ArticleBiophysical journal2005
Gapped DNA and cyclization of short DNA fragments.
Article in Biophysical journal, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 35 citations in OpenAlex.
- Article
- Kinetics of DNA looping by Anabaena sensory rhodopsin transducer (ASRT) by using DNA cyclization assay.Scientific reports · 2021Article
- Mechanical Flexibility of DNA: A Quintessential Tool for DNA Nanotechnology.Sensors (Basel, Switzerland) · 2020Review
- Revealing thermodynamics of DNA origami folding via affine transformations.Nucleic acids research · 2020Article
- Single-molecule analysis of i-motif within self-assembled DNA duplexes and nanocircles.Nucleic acids research · 2019Article
- Nucleosome DNA unwrapping does not affect prototype foamy virus integration efficiency or site selection.PloS one · 2019Article
- Motor-like DNA motion due to an ATP-hydrolyzing protein under nanoconfinement.Scientific reports · 2018Article
- Probing the elastic limit of DNA bending.Nucleic acids research · 2014Article
- DNA A-tracts are not curved in solutions containing high concentrations of monovalent cations.Biochemistry · 2013Article
- DNA looping by FokI: the impact of twisting and bending rigidity on protein-induced looping dynamics.Nucleic acids research · 2012Article
- Effect of magnesium ions and temperature on the sequence-dependent curvature of DNA restriction fragments.Journal of physics. Condensed matter : an Institute of Physics journal · 2010Article
- Effect of spontaneous twist on DNA minicircles.Biophysical journal · 2010Article
- First-principles calculation of DNA looping in tethered particle experiments.Physical biology · 2009Article
- Protein-induced local DNA bends regulate global topology of recombination products.Journal of molecular biology · 2007Article
- When a helicase is not a helicase: dsDNA tracking by the motor protein EcoR124I.The EMBO journal · 2006Article
- Loops in DNA: an overview of experimental and theoretical approaches.The European physical journal. E, Soft matter · 2006Review
- DNA conformation on surfaces measured by fluorescence self-interference.Proceedings of the National Academy of Sciences of the United States of America · 2006Article
- Base-stacking and base-pairing contributions into thermal stability of the DNA double helix.Nucleic acids research · 2006Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
We use the cyclization of small DNA molecules, approximately 200 bp in length, to study conformational properties of DNA fragments with single-stranded gaps. The approach is extremely sensitive to DNA conformational properties and, being complemented by computations, allows a very accurate determination of the fragment's conformational parameters. Sequence-specific nicking endonucleases are used to create the 4-nt-long gap. We determined the bending rigidity of the single-stranded region in the gapped DNA. We found that the gap of 4 nt in length makes all torsional orientations of DNA ends equally probable. Our results also show that the gap has isotropic bending rigidity. This makes it very attractive to use gapped DNA in the cyclization experiments to determine DNA conformational properties, since the gap eliminates oscillations of the cyclization efficiency with the DNA length. As a result, the number of measurements is greatly reduced in the approach, and the analysis of the data is greatly simplified. We have verified our approach on DNA fragments containing well-characterized intrinsic bends caused by A-tracts. The obtained experimental results and theoretical analysis demonstrate that gapped-DNA cyclization is an exceedingly sensitive and accurate approach for the determination of DNA bending.
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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.