Single-molecule DNA unzipping reveals asymmetric modulation of a transcription factor by its binding site sequence and context

Pausing kinetics dominates strand-displacement polymerization by reverse transcriptase

(2017) Omri Malik et al.   NUCLEIC ACIDS RESEARCH

Thermodynamic Additivity for Impacts of Base-Pair Substitutions on Association of the Egr-1 Zinc-Finger Protein with DNA

(2016) Abhijnan Chattopadhyay et al.   BIOCHEMISTRY

The Genetics of Transcription Factor DNA Binding Variation

(2016) Bart Deplancke et al.   CELL

H2A.Z controls the stability and mobility of nucleosomes to regulate expression of the LH genes

(2016) Sergei Rudnizky et al.   Nature Communications

Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity

(2016) Stefanie Schöne et al.   Nature Communications

Influence of Quasi-Specific Sites on Kinetics of Target DNA Search by a Sequence-Specific DNA-Binding Protein

(2015) Catherine A. Kemme et al.   BIOCHEMISTRY

Unraveling determinants of transcription factor binding outside the core binding site

(2015) Michal Levo et al.   GENOME RESEARCH

A widespread role of the motif environment in transcription factor binding across diverse protein families

(2015) Iris Dror et al.   GENOME RESEARCH

Sequence heterogeneity accelerates protein search for targets on DNA

(2015) Alexey A. Shvets et al.   JOURNAL OF CHEMICAL PHYSICS

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Balancing between affinity and speed in target DNA search by zinc-finger proteins via modulation of dynamic conformational ensemble

(2015) Levani Zandarashvili et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nanopore sensing of individual transcription factors bound to DNA

(2015) Allison Squires et al.   Scientific Reports

Dynamic regulation of transcription factors by nucleosome remodeling

(2015) Ming Li et al.   eLife

Conservation of transcription factor binding specificities across 600 million years of bilateria evolution

(2015) Kazuhiro R Nitta et al.   eLife

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

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

TFBSshape: a motif database for DNA shape features of transcription factor binding sites

(2013) Lin Yang et al.   NUCLEIC ACIDS RESEARCH

Probing DNA shape and methylation state on a genomic scale with DNase I

(2013) A. Lazarovici et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Generalized Facilitated Diffusion Model for DNA-Binding Proteins with Search and Recognition States

(2012) Maximilian Bauer et al.   BIOPHYSICAL JOURNAL

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

Rapid search for specific sites on DNA through conformational switch of nonspecifically bound proteins

(2011) H.-X. Zhou   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-molecule imaging reveals mechanisms of protein disruption by a DNA translocase

(2010) Ilya J. Finkelstein et al.   NATURE

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

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

Nucleosome-mediated cooperativity between transcription factors

(2010) L. A. Mirny   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An ensemble model of competitive multi-factor binding of the genome

(2009) T. Wasson et al.   GENOME RESEARCH

Incorporating nucleosomes into thermodynamic models of transcription regulation

(2009) T. Raveh-Sadka et al.   GENOME RESEARCH

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

The role of DNA shape in protein–DNA recognition

(2009) Remo Rohs et al.   NATURE

Nonspecifically bound proteins spin while diffusing along DNA

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

DNA Binding Site Sequence Directs Glucocorticoid Receptor Structure and Activity

(2009) S. H. Meijsing et al.   SCIENCE

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

(2008) Anahita Tafvizi et al.   BIOPHYSICAL JOURNAL

The enhanceosome

(2008) Daniel Panne   CURRENT OPINION IN STRUCTURAL BIOLOGY

Visualizing one-dimensional diffusion of proteins along DNA

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

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