How do site-specific DNA-binding proteins find their targets? (Q24563835)

Crystal structure of the lactose operon repressor and its complexes with DNA and inducer

Europe PubMed Central

title

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

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author name string

Stephen E Halford

series ordinal

1

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John F Marko

series ordinal

2

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language of work or name

English

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publication date

2004

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published in

Nucleic Acids Research

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volume

32

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issue

10

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page(s)

3040-52

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cites work

1 reference

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The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments

24 March 2017

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

24 March 2017

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Dynamic binding of histone H1 to chromatin in living cells

24 March 2017

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Rapid exchange of histone H1.1 on chromatin in living human cells

24 March 2017

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Comparison of the DNA association kinetics of the Lac repressor tetramer, its dimeric mutant LacIadi, and the native dimeric Gal repressor

24 March 2017

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The lac repressor-operator interaction. 3. Kinetic studies

24 March 2017

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

24 March 2017

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Myosin V walks hand-over-hand: single fluorophore imaging with 1.5-nm localization

24 March 2017

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High mobility of proteins in the mammalian cell nucleus

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Enzyme-mediated DNA looping

7 April 2017

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Kinesin walks hand-over-hand

27 September 2017

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

27 September 2017

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Physical constraints and functional characteristics of transcription factor-DNA interaction.

27 September 2017

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

27 September 2017

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27 September 2017

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Recognition of specific DNA sequences.

27 September 2017

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Protein dynamics: implications for nuclear architecture and gene expression.

27 September 2017

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Twisting and stretching single DNA molecules.

27 September 2017

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

27 September 2017

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Direct observation of one-dimensional diffusion and transcription by Escherichia coli RNA polymerase

27 September 2017

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Action of DNA repair endonuclease ERCC1/XPF in living cells

27 September 2017

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

27 September 2017

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

27 September 2017

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Reactions of the eco RV restriction endonuclease with fluorescent oligodeoxynucleotides: identical equilibrium constants for binding to specific and non-specific DNA.

27 September 2017

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Rapid-reaction analysis of plasmid DNA cleavage by the EcoRV restriction endonuclease.

27 September 2017

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Effect of supercoiling on the juxtaposition and relative orientation of DNA sites

27 September 2017

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

27 September 2017

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

27 September 2017

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

27 September 2017

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Diffusion-controlled macromolecular interactions

27 September 2017

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lac repressor forms loops with linear DNA carrying two suitably spaced lac operators

27 September 2017

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27 September 2017

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One-dimensional diffusion of Escherichia coli DNA-dependent RNA polymerase: a mechanism to facilitate promoter location

27 September 2017

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Facilitated target location in biological systems

27 September 2017

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Stable DNA loops in vivo and in vitro: roles in gene regulation at a distance and in biophysical characterization of DNA.

27 September 2017

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The three operators of the lac operon cooperate in repression

27 September 2017

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How Lac repressor finds lac operator in vitro

27 September 2017

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Nonspecific DNA binding of genome-regulating proteins as a biological control mechanism: Measurement of DNA-bound Escherichia coli lac repressor in vivo

27 September 2017

1 reference

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Association kinetics with coupled diffusion. An extension to coiled-chain macromolecules applied to the LAC repressor-operator system

27 September 2017

1 reference

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Promoter recognition and promoter strength in the Escherichia coli system

27 September 2017

1 reference

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Single-molecule studies of DNA mechanics

27 September 2017

1 reference

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Transposition and site-specific recombination: adapting DNA cut-and-paste mechanisms to a variety of genetic rearrangements

30 May 2018

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Use of surface plasmon resonance to probe the equilibrium and dynamic aspects of interactions between biological macromolecules.

30 May 2018

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

30 May 2018

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Facilitated diffusion of a DNA binding protein on chromatin.

30 May 2018

1 reference

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Upstream operators enhance repression of the lac promoter

30 May 2018

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Dynamics of repressor-operator recognition: the Tn10-encoded tetracycline resistance control.

30 May 2018

1 reference

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Equilibrium, kinetic, and footprinting studies of the Tus-Ter protein-DNA interaction

30 May 2018

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

30 May 2018

1 reference

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Association kinetics with coupled diffusion III. Ionic-strength dependence of the lac repressor-operator association

30 May 2018

1 reference

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Visualization of single molecules of RNA polymerase sliding along DNA.

30 May 2018

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Kinetic analysis of yeast TFIID-TATA box complex formation suggests a multi-step pathway

30 May 2018

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Variability of the intracellular ionic environment of Escherichia coli. Differences between in vitro and in vivo effects of ion concentrations on protein-DNA interactions and gene expression.

30 May 2018

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Monomeric and dimeric bZIP transcription factor GCN4 bind at the same rate to their target DNA site

19 June 2018

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

28 November 2018

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Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity.

28 November 2018

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Concerted binding and bending of DNA by Escherichia coli integration host factor.

28 November 2018

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28 November 2018

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DNA excision by the Sfi I restriction endonuclease.

28 November 2018

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Analysis of effects of salts and uncharged solutes on protein and nucleic acid equilibria and processes: a practical guide to recognizing and interpreting polyelectrolyte effects, Hofmeister effects, and osmotic effects of salts.

28 November 2018

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Facilitated diffusion of the EcoRI DNA methyltransferase is described by a novel mechanism

28 November 2018

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Protein-protein interactions in colicin E9 DNase-immunity protein complexes. 1. Diffusion-controlled association and femtomolar binding for the cognate complex.

28 November 2018

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

28 November 2018

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Diffusion-controlled protein-DNA association: influence of segmental diffusion of the DNA.

28 November 2018

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Template supercoiling by a chimera of yeast GAL4 protein and phage T7 RNA polymerase

28 November 2018

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12 December 2020

Statistical mechanics of supercoiled DNA

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12 December 2020

Salt dependence of the kinetics of the lac repressor-operator interaction: role of nonoperator deoxyribonucleic acid in the association reaction

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12 December 2020

Kinetic studies on Cro repressor-operator DNA interaction

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12 December 2020

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

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12 December 2020

Two are better than one

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12 December 2020

Linear diffusion of restriction endonucleases on DNA

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12 December 2020

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

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12 December 2020

Facilitated diffusion during catalysis by EcoRI endonuclease. Nonspecific interactions in EcoRI catalysis

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12 December 2020

Structural and thermodynamic strategies for site-specific DNA binding proteins

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12 December 2020

Identifiers

DOI

10.1093/NAR/GKH624

1 reference

163611

163611

1 reference

1 reference

1 reference