Multiple LacI-mediated loops revealed by Bayesian statistics and tethered particle motion

Empirical Bayes Methods Enable Advanced Population-Level Analyses of Single-Molecule FRET Experiments

(2014) Jan-Willem van de Meent et al.   BIOPHYSICAL JOURNAL

Tethered Particle Motion Reveals that LacI·DNA Loops Coexist with a Competitor-Resistant but Apparently Unlooped Conformation

(2014) Joel D. Revalee et al.   BIOPHYSICAL JOURNAL

Direct measurement of transcription factor dissociation excludes a simple operator occupancy model for gene regulation

(2014) Petter Hammar et al.   NATURE GENETICS

LacI-DNA-IPTG Loops: Equilibria among Conformations by Single-Molecule FRET

(2013) Kathy A. Goodson et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Extracting intracellular diffusive states and transition rates from single-molecule tracking data

(2013) Fredrik Persson et al.   NATURE METHODS

Dynamic analysis of a diffusing particle in a trapping potential

(2013) Moshe Lindner et al.   PHYSICAL REVIEW E

Interplay of Protein and DNA Structure Revealed in Simulations of the lac Operon

(2013) Luke Czapla et al.   PLoS One

Poly(dA:dT)-Rich DNAs Are Highly Flexible in the Context of DNA Looping

(2013) Stephanie Johnson et al.   PLoS One

The Effect of Nonspecific Binding of Lambda Repressor on DNA Looping Dynamics

(2012) Carlo Manzo et al.   BIOPHYSICAL JOURNAL

Variational Bayes Analysis of a Photon-Based Hidden Markov Model for Single-Molecule FRET Trajectories

(2012) Kenji Okamoto et al.   BIOPHYSICAL JOURNAL

FRET studies of a landscape of Lac repressor-mediated DNA loops

(2012) Aaron R. Haeusler et al.   NUCLEIC ACIDS RESEARCH

High-throughput single-molecule analysis of DNA–protein interactions by tethered particle motion

(2012) Thomas Plénat et al.   NUCLEIC ACIDS RESEARCH

Real-time single-molecule tethered particle motion experiments reveal the kinetics and mechanisms of Cre-mediated site-specific recombination

(2012) Hsiu-Fang Fan   NUCLEIC ACIDS RESEARCH

DNA looping by FokI: the impact of twisting and bending rigidity on protein-induced looping dynamics

(2012) Niels Laurens et al.   NUCLEIC ACIDS RESEARCH

Sequence dependence of transcription factor-mediated DNA looping

(2012) Stephanie Johnson et al.   NUCLEIC ACIDS RESEARCH

Force-free measurements of the conformations of DNA molecules tethered to a wall

(2011) Moshe Lindner et al.   PHYSICAL REVIEW E

Single-Molecule TPM Studies on the Conversion of Human Telomeric DNA

(2010) Jen-Fei Chu et al.   BIOPHYSICAL JOURNAL

A model for the molecular organisation of the IS911 transpososome

(2010) Philippe Rousseau et al.   Mobile DNA

Hidden Markov Analysis of Nucleosome Unwrapping Under Force

(2009) M. Kruithof et al.   BIOPHYSICAL JOURNAL

Learning Rates and States from Biophysical Time Series: A Bayesian Approach to Model Selection and Single-Molecule FRET Data

(2009) Jonathan E. Bronson et al.   BIOPHYSICAL JOURNAL

High Local Concentration: A Fundamental Strategy of Life

(2009) Stefan Oehler et al.   JOURNAL OF MOLECULAR BIOLOGY

Dissecting protein-induced DNA looping dynamics in real time

(2009) Niels Laurens et al.   NUCLEIC ACIDS RESEARCH

Concentration and Length Dependence of DNA Looping in Transcriptional Regulation

(2009) Lin Han et al.   PLoS One

Tetramer opening in LacI-mediated DNA looping

(2009) D. Rutkauskas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Eukaryotic HMGB proteins as replacements for HU in E. coli repression loop formation

(2008) Nicole A. Becker et al.   NUCLEIC ACIDS RESEARCH

Single-molecule manipulation reveals supercoiling-dependent modulation of lac repressor-mediated DNA looping

(2008) Davide Normanno et al.   NUCLEIC ACIDS RESEARCH

Interconvertible Lac Repressor–DNA Loops Revealed by Single-Molecule Experiments

(2008) Oi Kwan Wong et al.   PLOS BIOLOGY

Ligand-induced Conformational Changes and Conformational Dynamics in the Solution Structure of the Lactose Repressor Protein

(2007) Marc Taraban et al.   JOURNAL OF MOLECULAR BIOLOGY