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

doi:10.1016/j.bpj.2011.09.064

Title: Visual Analysis of Concerted Cleavage by Type IIF Restriction Enzyme SfiI in Subsecond Time Region

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

Publication Date:: Thu Dec 01 00:00:00 EST 2011

Sponsoring Org.:: USDOE

OSTI Identifier:: 1197942

Grant/Contract Number:: FG02-08ER64579

Resource Type:: Published Article

Journal Name:: Biophysical Journal

Additional Journal Information:: Journal Name: Biophysical Journal Journal Volume: 101 Journal Issue: 12; Journal ID: ISSN 0006-3495

Publisher:: Elsevier

Country of Publication:: United States

Language:: English

Citation Formats


                    Suzuki, Yuki, Gilmore, Jamie L., Yoshimura, Shige H., Henderson, Robert M., Lyubchenko, Yuri L., and Takeyasu, Kunio. Visual Analysis of Concerted Cleavage by Type IIF Restriction Enzyme SfiI in Subsecond Time Region.  United States: N. p., 2011. 
Web.  doi:10.1016/j.bpj.2011.09.064.

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                    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.  United States.  https://doi.org/10.1016/j.bpj.2011.09.064

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                    Suzuki, Yuki, Gilmore, Jamie L., Yoshimura, Shige H., Henderson, Robert M., Lyubchenko, Yuri L., and Takeyasu, Kunio. Thu .  
"Visual Analysis of Concerted Cleavage by Type IIF Restriction Enzyme SfiI in Subsecond Time Region".  United States.  https://doi.org/10.1016/j.bpj.2011.09.064.

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@article{osti_1197942,

  title        = {Visual Analysis of Concerted Cleavage by Type IIF Restriction Enzyme SfiI in Subsecond Time Region},

  author       = {Suzuki, Yuki and Gilmore, Jamie L. and Yoshimura, Shige H. and Henderson, Robert M. and Lyubchenko, Yuri L. and Takeyasu, Kunio},

  abstractNote = {},

  doi          = {10.1016/j.bpj.2011.09.064},

  journal      = {Biophysical Journal},

  number       = 12,

  volume       = 101,

  place        = {United States},

  year         = {Thu Dec 01 00:00:00 EST 2011},

  month        = {Thu Dec 01 00:00:00 EST 2011}

}

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https://doi.org/10.1016/j.bpj.2011.09.064

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Works referenced in this record:

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Title: Visual Analysis of Concerted Cleavage by Type IIF Restriction Enzyme SfiI in Subsecond Time Region

Citation Formats

DNA cleavage reactions by type II restriction enzymes that require two copies of their recognition sites 1 1Edited by J. Karn journal, August 2001

Analysis of DNA looping interactions by type II restriction enzymes that require two copies of their recognition sites 1 1Edited by J. Karn journal, August 2001

A type II restriction endonuclease with an eight nucleotide specificity from Streptomyces fimbriatus journal, January 1984

Effect of DNA Supercoiling on the Geometry of Holliday Junctions journal, October 2006

Direct Visualization of Dynamic Protein-DNA Interactions with a Dedicated Atomic Force Microscope journal, June 1998

Dynamics of Nucleosomes Revealed by Time-Lapse Atomic Force Microscopy journal, August 2009

Single-Molecule Dynamics of the DNA− Eco RII Protein Complexes Revealed with High-Speed Atomic Force Microscopy journal, October 2009

Molecular dynamics of DNA and nucleosomes in solution studied by fast-scanning atomic force microscopy journal, May 2010

SfiI endonuclease activity is strongly influenced by the non-specific sequence in the middle of its recognition site journal, April 2001

Direct real-time molecular scale visualisation of the degradation of condensed DNA complexes exposed to DNase I journal, July 2003

Recombination by resolvase to analyse DNA communications by the SfiI restriction endonuclease. journal, March 1996

Dissecting protein-induced DNA looping dynamics in real time journal, July 2009

A high-speed atomic force microscope for studying biological macromolecules journal, October 2001

Changing endonuclease EcoRII Tyr308 to Phe abolishes cleavage but not recognition: possible homology with the int-family of recombinases journal, January 1993

Dynamics of DNA Loop Capture by the SfiI Restriction Endonuclease on Supercoiled and Relaxed DNA journal, May 2004

Fast-scanning atomic force microscopy reveals the ATP/ADP-dependent conformational changes of GroEL journal, September 2006

Direct Observation of One-Dimensional Diffusion and Transcription by Escherichia coli RNA Polymerase journal, October 1999

Diversity of Type II restriction endonucleases that require two DNA recognition sites journal, November 2003

DNA excision by the SfiI restriction endonuclease journal, August 1998

AFM for analysis of structure and dynamics of DNA and protein–DNA complexes journal, March 2009

DNA looping by the SfiI restriction endonuclease journal, August 1998

Probing Interactions within the Synaptic DNA-SfiI Complex by AFM Force Spectroscopy journal, February 2007

DNA topoisomerase and recombinase activities in Nae I restriction endonuclease journal, March 1995

Differences between Ca 2+ and Mg 2+ in DNA binding and release by the SfiI restriction endonuclease: implications for DNA looping journal, July 2009

Site-specific labeling of supercoiled DNA journal, September 2006

Specificity from the Synapsis of DNA Elements by the Sfi I Endonuclease journal, June 1999

