Transient non-specific DNA binding dominates the target search of bacterial DNA-binding proteins

Chromosome-free bacterial cells are safe and programmable platforms for synthetic biology

(2020) Catherine Fan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA surface exploration and operator bypassing during target search

(2020) Emil Marklund et al.   NATURE

Clusters of bacterial RNA polymerase are biomolecular condensates that assemble through liquid–liquid phase separation

(2020) Anne-Marie Ladouceur et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phase separation by ssDNA binding protein controlled via protein−protein and protein−DNA interactions

(2020) Gábor M. Harami et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Receptor-Ligand Rebinding Kinetics in Confinement

(2019) Aykut Erbaş et al.   BIOPHYSICAL JOURNAL

Recent Advances in Understanding σ70-Dependent Transcription Initiation Mechanisms

(2019) Abhishek Mazumder et al.   JOURNAL OF MOLECULAR BIOLOGY

Role of AcrAB-TolC multidrug efflux pump in drug-resistance acquisition by plasmid transfer

(2019) Sophie Nolivos et al.   SCIENCE

Quantification of very low-abundant proteins in bacteria using the HaloTag and epi-fluorescence microscopy

(2019) Alessia Lepore et al.   Scientific Reports

DEAD-box ATPases are global regulators of phase-separated organelles

(2019) Maria Hondele et al.   NATURE

How do DNA-bound proteins leave their binding sites? The role of facilitated dissociation

(2019) Aykut Erbaş et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Visualizing bacterial DNA replication and repair with molecular resolution

(2018) Yilai Li et al.   CURRENT OPINION IN MICROBIOLOGY

Understanding Protein Mobility in Bacteria by Tracking Single Molecules

(2018) Achillefs N. Kapanidis et al.   JOURNAL OF MOLECULAR BIOLOGY

α-Proteobacterial RNA Degradosomes Assemble Liquid-Liquid Phase-Separated RNP Bodies

(2018) Nadra Al-Husini et al.   MOLECULAR CELL

Single-molecule imaging of DNA gyrase activity in living Escherichia coli

(2018) Mathew Stracy et al.   NUCLEIC ACIDS RESEARCH

Ribosome surface properties may impose limits on the nature of the cytoplasmic proteome

(2017) Paul E Schavemaker et al.   eLife

Mechanism of environmentally driven conformational changes that modulate H-NS DNA-bridging activity

(2017) Ramon A van der Valk et al.   eLife

Scc2/Nipbl hops between chromosomal cohesin rings after loading

(2017) James Rhodes et al.   eLife

Development of SimCells as a novel chassis for functional biosensors

(2017) Cordelia P. N. Rampley et al.   Scientific Reports

Stochastic activation of a DNA damage response causes cell-to-cell mutation rate variation

(2016) S. Uphoff et al.   SCIENCE

Single-molecule imaging of UvrA and UvrB recruitment to DNA lesions in living Escherichia coli

(2016) Mathew Stracy et al.   Nature Communications

MatP regulates the coordinated action of topoisomerase IV and MukBEF in chromosome segregation

(2016) Sophie Nolivos et al.   Nature Communications

MicrobeJ, a tool for high throughput bacterial cell detection and quantitative analysis

(2016) Adrien Ducret et al.   Nature Microbiology

Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology

(2015) Michael Feig et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

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

Live-cell superresolution microscopy reveals the organization of RNA polymerase in the bacterial nucleoid

(2015) Mathew Stracy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Concentration- and chromosome-organization-dependent regulator unbinding from DNA for transcription regulation in living cells

(2015) Tai-Yen Chen et al.   Nature Communications

Probing the target search of DNA-binding proteins in mammalian cells using TetR as model searcher

(2015) Davide Normanno et al.   Nature Communications

Targeted DNA degradation using a CRISPR device stably carried in the host genome

(2015) Brian J. Caliando et al.   Nature Communications

The Localization and Action of Topoisomerase IV in Escherichia coli Chromosome Segregation Is Coordinated by the SMC Complex, MukBEF

(2015) Pawel Zawadzki et al.   Cell Reports

MukBEF, a Chromosomal Organizer

(2015) Valentin V. Rybenkov et al.   JOURNAL OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY

Cytoplasmic Dynamics Reveals Two Modes of Nucleoid-Dependent Mobility

(2014) Stella Stylianidou et al.   BIOPHYSICAL JOURNAL

Multilayer chromosome organization through DNA bending, bridging and extrusion

(2014) Stephan Gruber   CURRENT OPINION IN MICROBIOLOGY

What Macromolecular Crowding Can Do to a Protein

(2014) Irina Kuznetsova et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Concentration-Dependent Exchange of Replication Protein A on Single-Stranded DNA Revealed by Single-Molecule Imaging

(2014) Bryan Gibb et al.   PLoS One

A New Coarse-Grained Model for E. coli Cytoplasm: Accurate Calculation of the Diffusion Coefficient of Proteins and Observation of Anomalous Diffusion

(2014) Sabeeha Hasnain et al.   PLoS One

Single-particle tracking reveals that free ribosomal subunits are not excluded from the Escherichia coli nucleoid

(2014) A. Sanamrad et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-molecule tracking in live cells reveals distinct target-search strategies of transcription factors in the nucleus

(2014) Ignacio Izeddin et al.   eLife

Partitioning of RNA Polymerase Activity in Live Escherichia coli from Analysis of Single-Molecule Diffusive Trajectories

(2013) Somenath Bakshi et al.   BIOPHYSICAL JOURNAL

Multiscale Spatial Organization of RNA Polymerase in Escherichia coli

(2013) Ulrike Endesfelder et al.   BIOPHYSICAL JOURNAL

The Bacterial Cytoplasm Has Glass-like Properties and Is Fluidized by Metabolic Activity

(2013) Bradley R. Parry et al.   CELL

How do proteins locate specific targets in DNA?

