Effects of osmolytes on RNA secondary and tertiary structure stabilities and RNA-Mg2+ interactions (Q41350567)

29 September 2017

Effects of osmolytes on RNA secondary and tertiary structure stabilities and RNA-Mg2+ interactions (English)

1 reference

29 September 2017

Dominic Lambert

1

1 reference

PMCID

1995082

29 September 2017

David E Draper

series ordinal

2

1 reference

PMCID

1995082

29 September 2017

language of work or name

English

0 references

publication date

5 May 2007

1 reference

Journal of Molecular Biology

29 September 2017

1 reference

29 September 2017

370

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29 September 2017

5

1 reference

29 September 2017

993-1005

1 reference

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

Predicting the energetics of osmolyte-induced protein folding/unfolding.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

An abundance of RNA regulators

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

Protein adaptations to temperature and pressure: complementary roles of adaptive changes in amino acid sequence and internal milieu

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

Osmolytes stimulate the reconstitution of functional 50S ribosomes from in vitro transcripts of Escherichia coli 23S rRNA.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

Metal ions and flexibility in a viral RNA pseudoknot at atomic resolution

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

Thermodynamics of interactions of urea and guanidinium salts with protein surface: relationship between solute effects on protein processes and changes in water-accessible surface area

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

A thermodynamic framework for Mg2+ binding to RNA.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

Translational repression of the Escherichia coli alpha operon mRNA: importance of an mRNA conformational switch and a ternary entrapment complex

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

Crystal structure of a conserved ribosomal protein-RNA complex

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

The structure of an RNA "kissing" hairpin complex of the HIV TAR hairpin loop and its complement

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

Betaine can eliminate the base pair composition dependence of DNA melting

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

Living with water stress: evolution of osmolyte systems

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

How do proteins recognize specific RNA sites? New clues from autogenously regulated ribosomal proteins

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

Control of prokaryotic translational initiation by mRNA secondary structure

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

Water as ligand: preferential binding and exclusion of denaturants in protein unfolding

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

Counteraction of urea destabilization of protein structure by methylamine osmoregulatory compounds of elasmobranch fishes

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

The Stability of Globular Protein

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

Solute probes of conformational changes in open complex (RPo) formation by Escherichia coli RNA polymerase at the lambdaPR promoter: evidence for unmasking of the active site in the isomerization step and for large-scale coupled folding in the subse

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

Use of urea and glycine betaine to quantify coupled folding and probe the burial of DNA phosphates in lac repressor-lac operator binding

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

Effects of osmolarity, ions and compatible osmolytes on cell-free protein synthesis

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

Bases defining an ammonium and magnesium ion-dependent tertiary structure within the large subunit ribosomal RNA.

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

Thermodynamics of RNA folding in a conserved ribosomal RNA domain.

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

Solution studies of the nucleic acid bases and related model compounds. Solubility in aqueous alcohol and glycol solutions

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

A test of the linear extrapolation of unfolding free energy changes over an extended denaturant concentration range

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

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

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

Preferential interactions of glycine betaine and of urea with DNA: implications for DNA hydration and for effects of these solutes on DNA stability

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

The exclusion of glycine betaine from anionic biopolymer surface: why glycine betaine is an effective osmoprotectant but also a compatible solute

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

Additive transfer free energies of the peptide backbone unit that are independent of the model compound and the choice of concentration scale

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

Trimethylamine N-oxide stabilizes RNA tertiary structure and attenuates the denaturating effects of urea

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

The linkage between magnesium binding and RNA folding.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

Quantitative analysis of nucleic acid three-dimensional structures.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

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

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

The interpretation of Mg(2+) binding isotherms for nucleic acids using Poisson-Boltzmann theory.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

An integrated model of the transcription complex in elongation, termination, and editing.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

Biophysical compensation mechanisms buffering E. coli protein-nucleic acid interactions against changing environments.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1995082

Effects of hydration, ion release, and excluded volume on the melting of triplex and duplex DNA

19 August 2018

1 reference

12 December 2020

The first crystal structure of an RNA racemate

1 reference

12 December 2020

Effect of ethylene glycol, urea, and N-methylated glycines on DNA thermal stability: the role of DNA base pair composition and hydration

1 reference

12 December 2020

Enthalpies of DNA melting in the presence of osmolytes

1 reference

12 December 2020

Applicability of urea in the thermodynamic analysis of secondary and tertiary RNA folding

1 reference

12 December 2020

Energetics of a strongly pH dependent RNA tertiary structure in a frameshifting pseudoknot

1 reference

12 December 2020

Vapor pressure osmometry studies of osmolyte-protein interactions: implications for the action of osmoprotectants in vivo and for the interpretation of "osmotic stress" experiments in vitro

1 reference

12 December 2020

Stabilization of RNA tertiary structure by monovalent cations

1 reference

12 December 2020

Mg2+-dependent compaction and folding of yeast tRNAPhe and the catalytic domain of the B. subtilis RNase P RNA determined by small-angle X-ray scattering

1 reference

12 December 2020

Solution studies of the nucleic acid bases and related model compounds. Solubility in aqueous urea and amide solutions

1 reference

12 December 2020

Solvent-accessible surfaces of nucleic acids

1 reference

12 December 2020

Base-stacking and base-pairing contributions to helix stability: thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp

1 reference

12 December 2020

Selective binding and solvent denaturation

1 reference

12 December 2020

Complexes formed by complementary RNA stem-loops. Their formations, structures and interaction with ColE1 Rom protein

1 reference

12 December 2020

The peptide backbone plays a dominant role in protein stabilization by naturally occurring osmolytes

1 reference

12 December 2020

Forcing thermodynamically unfolded proteins to fold

1 reference

12 December 2020

Responses of E. coli to osmotic stress: large changes in amounts of cytoplasmic solutes and water

1 reference

12 December 2020

10.1016/J.JMB.2007.03.080

Identifiers

DOI

1 reference

29 September 2017

1 reference

29 September 2017

1 reference

PMCID

1995082