Spatial effects on the speed and reliability of protein-DNA search (Q36740092)

16 August 2017

Spatial effects on the speed and reliability of protein-DNA search (English)

1 reference

16 August 2017

1

Zeba Wunderlich

1 reference

16 August 2017

Leonid A Mirny

2

1 reference

PMCID

2441786

16 August 2017

language of work or name

English

0 references

publication date

3 May 2008

1 reference

16 August 2017

Nucleic Acids Research

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16 August 2017

36

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16 August 2017

3570-3578

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16 August 2017

11

1 reference

How gene order is influenced by the biophysics of transcription regulation

16 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441786

Probing transcription factor dynamics at the single-molecule level in a living cell

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441786

Living with noisy genes: how cells function reliably with inherent variability in gene expression

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441786

Strong physical constraints on sequence-specific target location by proteins on DNA molecules.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441786

A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441786

How proteins search for their specific sites on DNA: the role of DNA conformation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441786

Real-time kinetics of gene activity in individual bacteria

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441786

Measurement of the contributions of 1D and 3D pathways to the translocation of a protein along DNA.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441786

The choreographed dynamics of bacterial chromosomes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441786

Transcriptional regulation by the numbers: applications

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441786

Transcriptional regulation by the numbers: models.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441786

Chromosomal organization is shaped by the transcription regulatory network

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441786

EcoCyc: a comprehensive database resource for Escherichia coli

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441786

Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441786

Kinetics of target site localization of a protein on DNA: a stochastic approach.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441786

How do site-specific DNA-binding proteins find their targets?

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441786

Control of stochasticity in eukaryotic gene expression

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441786

Gene Organization: Selection, Selfishness, and Serendipity

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441786

Protein motion from non-specific to specific DNA by three-dimensional routes aided by supercoiling

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441786

Stochastic gene expression in a single cell

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441786

Regulation of noise in the expression of a single gene

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441786

High local protein concentrations at promoters: strategies in prokaryotic and eukaryotic cells

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441786

Protein mobility in the cytoplasm of Escherichia coli.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441786

The complete genome sequence of Escherichia coli K-12

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441786

Selfish operons: horizontal transfer may drive the evolution of gene clusters

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441786

Quality and position of the three lac operators of E. coli define efficiency of repression.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441786

The lac repressor-operator interaction. 3. Kinetic studies

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441786

Non-specific DNA binding of genome regulating proteins as a biological control mechanism: I. The lac operon: equilibrium aspects

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441786

Diffusion controlled reaction rates in spheroidal geometry. Application to repressor--operator association and membrane bound enzymes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441786

In vivo DNA-binding properties of a yeast transcription activator protein

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441786

Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441786

Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli lac repressor--operator interaction: kinetic measurements and conclusions.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441786

Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory.

28 June 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKN173

Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKN173

Diffusion of transcription factors can drastically enhance the noise in gene expression

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKN173

Stochastic protein expression in individual cells at the single molecule level

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKN173

Single molecule measurements of repressor protein 1D diffusion on DNA

21 January 2018

1 reference

12 December 2020

Optimal target search on a fast-folding polymer chain with volume exchange

1 reference

12 December 2020

One-dimensional diffusion of proteins along DNA. Its biological and chemical significance revealed by single-molecule measurements

1 reference

12 December 2020

Linking stochastic dynamics to population distribution: an analytical framework of gene expression

1 reference

12 December 2020

How does a protein search for the specific site on DNA: The role of disorder

1 reference

12 December 2020

Diffusion-driven mechanisms of protein translocation on nucleic acids. 2. The Escherichia coli lac repressor-operator interaction: equilibrium measurements

1 reference

12 December 2020

Micromechanical analysis of the binding of DNA-bending proteins HMGB1, NHP6A, and HU reveals their ability to form highly stable DNA-protein complexes

1 reference

12 December 2020

Thermodynamic origins of specificity in the lac repressor-operator interaction. Adaptability in the recognition of mutant operator sites

1 reference

12 December 2020

Statistical analysis of the spatial distribution of operons in the transcriptional regulation network of Escherichia coli

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKN173

1 reference

16 August 2017

1 reference

1 reference

16 August 2017

1 reference

PMCID

2441786