(2013) Sy Redding et al.   CHEMICAL PHYSICS LETTERS

Chromosome segregation by the Escherichia coli Min system

(2013) B. Di Ventura et al.   Molecular Systems Biology

RecA bundles mediate homology pairing between distant sisters during DNA break repair

(2013) Christian Lesterlin et al.   NATURE

Exploring bacterial cell biology with single-molecule tracking and super-resolution imaging

(2013) Andreas Gahlmann et al.   NATURE REVIEWS MICROBIOLOGY

Single-molecule DNA repair in live bacteria

(2013) S. Uphoff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MinC, MinD, and MinE Drive Counter-oscillation of Early-Cell-Division Proteins Prior to Escherichia coli Septum Formation

(2013) P. Bisicchia et al.   mBio

Chromosome Replication and Segregation in Bacteria

(2012) Rodrigo Reyes-Lamothe et al.   Annual Review of Genetics

Biologistics—Diffusion coefficients for complete proteome of Escherichia coli

(2012) Tomasz Kalwarczyk et al.   BIOINFORMATICS

Geometry-Induced Bursting Dynamics in Gene Expression

(2012) B. Meyer et al.   BIOPHYSICAL JOURNAL

Segregation of molecules at cell division reveals native protein localization

(2012) Dirk Landgraf et al.   NATURE METHODS

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Dissociation and re-association of RNA polymerase with DNA during osmotic stress response in Escherichia coli

(2012) Cedric Cagliero et al.   NUCLEIC ACIDS RESEARCH

Optimal diffusion coefficient estimation in single-particle tracking

(2012) Xavier Michalet et al.   PHYSICAL REVIEW E

In Vivo Architecture and Action of Bacterial Structural Maintenance of Chromosome Proteins

(2012) A. Badrinarayanan et al.   SCIENCE

The lac Repressor Displays Facilitated Diffusion in Living Cells

(2012) P. Hammar et al.   SCIENCE

Subdiffraction-Limit Study of Kaede Diffusion and Spatial Distribution in Live Escherichia coli

(2011) Somenath Bakshi et al.   BIOPHYSICAL JOURNAL

High-throughput, subpixel precision analysis of bacterial morphogenesis and intracellular spatio-temporal dynamics

(2011) Oleksii Sliusarenko et al.   MOLECULAR MICROBIOLOGY

Single-molecule investigations of the stringent response machinery in living bacterial cells

(2011) B. P. English et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Simultaneous single-molecule measurements of phage T7 replisome composition and function reveal the mechanism of polymerase exchange

(2011) Joseph J. Loparo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mobility of Cytoplasmic, Membrane, and DNA-Binding Proteins in Escherichia coli

(2010) Mohit Kumar et al.   BIOPHYSICAL JOURNAL

Macromolecule diffusion and confinement in prokaryotic cells

(2010) Jacek T Mika et al.   CURRENT OPINION IN BIOTECHNOLOGY

Size Dependence of Protein Diffusion in the Cytoplasm of Escherichia coli

(2010) A. Nenninger et al.   JOURNAL OF BACTERIOLOGY

Molecular sieving properties of the cytoplasm of Escherichia coli and consequences of osmotic stress

(2010) Jacek T. Mika et al.   MOLECULAR MICROBIOLOGY

Geometry-controlled kinetics

(2010) O. Bénichou et al.   Nature Chemistry

Concentration-dependent exchange accelerates turnover of proteins bound to double-stranded DNA

(2010) J. S. Graham et al.   NUCLEIC ACIDS RESEARCH

Active Transcription of rRNA Operons Condenses the Nucleoid in Escherichia coli: Examining the Effect of Transcription on Nucleoid Structure in the Absence of Transertion

(2009) J. E. Cabrera et al.   JOURNAL OF BACTERIOLOGY

DNA Ligases: Progress and Prospects

(2009) Stewart Shuman   JOURNAL OF BIOLOGICAL CHEMISTRY

Lateral Diffusion of Membrane Proteins

(2009) Sivaramakrishnan Ramadurai et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Photoactivatable mCherry for high-resolution two-color fluorescence microscopy

(2009) Fedor V Subach et al.   NATURE METHODS

Effects of macromolecular crowding and DNA looping on gene regulation kinetics

(2009) Gene-Wei Li et al.   Nature Physics

Investigating Intracellular Dynamics of FtsZ Cytoskeleton with Photoactivation Single-Molecule Tracking

(2008) Lili Niu et al.   BIOPHYSICAL JOURNAL

Highly inclined thin illumination enables clear single-molecule imaging in cells

(2008) Makio Tokunaga et al.   NATURE METHODS

High-density mapping of single-molecule trajectories with photoactivated localization microscopy

(2008) Suliana Manley et al.   NATURE METHODS

Asymmetric segregation of protein aggregates is associated with cellular aging and rejuvenation

(2008) A. B. Lindner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA