ArticleNucleic acids research2015
Probing a label-free local bend in DNA by single molecule tethered particle motion.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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Who cites it
8 citing papers in PubMed, 30 citations in OpenAlex.
- Single-Molecule Methods for Investigating the Double-Stranded DNA Bendability.Molecules and cells · 2022Review
- Post-replicative pairing of sister ter regions in Escherichia coli involves multiple activities of MatP.Nature communications · 2020Article
- Understanding the paradoxical mechanical response of in-phase A-tracts at different force regimes.Nucleic acids research · 2020Article
- Plasmon Rulers as a Probe for Real-Time Microsecond Conformational Dynamics of Single Molecules.Nano letters · 2018Article
- Single-Molecule Tethered Particle Motion: Stepwise Analyses of Site-Specific DNA Recombination.Micromachines · 2018Review
- Article
- How does temperature impact the conformation of single DNA molecules below melting temperature?Nucleic acids research · 2018Article
- FtsK translocation permits discrimination between an endogenous and an imported Xer/dif recombination complex.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
Corrections and comments
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Authors and funding
8 authors at 5 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Being capable of characterizing DNA local bending is essential to understand thoroughly many biological processes because they involve a local bending of the double helix axis, either intrinsic to the sequence or induced by the binding of proteins. Developing a method to measure DNA bend angles that does not perturb the conformation of the DNA itself or the DNA-protein complex is a challenging task. Here, we propose a joint theory-experiment high-throughput approach to rigorously measure such bend angles using the Tethered Particle Motion (TPM) technique. By carefully modeling the TPM geometry, we propose a simple formula based on a kinked Worm-Like Chain model to extract the bend angle from TPM measurements. Using constructs made of 575 base-pair DNAs with in-phase assemblies of one to seven 6A-tracts, we find that the sequence CA6CGG induces a bend angle of 19° ± 4°. Our method is successfully compared to more theoretically complex or experimentally invasive ones such as cyclization, NMR, FRET or AFM. We further apply our procedure to TPM measurements from the literature and demonstrate that the angles of bends induced by proteins, such as Integration Host Factor (IHF) can be reliably evaluated as well.
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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.