DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Probing DNA-protein interactions using single-molecule diffusivity contrast

Journal Article · · Biophysical Reports

Not Available

Sponsoring Organization:
USDOE
OSTI ID:
1810170
Journal Information:
Biophysical Reports, Journal Name: Biophysical Reports Journal Issue: 1 Vol. 1; ISSN 2667-0747
Publisher:
ElsevierCopyright Statement
Country of Publication:
United States
Language:
English

References (56)

The energetics of the interaction of BamHI endonuclease with its recognition site GGATCC11Edited by R. Ebright journal March 2001
Optimal strategy for trapping single fluorescent molecules in solution using the ABEL trap journal December 2009
Analytical ultracentrifugation as a tool for studying protein interactions journal March 2013
Prediction of Hydrodynamic and Other Solution Properties of Rigid Proteins from Atomic- and Residue-Level Models journal August 2011
HullRad: Fast Calculations of Folded and Disordered Protein and Nucleic Acid Hydrodynamic Properties journal February 2018
Protein Environment and DNA Orientation Affect Protein-Induced Cy3 Fluorescence Enhancement journal July 2019
New insights into the spliceosome by single molecule fluorescence microscopy journal December 2011
Mechanism of Transcription Initiation at an Activator-Dependent Promoter Defined by Single-Molecule Observation journal February 2012
Single-molecule approaches to characterizing kinetics of biomolecular interactions journal February 2011
Hydrodynamic Properties of Biomacromolecules and Macromolecular Complexes: Concepts and Methods. A Tutorial Mini-review journal April 2020
Multicolor single-molecule FRET for DNA and RNA processes journal October 2021
Single-molecule views on homologous recombination journal September 2013
Single Particle Tracking: From Theory to Biophysical Applications journal May 2017
Single-Molecule Analysis and Engineering of DNA Motors journal August 2019
A Quantitative Theoretical Framework For Protein-Induced Fluorescence Enhancement–Förster-Type Resonance Energy Transfer (PIFE-FRET) journal April 2016
Conformational Changes Spanning Angstroms to Nanometers via a Combined Protein-Induced Fluorescence Enhancement–Förster Resonance Energy Transfer Method journal February 2017
Demystifying PIFE: The Photophysics Behind the Protein-Induced Fluorescence Enhancement Phenomenon in Cy3 journal May 2015
Resolving Mixtures in Solution by Single-Molecule Rotational Diffusivity journal July 2018
Comparative Thermodynamic Analysis of DNA−Protein Interactions Using Surface Plasmon Resonance and Fluorescence Correlation Spectroscopy journal September 2003
Single-Molecule Studies of RNA Polymerases journal September 2013
Detection of Intensity Change Points in Time-Resolved Single-Molecule Measurements journal January 2005
Binding Kinetics and Affinities of Heterodimeric versus Homodimeric HIV-1 Reverse Transcriptase on DNA–DNA Substrates at the Single-Molecule Level journal November 2012
An Adaptive Anti-Brownian Electrokinetic Trap with Real-Time Information on Single-Molecule Diffusivity and Mobility journal June 2011
A general approach to visualize protein binding and DNA conformation without protein labelling journal March 2016
Single-molecule motions enable direct visualization of biomolecular interactions in solution journal March 2014
Nonblinking and long-lasting single-molecule fluorescence imaging journal October 2006
Super-resolution imaging of multiple cells by optimized flat-field epi-illumination journal October 2016
Electrophoretic mobility shift assay (EMSA) for detecting protein–nucleic acid interactions journal July 2007
Interferometric scattering microscopy and its combination with single-molecule fluorescence imaging journal March 2016
ErbB1 dimerization is promoted by domain co-confinement and stabilized by ligand binding journal October 2011
Initial state of DNA-Dye complex sets the stage for protein induced fluorescence modulation journal May 2019
ABEL-FRET: tether-free single-molecule FRET with hydrodynamic profiling journal June 2021
Protein induced fluorescence enhancement (PIFE) for probing protein–nucleic acid interactions journal January 2014
Breaking the concentration limit of optical single-molecule detection journal January 2014
Recent advances in twisted intramolecular charge transfer (TICT) fluorescence and related phenomena in materials chemistry journal January 2016
Single-molecule and ensemble fluorescence assays for a functionally important conformational change in T7 DNA polymerase journal July 2007
Orientation dependence in fluorescent energy transfer between Cy3 and Cy5 terminally attached to double-stranded nucleic acids journal August 2008
Single-molecule measurements of synthesis by DNA polymerase with base-pair resolution journal December 2009
Protein induced fluorescence enhancement as a single molecule assay with short distance sensitivity journal April 2011
Ionic effects on the elasticity of single DNA molecules journal June 1997
Changes in solvation during DNA binding and cleavage are critical to altered specificity of the EcoRI endonuclease journal March 1998
A simple procedure to improve the surface passivation for single molecule fluorescence studies journal June 2015
How do site-specific DNA-binding proteins find their targets? journal June 2004
Asymmetric DNA recognition by the OkrAI endonuclease, an isoschizomer of BamHI journal September 2010
Single-molecule multiparameter fluorescence spectroscopy reveals directional MutS binding to mismatched bases in DNA journal February 2012
Single-molecule microscopy reveals new insights into nucleotide selection by DNA polymerase I journal June 2012
Nucleosomes accelerate transcription factor dissociation journal December 2013
Direct observation of mobility state transitions in RNA trajectories by sensitive single molecule feedback tracking journal November 2014
Cytosolic Viral Sensor RIG-I Is a 5'-Triphosphate-Dependent Translocase on Double-Stranded RNA journal February 2009
Probing Allostery Through DNA journal February 2013
Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes journal December 2016
Mechanics and Single-Molecule Interrogation of DNA Recombination journal June 2016
Single-Molecule Views of Protein Movement on Single-Stranded DNA journal June 2012
Molecular Traffic Jams on DNA journal May 2013
Flexibility of DNA journal June 1988
Robust model-based analysis of single-particle tracking experiments with Spot-On journal January 2018

Related Subjects