(Q36847510)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23510511%20AND%20SRC:MED&resulttype=core&format=json

26 February 2020

title

Quantifying functional group interactions that determine urea effects on nucleic acid helix formation (English)

1 reference

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26 February 2020

11

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26 February 2020

author name string

Emily J Guinn

1

1 reference

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26 February 2020

Jeffrey J Schwinefus

2

1 reference

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26 February 2020

Hyo Keun Cha

3

1 reference

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26 February 2020

Joseph L McDevitt

4

1 reference

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26 February 2020

Wolf E Merker

5

1 reference

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26 February 2020

Ryan Ritzer

6

1 reference

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26 February 2020

Gregory W Muth

7

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26 February 2020

Samuel W Engelsgjerd

8

1 reference

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26 February 2020

Kathryn E Mangold

9

1 reference

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26 February 2020

Perry J Thompson

10

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26 February 2020

M Thomas Record

12

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26 February 2020

language of work or name

English

0 references

publication date

3 April 2013

1 reference

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Journal of the American Chemical Society

26 February 2020

published in

1 reference

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26 February 2020

volume

135

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26 February 2020

issue

15

1 reference

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26 February 2020

page(s)

5828-5838

1 reference

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Denaturation of RNA secondary and tertiary structure by urea: simple unfolded state models and free energy parameters account for measured m-values

26 February 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655208

Molecular mechanisms of ion-specific effects on proteins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655208

Quantifying why urea is a protein denaturant, whereas glycine betaine is a protein stabilizer

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655208

Separation of preferential interaction and excluded volume effects on DNA duplex and hairpin stability

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655208

Mechanism of bacterial transcription initiation: RNA polymerase - promoter binding, isomerization to initiation-competent open complexes, and initiation of RNA synthesis

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655208

Why Hofmeister effects of many salts favor protein folding but not DNA helix formation.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655208

Urea destabilizes RNA by forming stacking interactions and multiple hydrogen bonds with nucleic acid bases

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655208

Interactions of the osmolyte glycine betaine with molecular surfaces in water: thermodynamics, structural interpretation, and prediction of m-values.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655208

Urea, but not guanidinium, destabilizes proteins by forming hydrogen bonds to the peptide group.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655208

Late steps in the formation of E. coli RNA polymerase-lambda P R promoter open complexes: characterization of conformational changes by rapid [perturbant] upshift experiments

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655208

Hydrophobicity of Long Chain n-Alkyl Carboxylic Acids, as Measured by Their Distribution Between Heptane and Aqueous Solutions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655208

Towards understanding the catalytic core structure of the spliceosome

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655208

Thermal and urea-induced unfolding of the marginally stable lac repressor DNA-binding domain: a model system for analysis of solute effects on protein processes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655208

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655208

Cation-pi bonding and amino-aromatic interactions in the biomolecular recognition of substituted ammonium ligands

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655208

Denaturant m values and heat capacity changes: relation to changes in accessible surface areas of protein unfolding

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655208

Areas, volumes, packing and protein 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=3655208

Introductory lecture: interpreting and predicting Hofmeister salt ion and solute effects on biopolymer and model processes using the solute partitioning model

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655208

Key roles of the downstream mobile jaw of Escherichia coli RNA polymerase in transcription initiation.

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655208

Probing DNA binding, DNA opening, and assembly of a downstream clamp/jaw in Escherichia coli RNA polymerase-lambdaP(R) promoter complexes using salt and the physiological anion glutamate

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655208

Thermodynamic origin of hofmeister ion effects

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655208

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

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655208

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

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655208

The effects of salts on the free energies of nonpolar groups in model peptides

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655208

Calorimetric measurements of the transition enthalpy of DNA in aqueous urea solutions

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655208

Investigating the hydrogen-bonding model of urea denaturation.

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655208

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

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655208

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

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655208

Preferential interactions in aqueous solutions of urea and KCl

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655208

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

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655208

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

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3655208

Human telomerase RNA pseudoknot and hairpin thermal stability with glycine betaine and urea: preferential interactions with RNA secondary and tertiary structures

5 September 2018

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

Physical and chemical characterization of two- and three-stranded adenine-thymine and adenine-uracil homopolymer complexes

1 reference

12 December 2020

Enthalpy and heat capacity changes for formation of an oligomeric DNA duplex: interpretation in terms of coupled processes of formation and association of single-stranded helices

1 reference

12 December 2020

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

1 reference

12 December 2020

Hydrophobicities of the nucleic acid bases: distribution coefficients from water to cyclohexane

1 reference

12 December 2020

Thermodynamic analysis of interactions between denaturants and protein surface exposed on unfolding: interpretation of urea and guanidinium chloride m-values and their correlation with changes in accessible surface area (ASA) using preferential inte

1 reference

12 December 2020

Sequence dependent rigidity of single stranded DNA

1 reference

12 December 2020

Folding of an mRNA pseudoknot required for stop codon readthrough: effects of mono- and divalent ions on stability

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

Aromatic rings act as hydrogen bond acceptors

1 reference

12 December 2020

Identifiers

DOI

10.1021/JA400965N

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23510511%20AND%20SRC:MED&resulttype=core&format=json

26 February 2020

1 reference

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26 February 2020

PubMed publication ID

23510511

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23510511%20AND%20SRC:MED&resulttype=core&format=json