ArticleNucleic acids research2016
DNA binding proteins explore multiple local configurations during docking via rapid rebinding.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
16 citing papers in PubMed.
- Comparative Analysis of Biochemical and Cellular Assay Conditions and the Need for a Buffer That Mimics Cytoplasmic Environments.Molecules (Basel, Switzerland) · 2025Review
- Bridging DNA contacts allow Dps from E. coli to condense DNA.Nucleic acids research · 2024Article
- Bridging DNA contacts allow Dps frombioRxiv : the preprint server for biology · 2024Article
- Polymer modification of SARS-CoV-2 spike protein impacts its ability to bind key receptor.European polymer journal · 2023Article
- Article
- Macromolecular crowding in solution alters huntingtin interaction and aggregation at interfaces.Colloids and surfaces. B, Biointerfaces · 2021Article
- Interference-free photoelectrochemical immunoassays using carboxymethylated dextran-coated and gold-modified TiOAnalytical and bioanalytical chemistry · 2021Article
- Manipulating polymer composition to create low-cost, high-fidelity sensors for indoor COScientific reports · 2021Article
- Enhancement of Adhesion Characteristics of Low-Density Polyethylene Using Atmospheric Plasma Initiated-Grafting of Polyethylene Glycol.Polymers · 2021Article
- Alternative transcription cycle for bacterial RNA polymerase.Nature communications · 2020Article
- Disordered RNA chaperones can enhance nucleic acid folding via local charge screening.Nature communications · 2019Article
- Amino Acid Sequence of Oligopeptide Causes Marked Difference in DNA Compaction and Transcription.Biophysical journal · 2019Article
- Article
- DNA origami scaffold for studying intrinsically disordered proteins of the nuclear pore complex.Nature communications · 2018Article
- How proteins bind to DNA: target discrimination and dynamic sequence search by the telomeric protein TRF1.Nucleic acids research · 2017Article
- Arm-specific cleavage and mutation during reverse transcription of 2΄,5΄-branched RNA by Moloney murine leukemia virus reverse transcriptase.Nucleic acids research · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Finding the target site and associating in a specific orientation are essential tasks for DNA-binding proteins. In order to make the target search process as efficient as possible, proteins should not only rapidly diffuse to the target site but also dynamically explore multiple local configurations before diffusing away. Protein flipping is an example of this second process that has been observed previously, but the underlying mechanism of flipping remains unclear. Here, we probed the mechanism of protein flipping at the single molecule level, using HIV-1 reverse transcriptase (RT) as a model system. In order to test the effects of long-range attractive forces on flipping efficiency, we varied the salt concentration and macromolecular crowding conditions. As expected, increased salt concentrations weaken the binding of RT to DNA while increased crowding strengthens the binding. Moreover, when we analyzed the flipping kinetics, i.e. the rate and probability of flipping, at each condition we found that flipping was more efficient when RT bound more strongly. Our data are consistent with a view that DNA bound proteins undergo multiple rapid re-binding events, or short hops, that allow the protein to explore other configurations without completely dissociating from the DNA.
Indexed as
Identifiers
What OpenQuestion holds
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.