(Q35218272)

7 August 2017

title

Theoretical and computational modeling of target-site search kinetics in vitro and in vivo (English)

1 reference

7 August 2017

Elena F Koslover

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7 August 2017

Mario A Díaz de la Rosa

series ordinal

1 reference

7 August 2017

Andrew J Spakowitz

series ordinal

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7 August 2017

language of work or name

English

0 references

publication date

1 August 2011

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7 August 2017

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inferred from page(s)

published in

Biophysical Journal

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7 August 2017

volume

101

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7 August 2017

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7 August 2017

page(s)

856-865

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Physics of protein–DNA interactions: mechanisms of facilitated target search

7 August 2017

cites work

1 reference

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Bacterial Chromosomal Loci Move Subdiffusively through a Viscoelastic Cytoplasm

13 July 2018

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Visualizing one-dimensional diffusion of eukaryotic DNA repair factors along a chromatin lattice

13 July 2018

1 reference

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Dynamic strategies for target-site search by DNA-binding proteins

13 July 2018

1 reference

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Facilitated diffusion with DNA coiling.

13 July 2018

1 reference

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

13 July 2018

1 reference

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How DNA coiling enhances target localization by proteins

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175062

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

13 July 2018

1 reference

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175062

Dynamic basis for one-dimensional DNA scanning by the mismatch repair complex Msh2-Msh6.

13 July 2018

1 reference

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How gene order is influenced by the biophysics of transcription regulation

13 July 2018

1 reference

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175062

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175062

Isolation of the lac repressor

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175062

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

13 July 2018

1 reference

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

13 July 2018

1 reference

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175062

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175062

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175062

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175062

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175062

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175062

Protein mobility in the cytoplasm of Escherichia coli.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175062

Linear diffusion of the restriction endonuclease EcoRV on DNA is essential for the in vivo function of the enzyme

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175062

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175062

The lac repressor-operator interaction. 3. Kinetic studies

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175062

Facilitated target location in biological systems

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175062

Nonspecific interaction of lac repressor with DNA: an association reaction driven by counterion release.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175062

How proteins squeeze through polymer networks: a Cartesian lattice study.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175062

The effects of intersegmental transfers on target location by proteins.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175062

The role of chromatin conformations in diffusional transport of chromatin-binding proteins: Cartesian lattice simulations

26 September 2018

1 reference

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Physical nature of bacterial cytoplasm.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175062

Periodic transcriptional organization of the E.coli genome

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175062

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

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175062

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

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175062

Facilitated Diffusion of Proteins on Chromatin

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175062

Facilitated Diffusion of DNA-Binding Proteins

8 December 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175062

Single molecule measurements of repressor protein 1D diffusion on DNA

8 December 2018

1 reference

12 December 2020

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

1 reference

12 December 2020

Facilitated diffusion of DNA-binding proteins: efficient simulation with the method of excess collisions

1 reference

12 December 2020

Geometry-controlled kinetics

1 reference

12 December 2020

Protein--DNA interactions: reaching and recognizing the targets

1 reference

12 December 2020

Facilitated search of proteins on DNA: correlations are important

1 reference

12 December 2020

10.1016/J.BPJ.2011.06.066

Identifiers

DOI

1 reference

7 August 2017

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7 August 2017

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