Development of a "modular" scheme to describe the kinetics of transcript elongation by RNA polymerase (Q35187537)

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12 February 2020

title

Development of a "modular" scheme to describe the kinetics of transcript elongation by RNA polymerase (English)

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12 February 2020

1

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12 February 2020

author name string

Jim P Goodarzi

series ordinal

2

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12 February 2020

Steven E Weitzel

series ordinal

3

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12 February 2020

Peter H von Hippel

series ordinal

4

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12 February 2020

language of work or name

English

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publication date

1 September 2011

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12 February 2020

number of pages

11

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inferred from page(s)

published in

Biophysical Journal

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12 February 2020

volume

101

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12 February 2020

issue

5

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12 February 2020

page(s)

1155-1165

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Fitting experimental transcription data with a comprehensive template-dependent modular kinetic model

12 February 2020

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1 reference

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Cooperation between translating ribosomes and RNA polymerase in transcription elongation

28 July 2018

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Macromolecular micromovements: how RNA polymerase translocates

28 July 2018

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Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II.

28 July 2018

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Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA

28 July 2018

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Mechanism of sequence-specific pausing of bacterial RNA polymerase

28 July 2018

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A look-ahead model for the elongation dynamics of transcription

28 July 2018

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Dynamics of backtracking long pauses of RNA polymerase.

28 July 2018

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Applied force reveals mechanistic and energetic details of transcription termination

28 July 2018

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Monitoring RNA transcription in real time by using surface plasmon resonance

28 July 2018

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RNA polymerase: the vehicle of transcription

28 July 2018

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An Allosteric Path to Transcription Termination

28 July 2018

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Direct spectroscopic study of reconstituted transcription complexes reveals that intrinsic termination is driven primarily by thermodynamic destabilization of the nucleic acid framework

28 July 2018

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The regulatory roles and mechanism of transcriptional pausing

28 July 2018

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The role of the lid element in transcription by E. coli RNA polymerase

28 July 2018

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Sequence-resolved detection of pausing by single RNA polymerase molecules.

28 July 2018

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Terminating the transcript: breaking up is hard to do.

28 July 2018

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Thermodynamic and kinetic modeling of transcriptional pausing

28 July 2018

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Thinking quantitatively about transcriptional regulation.

28 July 2018

1 reference

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General Methods for Analysis of Sequential “n-step” Kinetic Mechanisms: Application to Single Turnover Kinetics of Helicase-Catalyzed DNA Unwinding

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3164141

Nonequilibrium mechanism of transcription termination from observations of single RNA polymerase molecules

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3164141

The mechanism of intrinsic transcription termination.

28 July 2018

1 reference

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Regulation of the elongation-termination decision at intrinsic terminators by antitermination protein N of phage lambda

28 July 2018

1 reference

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Basic mechanisms of transcript elongation and its regulation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3164141

A model for the mechanism of polymerase translocation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3164141

Specificity mechanisms in the control of transcription

28 July 2018

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Transcription termination at intrinsic terminators: the role of the RNA hairpin

28 July 2018

1 reference

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Pausing of RNA polymerase during in vitro transcription through the ilvB and ilvGEDA attenuator regions of Escherichia coli K12.

28 July 2018

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Transcription by single molecules of RNA polymerase observed by light microscopy

28 July 2018

1 reference

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A quantitative assay for bacterial RNA polymerases

28 July 2018

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Backtracking and proofreading in DNA transcription.

28 July 2018

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Rapid kinetic analysis of transcription elongation by Escherichia coli RNA polymerase

27 September 2018

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Fluctuations, pauses, and backtracking in DNA transcription

27 September 2018

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Stochastic kinetics description of a simple transcription model.

27 September 2018

1 reference

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Transcriptional pausing caught in the act.

27 September 2018

1 reference

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Kinetic investigation of Escherichia coli RNA polymerase mutants that influence nucleotide discrimination and transcription fidelity.

27 September 2018

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Assembly of an RNA-protein complex. Binding of NusB and NusE (S10) proteins to boxA RNA nucleates the formation of the antitermination complex involved in controlling rRNA transcription in Escherichia coli.

27 September 2018

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Ubiquitous transcriptional pausing is independent of RNA polymerase backtracking.

27 September 2018

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Transcription termination: primary intermediates and secondary adducts.

27 September 2018

1 reference

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Transcription termination in Escherichia coli. Measurement of the rate of enzyme release from Rho-independent terminators

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3164141

Analytical theory of the nonequilibrium spatial distribution of RNA polymerase translocations

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3164141

Isolation and characterization of sigma(70)-retaining transcription elongation complexes from Escherichia coli

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3164141

Sequence-dependent kinetic model for transcription elongation by RNA polymerase

27 September 2018

1 reference

12 December 2020

Mechanochemical kinetics of transcription elongation

1 reference

12 December 2020

A central role of the RNA polymerase trigger loop in active-site rearrangement during transcriptional pausing

1 reference

12 December 2020

A dynamic model for transcription elongation and sequence-dependent short pauses by RNA polymerase

1 reference

12 December 2020

Delayed stochastic model of transcription at the single nucleotide level

1 reference

12 December 2020

Pausing and termination of transcription within the early region of bacteriophage T7 DNA in vitro

1 reference

12 December 2020

10.1016/J.BPJ.2011.07.042

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21889453%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21889453%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

PubMed publication ID

21889453

1 reference