(Q33908429)

29 July 2017

title

Dynamic strategies for target-site search by DNA-binding proteins (English)

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29 July 2017

author name string

Mario A Díaz de la Rosa

1

1 reference

29 July 2017

Elena F Koslover

2

1 reference

29 July 2017

Peter J Mulligan

3

1 reference

29 July 2017

Andrew J Spakowitz

4

1 reference

29 July 2017

language of work or name

English

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publication date

1 June 2010

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29 July 2017

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29 July 2017

volume

98

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29 July 2017

issue

12

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29 July 2017

page(s)

2943-2953

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Facilitated diffusion with DNA coiling.

29 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884260

An end to 40 years of mistakes in DNA-protein association kinetics?

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884260

How DNA coiling enhances target localization by proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884260

Visualizing one-dimensional diffusion of proteins along DNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884260

Sliding and jumping of single EcoRV restriction enzymes on non-cognate DNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884260

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884260

Tumor suppressor p53 slides on DNA with low friction and high stability

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884260

Single-molecule analysis of 1D diffusion and transcription elongation of T7 RNA polymerase along individual stretched DNA molecules

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884260

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884260

Isolation of the lac repressor

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884260

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884260

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884260

Long-distance lateral diffusion of human Rad51 on double-stranded DNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884260

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884260

Target search of N sliding proteins on a DNA

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884260

A model for the mediation of processivity of DNA-targeting proteins by nonspecific binding: dependence on DNA length and presence of obstacles

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884260

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884260

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884260

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884260

Analysis of a one-dimensional random walk with irreversible losses at each step: applications for protein movement on DNA

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884260

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884260

How to get from A to B: strategies for analysing protein motion on DNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884260

One- and three-dimensional pathways for proteins to reach specific DNA sites

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884260

Kinetic characterization of linear diffusion of the restriction endonuclease EcoRV on DNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884260

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884260

Energetics of DNA twisting. I. Relation between twist and cyclization probability.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884260

DNA flexibility studied by covalent closure of short fragments into circles

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884260

Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884260

Kinetics of protein-nucleic acid interactions: use of salt effects to probe mechanisms of interaction

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884260

Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884260

Direct measurement of association constants for the binding of Escherichia coli lac repressor to non-operator DNA

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884260

Quantifying hopping and jumping in facilitated diffusion of DNA-binding proteins.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884260

Protein association with circular DNA: rate enhancement by nonspecific binding.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884260

Biochemical characterization of the human RAD51 protein. III. Modulation of DNA binding by adenosine nucleotides

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884260

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

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884260

Association kinetics with coupled three- and one-dimensional diffusion. Chain-length dependence of the association rate of specific DNA sites.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884260

Thermodynamic parameters governing interaction of EcoRI endonuclease with specific and nonspecific DNA sequences

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884260

Single molecule measurements of repressor protein 1D diffusion on DNA

29 October 2018

1 reference

12 December 2020

Kinetic studies on Cro repressor-operator DNA interaction

1 reference

12 December 2020

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

1 reference

12 December 2020

Description of nonspecific DNA-protein interaction and facilitated diffusion with a dynamical model

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

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

1 reference

12 December 2020

Protein--DNA interactions: reaching and recognizing the targets

1 reference

12 December 2020

Base-sequence-dependent sliding of proteins on DNA

1 reference

12 December 2020

10.1016/J.BPJ.2010.02.055

Identifiers

DOI

1 reference

29 July 2017

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29 July 2017

1 reference