Substrate conformational dynamics facilitate structure-specific recognition of gapped DNA by DNA polymerase

Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study

(2018) Björn Hellenkamp et al.   NATURE METHODS

Enhanced spontaneous DNA twisting/bending fluctuations unveiled by fluorescence lifetime distributions promote mismatch recognition by the Rad4 nucleotide excision repair complex

(2017) Sagnik Chakraborty et al.   NUCLEIC ACIDS RESEARCH

DNA and Protein Requirements for Substrate Conformational Changes Necessary for Human Flap Endonuclease-1-catalyzed Reaction

(2016) Sana I. Algasaier et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The intrinsic mechanics of B-DNA in solution characterized by NMR

(2016) Akli Ben Imeddourene et al.   NUCLEIC ACIDS RESEARCH

In vivosingle-RNA tracking shows that most tRNA diffuses freely in live bacteria

(2016) Anne Plochowietz et al.   NUCLEIC ACIDS RESEARCH

Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability

(2016) Thuy T. M. Ngo et al.   Nature Communications

Real-time single-molecule studies of the motions of DNA polymerase fingers illuminate DNA synthesis mechanisms

(2015) Geraint W. Evans et al.   NUCLEIC ACIDS RESEARCH

Characterization of organic fluorophores for in vivo FRET studies based on electroporated molecules

(2014) A. Plochowietz et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Long-Lived Intracellular Single-Molecule Fluorescence Using Electroporated Molecules

(2013) Robert Crawford et al.   BIOPHYSICAL JOURNAL

Alternating-laser excitation: single-molecule FRET and beyond

(2013) Johannes Hohlbein et al.   CHEMICAL SOCIETY REVIEWS

Coarse-grained simulations of DNA overstretching

(2013) Flavio Romano et al.   JOURNAL OF CHEMICAL PHYSICS

Single-molecule characterization of Fen1 and Fen1/PCNA complexes acting on flap substrates

(2013) Timothy D. Craggs et al.   NUCLEIC ACIDS RESEARCH

On the biophysics and kinetics of toehold-mediated DNA strand displacement

(2013) Niranjan Srinivas et al.   NUCLEIC ACIDS RESEARCH

Coarse-graining DNA for simulations of DNA nanotechnology

(2013) Jonathan P. K. Doye et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

Conformational landscapes of DNA polymerase I and mutator derivatives establish fidelity checkpoints for nucleotide insertion

(2013) Johannes Hohlbein et al.   Nature Communications

Single-Stranded DNA within Nanopores: Conformational Dynamics and Implications for Sequencing; a Molecular Dynamics Simulation Study

(2012) Andrew T. Guy et al.   BIOPHYSICAL JOURNAL

The Transcription Bubble of the RNA Polymerase–Promoter Open Complex Exhibits Conformational Heterogeneity and Millisecond-Scale Dynamics: Implications for Transcription Start-Site Selection

(2012) Nicole C. Robb et al.   JOURNAL OF MOLECULAR BIOLOGY

A toolkit and benchmark study for FRET-restrained high-precision structural modeling

(2012) Stanislav Kalinin et al.   NATURE METHODS

Single-molecule multiparameter fluorescence spectroscopy reveals directional MutS binding to mismatched bases in DNA

(2012) Michele Cristóvão et al.   NUCLEIC ACIDS RESEARCH

Single-molecule microscopy reveals new insights into nucleotide selection by DNA polymerase I

(2012) Radoslaw P. Markiewicz et al.   NUCLEIC ACIDS RESEARCH

Interactions of replication versus repair DNA substrates with the Pol I DNA polymerases from Escherichia coli and Thermus aquaticus

(2011) Yanling Yang et al.   BIOPHYSICAL CHEMISTRY

Human Flap Endonuclease Structures, DNA Double-Base Flipping, and a Unified Understanding of the FEN1 Superfamily

(2011) Susan E. Tsutakawa et al.   CELL

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

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

Accurate Distance Determination of Nucleic Acids via Förster Resonance Energy Transfer: Implications of Dye Linker Length and Rigidity

(2011) Simon Sindbert et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Origins of Specificity in Protein-DNA Recognition

(2010) Remo Rohs et al.   Annual Review of Biochemistry

Single-Molecule FRET TACKLE Reveals Highly Dynamic Mismatched DNA−MutS Complexes

(2010) Lauryn E. Sass et al.   BIOCHEMISTRY

Sensing DNA Opening in Transcription Using Quenchable Förster Resonance Energy Transfer

(2010) Thorben Cordes et al.   BIOCHEMISTRY

Conformational Analysis of DNA Repair Intermediates by Time-Resolved Fluorescence Spectroscopy

(2009) Su Lin et al.   JOURNAL OF PHYSICAL CHEMISTRY A

PCNA and XPF cooperate to distort DNA substrates

(2009) Richard D. Hutton et al.   NUCLEIC ACIDS RESEARCH

3D-DART: a DNA structure modelling server

(2009) M. van Dijk et al.   NUCLEIC ACIDS RESEARCH

Conformational transitions in DNA polymerase I revealed by single-molecule FRET

(2009) Y. Santoso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Red light, green light: probing single molecules using alternating-laser excitation

(2008) Yusdi Santoso et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

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

(2008) Makio Tokunaga et al.   NATURE METHODS