Dissecting protein-induced DNA looping dynamics in real time
| Autor: | Stephen E. Halford, Stuart R.W. Bellamy, Niels Laurens, August F. Harms, Gijs J.L. Wuite, Yana S. Kovacheva |
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| Přispěvatelé: | Physics of Living Systems |
| Rok vydání: | 2009 |
| Předmět: |
Genetics
0303 health sciences Nucleic Acid Enzymes Reaction scheme Model system DNA Biology Multiple target Kinetics 03 medical and health sciences Restriction enzyme chemistry.chemical_compound 0302 clinical medicine Tethered particle motion Dna cleavage chemistry Nucleic Acid Conformation DNA Cleavage Deoxyribonucleases Type II Site-Specific Biological system 030217 neurology & neurosurgery 030304 developmental biology |
| Zdroj: | Nucleic Acids Research Nucleic Acids Research, 5454-5464. Oxford University Press STARTPAGE=5454;ENDPAGE=5464;ISSN=0305-1048;TITLE=Nucleic Acids Research Laurens, N, Bellamy, S R W, Harms, A F, Kovacheva, Y S, Halford, S E & Wuite, G J L 2009, ' Dissecting protein-induced DNA looping dynamics in real time ', Nucleic Acids Research, pp. 5454-5464 . https://doi.org/10.1093/nar/gkp570 Nucleic Acids Research, 37(16), 5454-5464 |
| ISSN: | 1362-4962 0305-1048 |
| DOI: | 10.1093/nar/gkp570 |
| Popis: | Many proteins that interact with DNA perform or enhance their specific functions by binding simultaneously to multiple target sites, thereby inducing a loop in the DNA. The dynamics and energies involved in this loop formation influence the reaction mechanism. Tethered particle motion has proven a powerful technique to study in real time protein-induced DNA looping dynamics while minimally perturbing the DNA-protein interactions. In addition, it permits many single-molecule experiments to be performed in parallel. Using as a model system the tetrameric Type II restriction enzyme SfiI, that binds two copies of its recognition site, we show here that we can determine the DNA-protein association and dissociation steps as well as the actual process of protein-induced loop capture and release on a single DNA molecule. The result of these experiments is a quantitative reaction scheme for DNA looping by SfiI that is rigorously compared to detailed biochemical studies of SfiI looping dynamics. We also present novel methods for data analysis and compare and discuss these with existing methods. The general applicability of the introduced techniques will further enhance tethered particle motion as a tool to follow DNA-protein dynamics in real time. © 2009 The Author(s). |
| Databáze: | OpenAIRE |
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