ArticleInternational journal of molecular sciences2013
Optical Methods to Study Protein-DNA Interactions in Vitro and in Living Cells at the Single-Molecule Level.
Article in International journal of molecular sciences, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Protein-DNA interaction in tight-binding paradigm.Scientific reports · 2025Article
- Mechanisms of DNA Damage Recognition by UDG and PARP1 in the Nucleosome.Biomolecules · 2025Article
- Protein target search diffusion-association/dissociation free energy landscape around DNA binding site with flanking sequences.Biophysical journal · 2025Article
- Observation of magnet-induced star-like radiation of a plasma created from cancer cells in a laser trap.European biophysics journal : EBJ · 2024Article
- Nonspecific vs. specific DNA binding free energetics of a transcription factor domain protein.Biophysical journal · 2023Article
- smFRET Detection of Cis and Trans DNA Interactions by the BfiI Restriction Endonuclease.The journal of physical chemistry. B · 2023Article
- Single-molecule characterization of target search dynamics of DNA-binding proteins in DNA-condensed droplets.Nucleic acids research · 2023Article
- Cognate DNA Recognition by Engrailed Homeodomain Involves a Conformational Change Controlled via an Electrostatic-Spring-Loaded Latch.International journal of molecular sciences · 2022Article
- Recognition and repair of oxidatively generated DNA lesions in plasmid DNA by a facilitated diffusion mechanism.The Biochemical journal · 2021Article
- Oriented Soft DNA Curtains for Single-Molecule Imaging.Langmuir : the ACS journal of surfaces and colloids · 2021Article
- Discrete-state stochastic kinetic models for target DNA search by proteins: Theory and experimental applications.Biophysical chemistry · 2021Review
- Data on the target search by a single protein on DNA measured with ultrafast force-clamp spectroscopy.Data in brief · 2019Article
- Facilitated Diffusion Mechanisms in DNA Base Excision Repair and Transcriptional Activation.Chemical reviews · 2018Review
- Sliding of a single lac repressor protein along DNA is tuned by DNA sequence and molecular switching.Nucleic acids research · 2018Article
- Hyperstretching DNA.Nature communications · 2017Article
- Recent insights from in vitro single-molecule studies into nucleosome structure and dynamics.Biophysical reviews · 2016Review
- Combining single-molecule manipulation and imaging for the study of protein-DNA interactions.Journal of visualized experiments : JoVE · 2014Article
- Single molecule techniques in DNA repair: a primer.DNA repair · 2014Review
- Positive and negative impacts of nonspecific sites during target location by a sequence-specific DNA-binding protein: origin of the optimal search at physiological ionic strength.Nucleic acids research · 2014Article
- Toward single-molecule optical mapping of the epigenome.ACS nano · 2014Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The maintenance of intact genetic information, as well as the deployment of transcription for specific sets of genes, critically rely on a family of proteins interacting with DNA and recognizing specific sequences or features. The mechanisms by which these proteins search for target DNA are the subject of intense investigations employing a variety of methods in biology. A large interest in these processes stems from the faster-than-diffusion association rates, explained in current models by a combination of 3D and 1D diffusion. Here, we present a review of the single-molecule approaches at the forefront of the study of protein-DNA interaction dynamics and target search in vitro and in vivo. Flow stretch, optical and magnetic manipulation, single fluorophore detection and localization as well as combinations of different methods are described and the results obtained with these techniques are discussed in the framework of the current facilitated diffusion model.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.