Visual analysis of concerted cleavage by type IIF restriction enzyme SfiI in subsecond time region

Yuki Suzuki, Jamie L. Gilmore, Shige H. Yoshimura, Robert M. Henderson, Yuri L Lyubchenko, Kunio Takeyasu

Research output: Contribution to journalArticle

27 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)2992-2998
Number of pages7
JournalBiophysical journal
Volume101
Issue number12
DOIs
StatePublished - Dec 21 2011

Fingerprint

DNA
Enzymes
Atomic Force Microscopy
DNA Cleavage
Proteins

ASJC Scopus subject areas

  • Biophysics

Cite this

Visual analysis of concerted cleavage by type IIF restriction enzyme SfiI in subsecond time region. / Suzuki, Yuki; Gilmore, Jamie L.; Yoshimura, Shige H.; Henderson, Robert M.; Lyubchenko, Yuri L; Takeyasu, Kunio.

In: Biophysical journal, Vol. 101, No. 12, 21.12.2011, p. 2992-2998.

Research output: Contribution to journalArticle

Suzuki, Yuki ; Gilmore, Jamie L. ; Yoshimura, Shige H. ; Henderson, Robert M. ; Lyubchenko, Yuri L ; Takeyasu, Kunio. / Visual analysis of concerted cleavage by type IIF restriction enzyme SfiI in subsecond time region. In: Biophysical journal. 2011 ; Vol. 101, No. 12. pp. 2992-2998.
@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",
year = "2011",
month = "12",
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",

}

TY - JOUR

T1 - Visual analysis of concerted cleavage by type IIF restriction enzyme SfiI in subsecond time region

AU - Suzuki, Yuki

AU - Gilmore, Jamie L.

AU - Yoshimura, Shige H.

AU - Henderson, Robert M.

AU - Lyubchenko, Yuri L

AU - Takeyasu, Kunio

PY - 2011/12/21

Y1 - 2011/12/21

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84055217526&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84055217526&partnerID=8YFLogxK

U2 - 10.1016/j.bpj.2011.09.064

DO - 10.1016/j.bpj.2011.09.064

M3 - Article

C2 - 22208198

AN - SCOPUS:84055217526

VL - 101

SP - 2992

EP - 2998

JO - Biophysical Journal

JF - Biophysical Journal

SN - 0006-3495

IS - 12

ER -