A mini-review of the diffusion dynamics of DNA-binding proteins: experiments and models

Fractional Brownian motion with random diffusivity: emerging residual nonergodicity below the correlation time

(2020) Wei Wang et al.   Journal of Physics A-Mathematical and Theoretical

DNA surface exploration and operator bypassing during target search

(2020) Emil Marklund et al.   NATURE

Single-molecule visualization reveals the damage search mechanism for the human NER protein XPC-RAD23B

(2019) Na Young Cheon et al.   NUCLEIC ACIDS RESEARCH

High Free-Energy Barrier of 1D Diffusion Along DNA by Architectural DNA-Binding Proteins

(2018) Kiyoto Kamagata et al.   JOURNAL OF MOLECULAR BIOLOGY

Random diffusivity from stochastic equations: comparison of two models for Brownian yet non-Gaussian diffusion

(2018) Vittoria Sposini et al.   NEW JOURNAL OF PHYSICS

Single-particle trajectories reveal two-state diffusion-kinetics of hOGG1 proteins on DNA

(2018) Christian L Vestergaard et al.   NUCLEIC ACIDS RESEARCH

Viscoelastic subdiffusion in a random Gaussian environment

(2018) Igor Goychuk   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Characterization of facilitated diffusion of tumor suppressor p53 along DNA using single-molecule fluorescence imaging

(2017) Kiyoto Kamagata et al.   JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS

PARP1 changes from three-dimensional DNA damage searching to one-dimensional diffusion after auto-PARylation or in the presence of APE1

(2017) Lili Liu et al.   NUCLEIC ACIDS RESEARCH

Connectivity, dynamics, and structure in a tetrahedral network liquid

(2017) Sándalo Roldán-Vargas et al.   Soft Matter

Activation of p53 Facilitates the Target Search in DNA by Enhancing the Target Recognition Probability

(2016) Yuji Itoh et al.   JOURNAL OF MOLECULAR BIOLOGY

Dynamic Coupling among Protein Binding, Sliding, and DNA Bending Revealed by Molecular Dynamics

(2016) Cheng Tan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Single-Molecule Imaging Reveals that Rad4 Employs a Dynamic DNA Damage Recognition Process

(2016) Muwen Kong et al.   MOLECULAR CELL

TALE proteins search DNA using a rotationally decoupled mechanism

(2016) Luke Cuculis et al.   Nature Chemical Biology

Functional interplay between SA1 and TRF1 in telomeric DNA binding and DNA–DNA pairing

(2016) Jiangguo Lin et al.   NUCLEIC ACIDS RESEARCH

Normal and anomalous diffusion of Brownian particles on disordered potentials

(2016) R. Salgado-García   PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS

Tracer diffusion in a sea of polymers with binding zones: mobile vs. frozen traps

(2016) Nairhita Samanta et al.   Soft Matter

Dynamic DNA binding licenses a repair factor to bypass roadblocks in search of DNA lesions

(2016) Maxwell W. Brown et al.   Nature Communications

Quantitative Aspects of Single-Molecule Microscopy: Information-theoretic analysis of single-molecule data

(2015) Raimund J. Ober et al.   IEEE SIGNAL PROCESSING MAGAZINE

One-Dimensional Sliding of p53 Along DNA Is Accelerated in the Presence of Ca 2+ or Mg 2+ at Millimolar Concentrations

(2015) Agato Murata et al.   JOURNAL OF MOLECULAR BIOLOGY

Ergodicity breaking, ageing, and confinement in generalized diffusion processes with position and time dependent diffusivity

(2015) Andrey G Cherstvy et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Direct observation of TALE protein dynamics reveals a two-state search mechanism

(2015) Luke Cuculis et al.   Nature Communications

Kinetic gating mechanism of DNA damage recognition by Rad4/XPC

(2015) Xuejing Chen et al.   Nature Communications

Real sequence effects on the search dynamics of transcription factors on DNA

(2015) Maximilian Bauer et al.   Scientific Reports

Diffusion on a rugged energy landscape with spatial correlations

(2014) Saikat Banerjee et al.   JOURNAL OF CHEMICAL PHYSICS

Localisation and universal fluctuations in ultraslow diffusion processes

(2014) Aljaž Godec et al.   Journal of Physics A-Mathematical and Theoretical

Anomalous diffusion models and their properties: non-stationarity, non-ergodicity, and ageing at the centenary of single particle tracking

(2014) Ralf Metzler et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Nonergodicity, fluctuations, and criticality in heterogeneous diffusion processes

(2014) A. G. Cherstvy et al.   PHYSICAL REVIEW E

Anomalous Features of Diffusion in Corrugated Potentials with Spatial Correlations: Faster than Normal, and Other Surprises

(2014) Igor Goychuk et al.   PHYSICAL REVIEW LETTERS

Diffusing Diffusivity: A Model for Anomalous, yet Brownian, Diffusion

(2014) Mykyta V. Chubynsky et al.   PHYSICAL REVIEW LETTERS

Two glycosylase families diffusively scan DNA using a wedge residue to probe for and identify oxidatively damaged bases

(2014) S. R. Nelson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-molecule analysis reveals human UV-damaged DNA-binding protein (UV-DDB) dimerizes on DNA via multiple kinetic intermediates

(2014) H. Ghodke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SA1 binds directly to DNA through its unique AT-hook to promote sister chromatid cohesion at telomeres

