ArticleJournal of physics. Condensed matter : an Institute of Physics journal2010
Determination of the number of proteins bound non-specifically to DNA.
Article in Journal of physics. Condensed matter : an Institute of Physics journal, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 22 citations in OpenAlex.
- Freezing shortens the lifetime of DNA molecules under tension.Journal of biological physics · 2017Article
- Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes.PLoS computational biology · 2015Article
- Article
- Protein-DNA binding in the absence of specific base-pair recognition.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Tethered particle motion reveals that LacI·DNA loops coexist with a competitor-resistant but apparently unlooped conformation.Biophysical journal · 2014Article
- Positive and negative design for nonconsensus protein-DNA binding affinity in the vicinity of functional binding sites.Biophysical journal · 2013Article
- Crenarchaeal chromatin proteins Cren7 and Sul7 compact DNA by inducing rigid bends.Nucleic acids research · 2013Article
- Stretching DNA to quantify nonspecific protein binding.Physical review. E, Statistical, nonlinear, and soft matter physics · 2012Article
- Nonspecific protein-DNA binding is widespread in the yeast genome.Biophysical journal · 2012Article
- Force-driven unbinding of proteins HU and Fis from DNA quantified using a thermodynamic Maxwell relation.Nucleic acids research · 2011Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
We have determined the change in the number of proteins bound non-specifically to DNA as a function of applied force using force-extension measurements on tethered DNA. Using magnetic tweezers, single molecules of λ DNA were repeatedly stretched and relaxed in the absence and presence of 170 nM λ repressor protein (CI). CI binds to six specific sites of λ DNA with nanomolar affinity and also binds non-specifically with micromolar affinity. The force versus extension data were analyzed using a recently developed theoretical framework for quantitative determination of protein binding to the DNA. The results indicate that the non-specific binding of CI changes the force-extension relation significantly in comparison to that of naked DNA. The DNA tether used in our experiment would have about 640 bound repressors, if it was completely saturated with bound proteins. We find that as the pulling force on DNA is reduced from 4.81 to 0.13 pN, approximately 138 proteins bind to DNA, which is about 22% of the length of the tethered DNA. Our results show that 0.13 pN is not low enough to cause saturation of DNA by repressor and 4.81 pN is also not high enough to eliminate all the repressors bound to DNA. This demonstrates that the force-extension relation provides an effective approach for estimating the number of proteins bound non-specifically to a DNA molecule.
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