Fast-scan atomic force microscopy reveals that the type III restriction enzyme EcoP15I is capable of DNA translocation and looping journal, July 2007

TheSfiI Restriction Endonuclease Makes a Four-strand DNA Break at Two Copies of its Recognition Sequence journal, May 1995

Direct observation of DNA translocation and cleavage by the EcoKI endonuclease using atomic force microscopy journal, January 1999

Direct Visualization of the EcoRII−DNA Triple Synaptic Complex by Atomic Force Microscopy journal, September 2007

Dynamics of Synaptic SfiI-DNA Complex: Single-Molecule Fluorescence Analysis journal, May 2007

DNA Strand Arrangement within the SfiI−DNA Complex: Atomic Force Microscopy Analysis journal, December 2005

DNA Cleavage at Two Recognition Sites by theSfiI Restriction Endonuclease: Salt Dependence ofCisandTransInteractions between Distant DNA Sites journal, September 1995

Fast-scanning atomic force microscopy reveals the molecular mechanism of DNA cleavage by ApaI endonuclease journal, January 2006

A Switch in the Mechanism of Communication between the Two DNA-Binding Sites in the SfiI Restriction Endonuclease journal, November 2007

DNA cleavage reactions by type II restriction enzymes that require two copies of their recognition sites 1 1Edited by J. Karn
journal, August 2001

Analysis of DNA looping interactions by type II restriction enzymes that require two copies of their recognition sites 1 1Edited by J. Karn
journal, August 2001

A type II restriction endonuclease with an eight nucleotide specificity from Streptomyces fimbriatus
journal, January 1984

Effect of DNA Supercoiling on the Geometry of Holliday Junctions
journal, October 2006

Direct Visualization of Dynamic Protein-DNA Interactions with a Dedicated Atomic Force Microscope
journal, June 1998

Dynamics of Nucleosomes Revealed by Time-Lapse Atomic Force Microscopy
journal, August 2009

Single-Molecule Dynamics of the DNA− Eco RII Protein Complexes Revealed with High-Speed Atomic Force Microscopy
journal, October 2009

Molecular dynamics of DNA and nucleosomes in solution studied by fast-scanning atomic force microscopy
journal, May 2010

SfiI endonuclease activity is strongly influenced by the non-specific sequence in the middle of its recognition site
journal, April 2001

Direct real-time molecular scale visualisation of the degradation of condensed DNA complexes exposed to DNase I
journal, July 2003

Recombination by resolvase to analyse DNA communications by the SfiI restriction endonuclease.
journal, March 1996

Dissecting protein-induced DNA looping dynamics in real time
journal, July 2009

A high-speed atomic force microscope for studying biological macromolecules
journal, October 2001

Changing endonuclease EcoRII Tyr308 to Phe abolishes cleavage but not recognition: possible homology with the int-family of recombinases
journal, January 1993

Dynamics of DNA Loop Capture by the SfiI Restriction Endonuclease on Supercoiled and Relaxed DNA
journal, May 2004

Fast-scanning atomic force microscopy reveals the ATP/ADP-dependent conformational changes of GroEL
journal, September 2006

Direct Observation of One-Dimensional Diffusion and Transcription by Escherichia coli RNA Polymerase
journal, October 1999

Diversity of Type II restriction endonucleases that require two DNA recognition sites
journal, November 2003

DNA excision by the SfiI restriction endonuclease
journal, August 1998

AFM for analysis of structure and dynamics of DNA and protein–DNA complexes
journal, March 2009

DNA looping by the SfiI restriction endonuclease
journal, August 1998

Probing Interactions within the Synaptic DNA-SfiI Complex by AFM Force Spectroscopy
journal, February 2007

DNA topoisomerase and recombinase activities in Nae I restriction endonuclease
journal, March 1995

Differences between Ca 2+ and Mg 2+ in DNA binding and release by the SfiI restriction endonuclease: implications for DNA looping
journal, July 2009

Site-specific labeling of supercoiled DNA
journal, September 2006

Specificity from the Synapsis of DNA Elements by the Sfi I Endonuclease
journal, June 1999

Fast-scan atomic force microscopy reveals that the type III restriction enzyme EcoP15I is capable of DNA translocation and looping
journal, July 2007

TheSfiI Restriction Endonuclease Makes a Four-strand DNA Break at Two Copies of its Recognition Sequence
journal, May 1995

Direct observation of DNA translocation and cleavage by the EcoKI endonuclease using atomic force microscopy
journal, January 1999

Direct Visualization of the EcoRII−DNA Triple Synaptic Complex by Atomic Force Microscopy
journal, September 2007

Dynamics of Synaptic SfiI-DNA Complex: Single-Molecule Fluorescence Analysis
journal, May 2007

DNA Strand Arrangement within the SfiI−DNA Complex: Atomic Force Microscopy Analysis
journal, December 2005

DNA Cleavage at Two Recognition Sites by theSfiI Restriction Endonuclease: Salt Dependence ofCisandTransInteractions between Distant DNA Sites
journal, September 1995

Fast-scanning atomic force microscopy reveals the molecular mechanism of DNA cleavage by ApaI endonuclease
journal, January 2006

A Switch in the Mechanism of Communication between the Two DNA-Binding Sites in the SfiI Restriction Endonuclease
journal, November 2007