Tethered multifluorophore motion reveals equilibrium transition kinetics of single DNA double helices

Identification of Individual Immobilized DNA Molecules by Their Hybridization Kinetics Using Single-Molecule Fluorescence Imaging

(2018) Eric M. Peterson et al.   ANALYTICAL CHEMISTRY

Predicting DNA hybridization kinetics from sequence

(2017) Jinny X. Zhang et al.   Nature Chemistry

Influence of thermodynamically unfavorable secondary structures on DNA hybridization kinetics

(2017) Hiroaki Hata et al.   NUCLEIC ACIDS RESEARCH

Single-Molecule Fluorescence Imaging of Interfacial DNA Hybridization Kinetics at Selective Capture Surfaces

(2016) Eric M. Peterson et al.   ANALYTICAL CHEMISTRY

Purification of Functionalized DNA Origami Nanostructures

(2015) Alan Shaw et al.   ACS Nano

Refinement of Generalized Born Implicit Solvation Parameters for Nucleic Acids and Their Complexes with Proteins

(2015) Hai Nguyen et al.   Journal of Chemical Theory and Computation

DNA hairpins destabilize duplexes primarily by promoting melting rather than by inhibiting hybridization

(2015) John S. Schreck et al.   NUCLEIC ACIDS RESEARCH

Assembly, translocation, and activation of XerCD-difrecombination by FtsK translocase analyzed in real-time by FRET and two-color tethered fluorophore motion

(2015) Peter F. J. May et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tethered Fluorophore Motion: Studying Large DNA Conformational Changes by Single-fluorophore Imaging

(2014) Peter F.J. May et al.   BIOPHYSICAL JOURNAL

Enhanced Tethered-Particle Motion Analysis Reveals Viscous Effects

(2014) Sandip Kumar 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

Cellular Incorporation of Unnatural Amino Acids and Bioorthogonal Labeling of Proteins

(2014) Kathrin Lang et al.   CHEMICAL REVIEWS

Coarse-grained modeling of DNA oligomer hybridization: Length, sequence, and salt effects

(2014) Daniel M. Hinckley et al.   JOURNAL OF CHEMICAL PHYSICS

Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA

(2014) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

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

(2014) Stephanie Johnson et al.   NUCLEIC ACIDS RESEARCH

Single-Molecule Kinetics Reveal Cation-Promoted DNA Duplex Formation Through Ordering of Single-Stranded Helices

(2013) Nicholas F. Dupuis et al.   BIOPHYSICAL JOURNAL

Conformational Dynamics of DNA Hairpins at Millisecond Resolution Obtained from Analysis of Single-Molecule FRET Histograms

(2013) Roman Tsukanov et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Detailed Study of DNA Hairpin Dynamics Using Single-Molecule Fluorescence Assisted by DNA Origami

(2013) Roman Tsukanov et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Coarse-Grained Simulations of RNA and DNA Duplexes

(2013) Tristan Cragnolini et al.   JOURNAL OF PHYSICAL CHEMISTRY B

DNA hybridization kinetics: zippering, internal displacement and sequence dependence

(2013) Thomas E. Ouldridge et al.   NUCLEIC ACIDS RESEARCH

Real-time single-molecule tethered particle motion analysis reveals mechanistic similarities and contrasts of Flp site-specific recombinase with Cre and   Int

(2013) H.-F. Fan et al.   NUCLEIC ACIDS RESEARCH

Conformational transitions during FtsK translocase activation of individual XerCD-dif recombination complexes

(2013) P. Zawadzki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) Carlo Manzo et al.   BIOPHYSICAL JOURNAL

Hidden Markov Analysis of Trajectories in Single-Molecule Experiments and the Effects of Missed Events

(2012) Johannes Stigler et al.   CHEMPHYSCHEM

Sequence-dependent thermodynamics of a coarse-grained DNA model

(2012) Petr Šulc et al.   JOURNAL OF CHEMICAL PHYSICS

A rule of seven in Watson-Crick base-pairing of mismatched sequences

(2012) Ibrahim I Cisse et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2012) Thomas Plénat et al.   NUCLEIC ACIDS RESEARCH

DNA looping by FokI: the impact of synapse geometry on loop topology at varied site orientations

(2012) David A. Rusling 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

Capturing reaction paths and intermediates in Cre-loxP recombination using single-molecule fluorescence

(2012) J. N. M. Pinkney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional Patterning of DNA Origami by Parallel Enzymatic Modification

(2011) Kasper Jahn et al.   BIOCONJUGATE CHEMISTRY

Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model

(2011) Thomas E. Ouldridge et al.   JOURNAL OF CHEMICAL PHYSICS

A primer to scaffolded DNA origami

(2011) Carlos Ernesto Castro et al.   NATURE METHODS

Developing Single-Molecule TPM Experiments for Direct Observation of Successful RecA-Mediated Strand Exchange Reaction

(2011) Hsiu-Fang Fan et al.   PLoS One

Single-Molecule Kinetics and Super-Resolution Microscopy by Fluorescence Imaging of Transient Binding on DNA Origami

(2010) Ralf Jungmann et al.   NANO LETTERS

Hidden Markov Analysis of Nucleosome Unwrapping Under Force

(2009) M. Kruithof et al.   BIOPHYSICAL JOURNAL

The persistence length of double stranded DNA determined using dark field tethered particle motion

(2009) Sanneke Brinkers et al.   JOURNAL OF CHEMICAL PHYSICS

Multilayer DNA Origami Packed on a Square Lattice

(2009) Yonggang Ke et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Control of DNA Strand Displacement Kinetics Using Toehold Exchange

(2009) David Yu Zhang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Self-assembly of DNA into nanoscale three-dimensional shapes

(2009) Shawn M. Douglas et al.   NATURE

Rapid prototyping of 3D DNA-origami shapes with caDNAno

(2009) Shawn M. Douglas et al.   NUCLEIC ACIDS RESEARCH

Direct demonstration and quantification of long-range DNA looping by the λ bacteriophage repressor

(2009) Chiara Zurla et al.   NUCLEIC ACIDS RESEARCH

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

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

(2008) Davide Normanno et al.   NUCLEIC ACIDS RESEARCH

Fast, bias-free algorithm for tracking single particles with variable size and shape

(2008) Andrew J. Berglund et al.   OPTICS EXPRESS

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

(2008) Oi Kwan Wong et al.   PLOS BIOLOGY