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Nucleic Acids Research 2004 32(22):6540-6547; doi:10.1093/nar/gkh999
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Published online 14 December 2004

Nucleic Acids Research, Vol. 32 No. 22 © Oxford University Press 2004; all rights reserved

Initiation of translocation by Type I restriction-modification enzymes is associated with a short DNA extrusion

John van Noort, Thijn van der Heijden, Christina F. Dutta1, Keith Firman1,* and Cees Dekker

Delft University of Technology, Faculty of Applied Sciences and Dimes, Lorentzweg 1, 2628 CJ Delft, The Netherlands and 1 IBBS Biophysics Laboratories, School of Biological Sciences, University of Portsmouth, King Henry Building, King Henry I Street, Portsmouth PO1 2DY, UK

* To whom correspondence should be addressed. Tel: +44 23 92842059; Fax: +44 23 92842070; Email: keith.firman{at}port.ac.uk
Present address: John van Noort, Department of Biophysics, Huygens Laboratory, Leiden University, 2300 RA Leiden, The Netherlands

Received as resubmission September 21, 2004; Revised and Accepted November 24, 2004

Recognition of ‘foreign’ DNA by Type I restriction–modification (R-M) enzymes elicits an ATP-dependent switch from methylase to endonuclease activity, which involves DNA translocation by the restriction subunit HsdR. Type I R-M enzymes are composed of three (Hsd) subunits with a stoichiometry of HsdR2:HsdM2:HsdS1 (R2-complex). However, the EcoR124I R-M enzyme can also exist as a cleavage deficient, sub-assembly of HsdR1:HsdM2:HsdS1 (R1-complex). ATP{gamma}S was used to trap initial translocation complexes, which were visualized by Atomic Force Microscopy (AFM). In the R1-complex, a small bulge, associated with a shortening in the contour-length of the DNA of 8 nm, was observed. This bulge was found to be sensitive to single-strand DNA nucleases, indicative of non-duplexed DNA. R2-complexes appeared larger in the AFM images and the DNA contour length showed a shortening of ~11 nm, suggesting that two bulges were formed. Disclosure of the structure of the first stage after the recognition-translocation switch of Type I restriction enzymes forms an important first step in resolving a detailed mechanistic picture of DNA translocation by SF-II DNA translocation motors.


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