(Q41761743)

9 October 2017

Semiautomated and rapid quantification of nucleic acid footprinting and structure mapping experiments (English)

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9 October 2017

2

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9 October 2017

Quentin Vicens

3

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Alain Laederach

object named as

Alain Laederach

1

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Russ Altman

7

object named as

Russ B Altman

1 reference

9 October 2017

Samuel M Pearlman

4

1 reference

9 October 2017

Michael Brenowitz

5

1 reference

9 October 2017

Daniel Herschlag

6

1 reference

9 October 2017

1 January 2008

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9 October 2017

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9 October 2017

3

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9 October 2017

1395-1401

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9 October 2017

9

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describes a project that uses

9 October 2017

ImageQuant

1 reference

11 June 2022

https://www.ebi.ac.uk/europepmc/webservices/rest/PMC2652576/fullTextXML

based on heuristic

inferred from PubMed Central ID database lookup

exact match

https://scigraph.springernature.com/pub.10.1038/nprot.2008.134

0 references

cites work

DMS footprinting of structured RNAs and RNA-protein complexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652576

Distinct contribution of electrostatics, initial conformational ensemble, and macromolecular stability in RNA folding

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652576

Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652576

Local RNA structural changes induced by crystallization are revealed by SHAPE

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652576

Fast Fenton footprinting: a laboratory-based method for the time-resolved analysis of DNA, RNA and proteins

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652576

Local kinetic measures of macromolecular structure reveal partitioning among multiple parallel pathways from the earliest steps in the folding of a large RNA molecule

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652576

SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652576

Semi-automated, single-band peak-fitting analysis of hydroxyl radical nucleic acid footprint autoradiograms for the quantitative analysis of transitions

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652576

Multiple folding pathways for the P4-P6 RNA domain

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652576

Directed hydroxyl radical probing of 16S rRNA using Fe(II) tethered to ribosomal protein S4

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652576

"Footprint" titrations yield valid thermodynamic isotherms

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652576

Secondary structure of the circular form of the Tetrahymena rRNA intervening sequence: a technique for RNA structure analysis using chemical probes and reverse transcriptase

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652576

Defining the inside and outside of a catalytic RNA molecule

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652576

Conformation of yeast 18S rRNA. Direct chemical probing of the 5' domain in ribosomal subunits and in deproteinized RNA by reverse transcriptase mapping of dimethyl sulfate-accessible.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652576

The RNA Ontology Consortium: an open invitation to the RNA community

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652576

RNA flexibility in the dimerization domain of a gamma retrovirus

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652576

Perturbation of the hierarchical folding of a large RNA by the destabilization of its Scaffold's tertiary structure

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652576

RNA SHAPE chemistry reveals nonhierarchical interactions dominate equilibrium structural transitions in tRNA(Asp) transcripts

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652576

Exploration of the transition state for tertiary structure formation between an RNA helix and a large structured RNA.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652576

Linkage of monovalent and divalent ion binding in the folding of the P4-P6 domain of the Tetrahymena ribozyme

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652576

Probing the folding landscape of the Tetrahymena ribozyme: commitment to form the native conformation is late in the folding pathway.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652576

Time-resolved synchrotron X-ray "footprinting", a new approach to the study of nucleic acid structure and function: application to protein-DNA interactions and RNA folding.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2652576

Monovalent ion-mediated folding of the Tetrahymena thermophila ribozyme

18 August 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.134

The Fastest Global Events in RNA Folding: Electrostatic Relaxation and Tertiary Collapse of the Tetrahymena Ribozyme

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.134

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.134

RNA Folding at Millisecond Intervals by Synchrotron Hydroxyl Radical Footprinting

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.134

Folding Mechanism of theTetrahymenaRibozyme P4−P6 Domain†

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.134

21 January 2018

Identifiers

DOI

10.1038/NPROT.2008.134

1 reference

9 October 2017

1 reference

9 October 2017

1 reference