Dancing on DNA: kinetic aspects of search processes on DNA (Q36110835)

12 August 2017

1 reference

title

Dancing on DNA: kinetic aspects of search processes on DNA (English)

1 reference

12 August 2017

3

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author name string

Anahita Tafvizi

series ordinal

1

1 reference

PMCID

4590286

12 August 2017

Leonid A Mirny

series ordinal

2

1 reference

12 August 2017

10 May 2011

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12 August 2017

1 reference

12 August 2017

12

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12 August 2017

8

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12 August 2017

1481-1489

1 reference

A single-molecule characterization of p53 search on DNA

12 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

Bacterial Chromosomal Loci Move Subdiffusively through a Viscoelastic Cytoplasm

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

Experimental snapshots of a protein-DNA binding landscape

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

Hopping enables a DNA repair glycosylase to search both strands and bypass a bound protein.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

Facilitated diffusion with DNA coiling.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

Proliferating cell nuclear antigen uses two distinct modes to move along DNA.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

Early Interrogation and Recognition of DNA Sequence by Indirect Readout

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

How DNA coiling enhances target localization by proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

Visualizing one-dimensional diffusion of proteins along DNA.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

Uracil DNA glycosylase uses DNA hopping and short-range sliding to trap extrahelical uracils

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

NMR structural and kinetic characterization of a homeodomain diffusing and hopping on nonspecific DNA.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

Transition from nonspecific to specific DNA interactions along the substrate-recognition pathway of dam methyltransferase.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

Specific interaction of p53 with target binding sites is determined by DNA conformation and is regulated by the C-terminal domain

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

Kinetic studies of protein-protein interactions

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

2 October 2017

Surfing the p53 network

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

Structure of BamHI bound to nonspecific DNA: a model for DNA sliding

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

Covalent and noncovalent modifiers of the p53 protein

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

Single-molecule imaging of RNA polymerase-DNA interactions in real time

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

Identification of an additional negative regulatory region for p53 sequence-specific DNA binding

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

Coupling of local folding to site-specific binding of proteins to DNA

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

Conformational shifts propagate from the oligomerization domain of p53 to its tetrameric DNA binding domain and restore DNA binding to select p53 mutants.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

Pausing of the restriction endonuclease EcoRI during linear diffusion on DNA.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

p53-catalyzed annealing of complementary single-stranded nucleic acids

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

Involvement of outside DNA sequences in the major kinetic path by which EcoRI endonuclease locates and leaves its recognition sequence

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

The lac repressor-operator interaction. 3. Kinetic studies

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

Diffusion-controlled macromolecular interactions

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

Facilitated target location in biological systems

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

Regulation of the specific DNA binding function of p53

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

Visualization of single molecules of RNA polymerase sliding along DNA.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

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

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

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

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

Association kinetics with coupled diffusional flows. Special application to the lac repressor--operator system.

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

Allelic frequency of p53 gene codon 72 polymorphism in urologic cancers.

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

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

2 July 2018

1 reference

https://api.crossref.org/works/10.1002%2FCPHC.201100112

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCPHC.201100112

Diffusion in correlated random potentials, with applications to DNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCPHC.201100112

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCPHC.201100112

DNA bending by Cro protein in specific and nonspecific complexes: implications for protein site recognition and specificity

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCPHC.201100112

p53 linear diffusion along DNA requires its C terminus

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCPHC.201100112

The one-dimensional diffusion coefficient of proteins absorbed on DNA. Hydrodynamic considerations

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCPHC.201100112

Obstacle bypass in protein motion along DNA by two-dimensional rather than one-dimensional sliding

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCPHC.201100112

Physical nature of bacterial cytoplasm.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCPHC.201100112

In vivo anomalous diffusion and weak ergodicity breaking of lipid granules.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCPHC.201100112

Facilitated Diffusion of DNA-Binding Proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCPHC.201100112

Thermodynamic Consequences of Bipartite Immunity Protein Binding to the Ribosomal Ribonuclease Colicin E3†

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCPHC.201100112

Enhancement of Association Rates by Nonspecific Binding to DNA and Cell Membranes

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCPHC.201100112

A residue-specific view of the association and dissociation pathway in protein–DNA recognition

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4590286

Single molecule measurements of repressor protein 1D diffusion on DNA

5 December 2018

1 reference

12 December 2020

Diffusion Constant of a Nonspecifically Bound Protein Undergoing Curvilinear Motion along DNA†

1 reference

12 December 2020

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

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

Identifiers

DOI

10.1002/CPHC.201100112

1 reference

12 August 2017

1 reference

12 August 2017

1 reference

PMCID

4590286