English

0 references

publication date

3 October 2008

1 reference

17 August 2017

1 reference

17 August 2017

95

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17 August 2017

5489-5495

1 reference

17 August 2017

12

1 reference

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

17 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599833

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599833

Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599833

Structure and mechanism of a metal-sensing regulatory RNA

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599833

Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599833

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599833

Folding of the adenine riboswitch

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599833

Evidence for preorganization of the glmS ribozyme ligand binding pocket

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599833

Ion-mediated nucleic acid helix-helix interactions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599833

Nucleic acid helix stability: effects of salt concentration, cation valence and size, and chain length

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599833

RNA tertiary interactions mediate native collapse of a bacterial group I ribozyme

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599833

Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599833

The contribution of metal ions to the structural stability of the large ribosomal subunit

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599833

Fluorescence measurements of free [Mg2+] by use of mag-fura 2 in Salmonella enterica

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599833

Freely diffusing single hairpin ribozymes provide insights into the role of secondary structure and partially folded states in RNA folding

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599833

Single-molecule studies highlight conformational heterogeneity in the early folding steps of a large ribozyme

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599833

A compact RNA tertiary structure contains a buried backbone-K+ complex

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599833

A thermodynamic framework for Mg2+ binding to RNA.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599833

Is counterion delocalization responsible for collapse in RNA folding?

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599833

Energetics and cooperativity of tertiary hydrogen bonds in RNA structure

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599833

Crystal structure of a group I ribozyme domain: principles of RNA packing

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599833

Conformational transitions of duplex and triplex nucleic acid helices: thermodynamic analysis of effects of salt concentration on stability using preferential interaction coefficients

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599833

Transfer RNA in solution: selected topics

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599833

Methods for measurement of intracellular magnesium: NMR and fluorescence

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599833

Electrostatic interactions in a peptide--RNA complex.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599833

Small angle X-ray scattering reveals a compact intermediate in RNA folding

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599833

Conformational changes of transfer RNA. The role of magnesium(II)

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599833

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

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599833

Inter-DNA attraction mediated by divalent counterions.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599833

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

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599833

Compaction of a bacterial group I ribozyme coincides with the assembly of core helices.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599833

The linkage between magnesium binding and RNA folding.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599833

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

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599833

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

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599833

Analysis of effects of salts and uncharged solutes on protein and nucleic acid equilibria and processes: a practical guide to recognizing and interpreting polyelectrolyte effects, Hofmeister effects, and osmotic effects of salts.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599833

Principles of RNA Compaction: Insights from the Equilibrium Folding Pathway of the P4-P6 RNA Domain in Monovalent Cations

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599833

Role of counterion condensation in folding of the Tetrahymena ribozyme. I. Equilibrium stabilization by cations

4 December 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2599833

A collapsed non-native RNA folding state

4 December 2018

1 reference

12 December 2020

Stabilization of RNA tertiary structure by monovalent cations

1 reference

12 December 2020

Counterion distribution around DNA probed by solution X-ray scattering

1 reference

12 December 2020

Interactions of polyelectrolytes with simple electrolytes. II. Donnan equilibria obtained with DNA in solutions of 1-1 electrolytes

1 reference

12 December 2020

Conformational changes of transfer ribonucleic acid. Equilibrium phase diagrams

1 reference

12 December 2020

Interactions of some naturally occurring cations with phenylalanine and initiator tRNA from yeast as reflected by their thermal stability

1 reference

12 December 2020

Characterization of the cytoplasm of Escherichia coli K-12 as a function of external osmolarity. Implications for protein-DNA interactions in vivo

1 reference

12 December 2020

RNA Folding at Millisecond Intervals by Synchrotron Hydroxyl Radical Footprinting

1 reference

12 December 2020

Structure of a folding intermediate reveals the interplay between core and peripheral elements in RNA folding

1 reference

12 December 2020

Calculation of the binding free energy for magnesium-RNA interactions

1 reference

12 December 2020

10.1529/BIOPHYSJ.108.131813

Identifiers

DOI

1 reference

17 August 2017

1 reference

17 August 2017

1 reference

PMCID

2599833