Dynamics and consequences of DNA looping by the FokI restriction endonuclease
| Autor: | Lucy E. Catto, Stuart R.W. Bellamy, Susan E. Retter, Stephen E. Halford |
|---|---|
| Rok vydání: | 2008 |
| Předmět: |
Dimer
Plasma protein binding 010402 general chemistry 01 natural sciences 03 medical and health sciences chemistry.chemical_compound 0103 physical sciences Genetics Binding site Deoxyribonucleases Type II Site-Specific 030304 developmental biology 0303 health sciences Binding Sites 010304 chemical physics biology DNA Superhelical Nucleic Acid Enzymes 030302 biochemistry & molecular biology FokI 0104 chemical sciences Kinetics Restriction enzyme chemistry Phosphodiester bond biology.protein Biophysics Nucleic Acid Conformation DNA supercoil Erratum Dimerization DNA Protein Binding |
| Zdroj: | Nucleic Acids Research |
| ISSN: | 1362-4962 0305-1048 |
| DOI: | 10.1093/nar/gkn051 |
| Popis: | Genetic events often require proteins to be activated by interacting with two DNA sites, trapping the intervening DNA in a loop. While much is known about looping equilibria, only a few studies have examined DNA-looping dynamics experimentally. The restriction enzymes that cut DNA after interacting with two recognition sites, such as FokI, can be used to exemplify looping reactions. The reaction pathway for FokI on a supercoiled DNA with two sites was dissected by fast kinetics to reveal, in turn: the initial binding of a protein monomer to each site; the protein-protein association to form the dimer, trapping the loop; the subsequent phosphodiester hydrolysis step. The DNA motion that juxtaposes the sites ought on the basis of Brownian dynamics to take approximately 2 ms, but loop capture by FokI took 230 ms. Hence, DNA looping by FokI is rate limited by protein association rather than DNA dynamics. The FokI endonuclease also illustrated activation by looping: it cut looped DNA 400 times faster than unlooped DNA. |
| Databáze: | OpenAIRE |
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