Sequence heterogeneity accelerates protein search for targets on DNA

Protein search for multiple targets on DNA

(2015) Martin Lange et al.   JOURNAL OF CHEMICAL PHYSICS

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

(2015) Maximilian Bauer et al.   Scientific Reports

Positive and negative impacts of nonspecific sites during target location by a sequence-specific DNA-binding protein: origin of the optimal search at physiological ionic strength

(2014) Alexandre Esadze et al.   NUCLEIC ACIDS RESEARCH

Protein−DNA binding in the absence of specific base-pair recognition

(2014) Ariel Afek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulation of the Nucleosome Repeat Length In Vivo by the DNA Sequence, Protein Concentrations and Long-Range Interactions

(2014) Daria A. Beshnova et al.   PLoS Computational Biology

Positive and Negative Design for Nonconsensus Protein-DNA Binding Affinity in the Vicinity of Functional Binding Sites

(2013) Ariel Afek et al.   BIOPHYSICAL JOURNAL

Obstacles May Facilitate and Direct DNA Search by Proteins

(2013) Amir Marcovitz et al.   BIOPHYSICAL JOURNAL

Speed-Selectivity Paradox in the Protein Search for Targets on DNA: Is It Real or Not?

(2013) Alex Veksler et al.   JOURNAL OF PHYSICAL CHEMISTRY B

In Vivo Facilitated Diffusion Model

(2013) Maximilian Bauer et al.   PLoS One

Nonspecific Protein-DNA Binding Is Widespread in the Yeast Genome

(2012) Ariel Afek et al.   BIOPHYSICAL JOURNAL

How to accelerate protein search on DNA: Location and dissociation

(2012) Anatoly B. Kolomeisky et al.   JOURNAL OF CHEMICAL PHYSICS

DNA target sequence identification mechanism for dimer-active protein complexes

(2012) Markita P. Landry et al.   NUCLEIC ACIDS RESEARCH

Facilitated Diffusion on Mobile DNA: Configurational Traps and Sequence Heterogeneity

(2012) C. A. Brackley et al.   PHYSICAL REVIEW LETTERS

Asymmetrical roles of zinc fingers in dynamic DNA-scanning process by the inducible transcription factor Egr-1

(2012) L. Zandarashvili et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Classes of fast and specific search mechanisms for proteins on DNA

(2012) M Sheinman et al.   REPORTS ON PROGRESS IN PHYSICS

The lac Repressor Displays Facilitated Diffusion in Living Cells

(2012) P. Hammar et al.   SCIENCE

Theoretical and Computational Modeling of Target-Site Search Kinetics In Vitro and In Vivo

(2011) Elena F. Koslover et al.   BIOPHYSICAL JOURNAL

Nonspecific Transcription-Factor-DNA Binding Influences Nucleosome Occupancy in Yeast

(2011) Ariel Afek et al.   BIOPHYSICAL JOURNAL

Real-Time Observation of Transcription Initiation and Elongation on an Endogenous Yeast Gene

(2011) D. R. Larson et al.   SCIENCE

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

(2010) Anatoly B. Kolomeisky   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

Diffusion of the Restriction Nuclease EcoRI along DNA

(2009) Donald C. Rau et al.   JOURNAL OF MOLECULAR BIOLOGY

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

A Closed-Form Analytic Expression for FRAP Formula for the Binding Diffusion Model

(2008) Minchul Kang et al.   BIOPHYSICAL JOURNAL

How DNA coiling enhances target localization by proteins

(2008) B. van den Broek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA