ArticleJournal of visualized experiments : JoVE2014
Studying DNA looping by single-molecule FRET.
Article in Journal of visualized experiments : JoVE, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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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.
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Who cites it
9 citing papers in PubMed, 13 citations in OpenAlex.
- First passage time study of DNA strand displacement.Biophysical journal · 2021Article
- Mechanical Flexibility of DNA: A Quintessential Tool for DNA Nanotechnology.Sensors (Basel, Switzerland) · 2020Review
- Determinants of cyclization-decyclization kinetics of short DNA with sticky ends.Nucleic acids research · 2020Article
- Base-Pair Mismatch Can Destabilize Small DNA Loops through Cooperative Kinking.Physical review letters · 2019Article
- Shining a Spotlight on DNA: Single-Molecule Methods to Visualise DNA.Molecules (Basel, Switzerland) · 2019Review
- Coordinated protein and DNA conformational changes govern mismatch repair initiation by MutS.Nucleic acids research · 2018Article
- Single-molecule fluorescence studies on DNA looping.Methods (San Diego, Calif.) · 2016Article
- The Effect of Basepair Mismatch on DNA Strand Displacement.Biophysical journal · 2016Article
- Probing the elastic limit of DNA bending.Nucleic acids research · 2014Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bending of double-stranded DNA (dsDNA) is associated with many important biological processes such as DNA-protein recognition and DNA packaging into nucleosomes. Thermodynamics of dsDNA bending has been studied by a method called cyclization which relies on DNA ligase to covalently join short sticky ends of a dsDNA. However, ligation efficiency can be affected by many factors that are not related to dsDNA looping such as the DNA structure surrounding the joined sticky ends, and ligase can also affect the apparent looping rate through mechanisms such as nonspecific binding. Here, we show how to measure dsDNA looping kinetics without ligase by detecting transient DNA loop formation by FRET (Fluorescence Resonance Energy Transfer). dsDNA molecules are constructed using a simple PCR-based protocol with a FRET pair and a biotin linker. The looping probability density known as the J factor is extracted from the looping rate and the annealing rate between two disconnected sticky ends. By testing two dsDNAs with different intrinsic curvatures, we show that the J factor is sensitive to the intrinsic shape of the dsDNA.
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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.