| Title | Diffusion of the Restriction Nuclease EcoRI along DNA. | | Author(s) | Rau DC, Sidorova NY | | Institution | Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-0924. | | Source | J Mol Biol 2009 Oct 26. | | Abstract | Many specific sequence DNA binding proteins locate their target sequence by first binding to DNA nonspecifically, then linearly diffusing or hopping along DNA until either the protein dissociates from the DNA or it finds the recognition sequence. We have devised a method for measuring 1-dimensional diffusion along DNA based on the ratio of the dissociation rates of EcoRI from DNA fragments containing one and two specific binding sites. Our extensive measurements of dissociation rates and specific-nonspecific relative binding constants of the restriction nuclease EcoRI enable us to determine the diffusion rate of nonspecifically bound protein along the DNA. By varying the distance between the two binding sites we confirm a linear diffusion mechanism. The sliding rate is relatively insensitive to salt concentration and osmotic pressure indicating the protein moves smoothly along the DNA probably following the helical phosphate-sugar backbone of DNA. We calculate a diffusion coefficient for EcoRI of 3 x 10(4) bp(2)sec(-1). EcoRI is able to diffuse approximately 150 base pairs on average along DNA in 1 second. This diffusion rate is about 2000-fold slower than the diffusion of the free protein in solution. A factor of 40-50 can be accounted for by a rotational friction resulting from following the helical path of the DNA backbone. Two possibilities could account for remaining activation energy: the salt bridges between the DNA and protein are transiently broken or the water structure at the protein-DNA interface is disrupted as the two surfaces move past one another. | | Language | ENG | | Pub Type(s) | JOURNAL ARTICLE
| | PubMed ID | 19874828 |
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