(2013) K. K. Bisht et al.   JOURNAL OF CELL SCIENCE

Anomalous diffusion and ergodicity breaking in heterogeneous diffusion processes

(2013) Andrey G Cherstvy et al.   NEW JOURNAL OF PHYSICS

TRF1 and TRF2 use different mechanisms to find telomeric DNA but share a novel mechanism to search for protein partners at telomeres

(2013) Jiangguo Lin et al.   NUCLEIC ACIDS RESEARCH

Real-time single-molecule imaging reveals a direct interaction between UvrC and UvrB on DNA tightropes

(2013) Craig D. Hughes et al.   NUCLEIC ACIDS RESEARCH

Population splitting, trapping, and non-ergodicity in heterogeneous diffusion processes

(2013) Andrey G. Cherstvy et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Subdiffusive rocking ratchets in viscoelastic media: Transport optimization and thermodynamic efficiency in overdamped regime

(2013) Vasyl O. Kharchenko et al.   PHYSICAL REVIEW E

Distance Matters: The Impact of Gene Proximity in Bacterial Gene Regulation

(2013) Otto Pulkkinen et al.   PHYSICAL REVIEW LETTERS

In Vivo Facilitated Diffusion Model

(2013) Maximilian Bauer et al.   PLoS One

p53 Searches on DNA by Rotation-Uncoupled Sliding at C-Terminal Tails and Restricted Hopping of Core Domains

(2012) Tsuyoshi Terakawa et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

When Brownian diffusion is not Gaussian

(2012) Bo Wang et al.   NATURE MATERIALS

The promoter-search mechanism of Escherichia coli RNA polymerase is dominated by three-dimensional diffusion

(2012) Feng Wang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The rotation-coupled sliding of EcoRV

(2012) Jasmina Dikić et al.   NUCLEIC ACIDS RESEARCH

Inequivalence of time and ensemble averages in ergodic systems: Exponential versus power-law relaxation in confinement

(2012) Jae-Hyung Jeon et al.   PHYSICAL REVIEW E

Sequence-dependent sliding kinetics of p53

(2012) J. S. Leith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Removal of Shelterin Reveals the Telomere End-Protection Problem

(2012) A. Sfeir et al.   SCIENCE

The lac Repressor Displays Facilitated Diffusion in Living Cells

(2012) P. Hammar et al.   SCIENCE

ATP Alters the Diffusion Mechanics of MutS on Mismatched DNA

(2012) Won-Ki Cho et al.   STRUCTURE

Protein-DNA Recognition Triggered by a DNA Conformational Switch

(2011) Benjamin Bouvier et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Dancing on DNA: Kinetic Aspects of Search Processes on DNA

(2011) Anahita Tafvizi et al.   CHEMPHYSCHEM

MutS switches between two fundamentally distinct clamps during mismatch repair

(2011) Cherlhyun Jeong et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Single Qdot-labeled glycosylase molecules use a wedge amino acid to probe for lesions while scanning along DNA

(2011) Andrew R. Dunn et al.   NUCLEIC ACIDS RESEARCH

Non-Gaussian athermal fluctuations in active gels

(2011) Toshihiro Toyota et al.   Soft Matter

Hopping Enables a DNA Repair Glycosylase To Search Both Strands and Bypass a Bound Protein

(2010) Mark Hedglin et al.   ACS Chemical Biology

Collaborative Dynamic DNA Scanning by Nucleotide Excision Repair Proteins Investigated by Single- Molecule Imaging of Quantum-Dot-Labeled Proteins

(2010) Neil M. Kad et al.   MOLECULAR CELL

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

(2010) Jason Gorman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs

(2010) Malka Kitayner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2010) Anatoly B. Kolomeisky   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Fractional Brownian motion and motion governed by the fractional Langevin equation in confined geometries

(2010) Jae-Hyung Jeon et al.   PHYSICAL REVIEW E

A single-molecule characterization of p53 search on DNA

(2010) A. Tafvizi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptional Regulation by P53

(2010) R. Beckerman et al.   Cold Spring Harbor Perspectives in Biology

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

(2009) Stephen E. Halford   BIOCHEMICAL SOCIETY TRANSACTIONS

Tracking of Single Quantum Dot Labeled EcoRV Sliding along DNA Manipulated by Double Optical Tweezers

(2009) Andreas Biebricher et al.   BIOPHYSICAL JOURNAL

Modes of p53 Regulation

(2009) Jan-Philipp Kruse et al.   CELL

Entrapment and Structure of an Extrahelical Guanine Attempting to Enter the Active Site of a Bacterial DNA Glycosylase, MutM

(2009) Yan Qi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

How a protein searches for its site on DNA: the mechanism of facilitated diffusion

(2009) Leonid Mirny et al.   Journal of Physics A-Mathematical and Theoretical

Nonspecifically bound proteins spin while diffusing along DNA

(2009) Paul C Blainey et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Nonspecific DNA-Protein Interaction: Why Proteins Can Diffuse along DNA

(2009) Vincent Dahirel et al.   PHYSICAL REVIEW LETTERS

Facilitated diffusion with DNA coiling

(2009) M. A. Lomholt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Anomalous yet Brownian

(2009) B. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural Biology of the Tumor Suppressor p53

(2008) Andreas C. Joerger et al.   Annual Review of Biochemistry

Tumor Suppressor p53 Slides on DNA with Low Friction and High Stability

(2008) Anahita Tafvizi et al.   BIOPHYSICAL JOURNAL

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

(2008) Biman Bagchi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Visualizing one-dimensional diffusion of proteins along DNA

(2008) Jason Gorman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2008) Isabelle Bonnet et al.   NUCLEIC ACIDS RESEARCH

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

(2008) R. H. Porecha et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA