Single-molecule tracking of the transcription cycle by sub-second RNA detection (Q41889407)

13 October 2017

Single-molecule tracking of the transcription cycle by sub-second RNA detection (English)

1 reference

13 October 2017

Luke D Lavis

0 references

Zhengjian Zhang

1 reference

13 October 2017

Andrey Revyakin

1 reference

13 October 2017

Jonathan B Grimm

1 reference

13 October 2017

Robert Tjian

1 reference

13 October 2017

PMC publication ID

3901038

language of work or name

English

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publication date

28 January 2014

1 reference

13 October 2017

1 reference

13 October 2017

1 reference

13 October 2017

e01775

1 reference

Transcription under torsion

13 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

RNA polymerase approaches its promoter without long-range sliding along DNA

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

The transcription bubble of the RNA polymerase-promoter open complex exhibits conformational heterogeneity and millisecond-scale dynamics: implications for transcription start-site selection

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

The promoter-search mechanism of Escherichia coli RNA polymerase is dominated by three-dimensional diffusion

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Opening and closing of the bacterial RNA polymerase clamp

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Copper-Catalyzed Azide-Alkyne Click Chemistry for Bioconjugation

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Transcription initiation by human RNA polymerase II visualized at single-molecule resolution

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Transcription goes digital

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Mechanism of transcription initiation at an activator-dependent promoter defined by single-molecule observation

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Stochastic state transitions give rise to phenotypic equilibrium in populations of cancer cells

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Real-time observation of the transition from transcription initiation to elongation of the RNA polymerase

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

5 June 2018

Transcription dynamics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Super-resolution fluorescence microscopy

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Single-molecule approaches to stochastic gene expression

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

T7 RNA polymerase studied by force measurements varying cofactor concentration.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

5 June 2018

The Vienna RNA websuite

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Secondary structure effects on DNA hybridization kinetics: a solution versus surface comparison

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Viewing dynamic assembly of molecular complexes by multi-wavelength single-molecule fluorescence

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Single-molecule analysis of RNA polymerase transcription

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Folding DNA to create nanoscale shapes and patterns

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Making all parts of the 16S rRNA of Escherichia coli accessible in situ to single DNA oligonucleotides.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Fluorescence quenching by TEMPO: a sub-30 A single-molecule ruler

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

tRNA dynamics on the ribosome during translation

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Complexity: an internet resource for analysis of DNA sequence complexity

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Backtracking by single RNA polymerase molecules observed at near-base-pair resolution

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Mfold web server for nucleic acid folding and hybridization prediction

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Hybridization kinetics and thermodynamics of molecular beacons

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Bacterial RNA polymerases: the wholo story

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Intramolecular dimers: a new strategy to fluorescence quenching in dual-labeled oligonucleotide probes

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Magnetic tweezers: micromanipulation and force measurement at the molecular level

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Hybridization of DNA and PNA molecular beacons to single-stranded and double-stranded DNA targets.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Effect of secondary structure on the thermodynamics and kinetics of PNA hybridization to DNA hairpins.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Fluorescence spectroscopy of single biomolecules.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

RNA polymerase-promoter interactions: the comings and goings of RNA polymerase

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

The biophysics of DNA hybridization with immobilized oligonucleotide probes.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Differentiation and proliferation of hematopoietic stem cells

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Kinetic analysis of T7 RNA polymerase transcription initiation from promoters containing single-stranded regions

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

T7 RNA polymerase mutants with altered promoter specificities

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Cyanine dye labeling reagents: sulfoindocyanine succinimidyl esters

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Characterization of T7-specific ribonucleic acid polymerase. IV. Resolution of the major in vitro transcripts by gel electrophoresis.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Implication of RNA structure on antisense oligonucleotide hybridization kinetics

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

A movie of RNA polymerase II transcription

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Backtracking determines the force sensitivity of RNAP II in a factor-dependent manner

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Observed instability of T7 RNA polymerase elongation complexes can be dominated by collision-induced "bumping".

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Ubiquitous transcriptional pausing is independent of RNA polymerase backtracking.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Promoter binding, initiation, and elongation by bacteriophage T7 RNA polymerase. A single-molecule view of the transcription cycle.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Cooperation between RNA polymerase molecules in transcription elongation

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

The +2 NTP binding drives open complex formation in T7 RNA polymerase

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Force and velocity measured for single molecules of RNA polymerase.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

Kinetic analysis of T7 RNA polymerase-promoter interactions with small synthetic promoters

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

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

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3901038

An open-source oligomicroarray standard for human and mouse

18 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.7554%2FELIFE.01775

Elite and stochastic models for induced pluripotent stem cell generation

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.7554%2FELIFE.01775

Characterization of a set of T7 RNA polymerase active site mutants

21 January 2018

1 reference

12 December 2020

Computational identification of antisense oligonucleotides that rapidly hybridize to RNA

1 reference

12 December 2020

Rapid binding of T7 RNA polymerase is followed by simultaneous bending and opening of the promoter DNA

1 reference

12 December 2020

T7 RNA polymerase elongation complex structure and movement

1 reference

12 December 2020

Easily calculable measure for the complexity of spatiotemporal patterns

1 reference

12 December 2020

Stretching single stranded DNA, a model polyelectrolyte

1 reference

12 December 2020

RNA polymerase II ternary complexes may become arrested after transcribing to within 10 bases of the end of linear templates

1 reference

12 December 2020

Identifiers

DOI

10.7554/ELIFE.01775

1 reference

13 October 2017

1 reference

PMC publication ID

3901038

13 October 2017

PubMed publication ID

24473079

1 reference

PMC publication ID

3901038