ArticleBiophysical journal2009
Determining protein-induced DNA bending in force-extension experiments: theoretical analysis.
Article in Biophysical journal, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
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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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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.
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Who cites it
7 citing papers in PubMed, 14 citations in OpenAlex.
- Dynamic coupling between conformations and nucleotide states in DNA gyrase.Nature chemical biology · 2018Article
- Simulation of DNA Supercoil Relaxation.Biophysical journal · 2016Article
- Gold rotor bead tracking for high-speed measurements of DNA twist, torque and extension.Nature methods · 2014Article
- DNA phosphate crowding correlates with protein cationic side chain density and helical curvature in protein/DNA crystal structures.Nucleic acids research · 2013Article
- Recent developments in single-molecule DNA mechanics.Current opinion in structural biology · 2012Review
- ATP binding controls distinct structural transitions of Escherichia coli DNA gyrase in complex with DNA.Nature structural & molecular biology · 2012Article
- Tightness of knots in a polymer chain.Physical review. E, Statistical, nonlinear, and soft matter physics · 2010Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author at 1 institution in 1 country.
Funding
Abstract
Computer simulations were used to investigate the possibility of determining protein-induced DNA bend angles by measuring the extension of a single DNA molecule. Analysis of the equilibrium sets of DNA conformations showed that shortening of DNA extension by a single protein-induced DNA bend can be as large as 35 nm. The shortening has a maximum value at the extending force of approximately 0.1 pN. At this force, the DNA extension experiences very large fluctuations that dramatically complicate the measurement. Using Brownian dynamics simulation of a DNA molecule extended by force, we were able to estimate the observation time needed to obtain the desired accuracy of the extension measurement. Also, the simulation revealed large fluctuations of the force, acting on the attached magnetic bead from the stretched DNA molecule.
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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.