Berlin 2008 – scientific programme
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BP: Fachverband Biologische Physik
BP 26: Posters II
BP 26.33: Poster
Thursday, February 28, 2008, 17:00–19:30, Poster A
1D diffusion model for inter-site communication by Type III restriction enzymes — •Subramanian Ramanathan1, Kara van Aelst2, Mark D. Szczelkun2, and Ralf Seidel1 — 1Biotechnology Center, Dresden University of Technology, Germany — 2Department of Biochemistry, University of Bristol, UK
Type III restriction enzymes use ATP hydrolysis to communicate between distant target sites on DNA, which subsequently triggers DNA cleavage. Due to amino acid sequence similarities these enzymes belong to the superfamily 2 of helicases. They are therefore generally believed to be molecular motors that directionally translocate DNA in order to communicate between their target sites. However, the low ATPase activity of these enzymes does not support DNA translocation and alternative models involving passive diffusive looping have been suggested. In order to gain insight into the communication mechanism of type III restriction enzymes we used magnetic tweezers to investigate DNA cleavage of multiple single molecules in parallel. This allowed us to measure the cleavage kinetics while keeping the DNA stretched. We observed rapid DNA cleavage even at the highest stretching forces, where DNA looping is completely abolished. Furthermore, the cleavage rates did not change over a large range of forces. These results provide direct evidence for a communication mechanism between the target sites in 1D, i.e. enzyme movement along the DNA contour, rather than in 3D by diffusive DNA looping. Therefore, given the low ATP consumption, we suggest diffusion rather than active translocation as being the mechanism by which the enzymes move along DNA.