@article{df119f8348e4415ea1692e8bf566a9a9,
title = "Visual analysis of concerted cleavage by type IIF restriction enzyme SfiI in subsecond time region",
abstract = "Many DNA regulatory factors require communication between distantly separated DNA sites for their activity. The type IIF restriction enzyme SfiI is often used as a model system of site communication. Here, we used fast-scanning atomic force microscopy to monitor the DNA cleavage process with SfiI and the changes in the single SfiI-DNA complex in the presence of either Mg 2+ or Ca 2+ at a scan rate of 1-2 fps. The increased time resolution allowed us to visualize the concerted cleavage of the protein at two cognate sites. The four termini generated by the cleavage were released in a multistep manner. The high temporal resolution enabled us to visualize the translocation of a DNA strand on a looped complex and intersegmental transfer of the SfiI protein in which swapping of the site is performed without protein dissociation. On the basis of our results, we propose that the SfiI tetramer can remain bound to one of the sites even after cleavage, allowing the other site on the DNA molecule to fill the empty DNA-binding cleft by combining a one-dimensional diffusion-mediated sliding and a segment transfer mechanism.",
author = "Yuki Suzuki and Gilmore, {Jamie L.} and Yoshimura, {Shige H.} and Henderson, {Robert M.} and Lyubchenko, {Yuri L.} and Kunio Takeyasu",
note = "Funding Information: This work was supported by a Human Frontier Science Program (K.T.) and by grants from the Japanese Ministry of Education, Culture, Sports, Science and Technology (Grant-in-Aid for Scientific Research on Priority Areas to K.T. and S.H.Y.) and from Japan Society for the Promotion of Science (Grant-in-Aid for Basic Research (A) to K.T. and (B) to S. H.Y., Japan-UK Bilateral Joint Project Award to K.T.), grants to Y.L.L. from National Science Foundation (NSF) (PHY-061590), U. S. Department of Energy (DOE) (DE-FG02-08ER64579), North Atlantic Treaty Organization (NATO) (CBN.NR.NRSFP 983204) and Nebraska Research Initiative (NRI), grant 0812853 (NSF East Asia and Pacific Summer Institutes (EAPSI) program) and a structural biology and biophysics fellowship to J.L.G. provided by Graduate Assistance in Areas of National Need (GAANN) funding (U.S. Department of Education grant P200A060150), and by SENTAN, JST (Japan Science and Technology Agency). R.M.H. holds a Biotechnology and Biological Sciences Research Council (BBSRC) Japan-Partnering Award. Y.S. is a recipient of the JSPS (Japan Society for the Promotion of Science) research fellow. ",
year = "2011",
month = dec,
day = "21",
doi = "10.1016/j.bpj.2011.09.064",
language = "English (US)",
volume = "101",
pages = "2992--2998",
journal = "Biophysical Journal",
issn = "0006-3495",
publisher = "Biophysical Society",
number = "12",
}