Published online 10 May 2005
Article |
DNA-tension dependence of restriction enzyme activity reveals mechanochemical properties of the reaction pathway
Laser Centre and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, 1081 HV, The Netherlands
*To whom correspondence should be addressed. Tel: +31205987987; Fax: +31205987991; Email: gwuite{at}nat.vu.nl
Received February 8, 2005. Revised April 8, 2005. Accepted April 21, 2005.
Type II restriction endonucleases protect bacteria against phage infections by cleaving recognition sites on foreign double-stranded DNA (dsDNA) with extraordinary specificity. This capability arises primarily from large conformational changes in enzyme and/or DNA upon target sequence recognition. In order to elucidate the connection between the mechanics and the chemistry of DNA recognition and cleavage, we used a single-molecule approach to measure rate changes in the reaction pathway of EcoRV and BamHI as a function of DNA tension. We show that the induced-fit rate of EcoRV is strongly reduced by such tension. In contrast, BamHI is found to be insensitive, providing evidence that both substrate binding and hydrolysis are not influenced by this force. Based on these results, we propose a mechanochemical model of induced-fit reactions on DNA, allowing determination of induced-fit rates and DNA bend angles. Finally, for both enzymes a strongly decreased association rate is obtained on stretched DNA, presumably due to the absence of intradomain dissociation/re-association between non-specific sites (jumping). The obtained results should apply to many other DNA-associated proteins.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  J. van Mameren, P. Gross, G. Farge, P. Hooijman, M. Modesti, M. Falkenberg, G. J. L. Wuite, and E. J. G. Peterman From the Cover: Unraveling the structure of DNA during overstretching by using multicolor, single-molecule fluorescence imaging PNAS, October 27, 2009; 106(43): 18231 - 18236. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. Laurens, S. R. W. Bellamy, A. F. Harms, Y. S. Kovacheva, S. E. Halford, and G. J. L. Wuite Dissecting protein-induced DNA looping dynamics in real time Nucleic Acids Res., September 1, 2009; 37(16): 5454 - 5464. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Kumar, B. C. Han, Z. Shi, J. Jia, Y. P. Wang, Y. T. Zhang, L. Liang, Q. F. Liu, Z. L. Ji, and Y. Z. Chen Update of KDBI: Kinetic Data of Bio-molecular Interaction database Nucleic Acids Res., January 1, 2009; 37(suppl_1): D636 - D641. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. van den Broek, M. A. Lomholt, S.-M. J. Kalisch, R. Metzler, and G. J. L. Wuite How DNA coiling enhances target localization by proteins PNAS, October 14, 2008; 105(41): 15738 - 15742. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. van Mameren, E. J. G. Peterman, and G. J. L. Wuite See me, feel me: methods to concurrently visualize and manipulate single DNA molecules and associated proteins Nucleic Acids Res., August 1, 2008; 36(13): 4381 - 4389. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Bonnet, A. Biebricher, P.-L. Porte, C. Loverdo, O. Benichou, R. Voituriez, C. Escude, W. Wende, A. Pingoud, and P. Desbiolles Sliding and jumping of single EcoRV restriction enzymes on non-cognate DNA Nucleic Acids Res., July 1, 2008; 36(12): 4118 - 4127. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. R. Morgan, R. P. Lyon, D. Y. Maeda, and J. A. Zebala Snap-to-it probes: chelate-constrained nucleobase oligomers with enhanced binding specificity Nucleic Acids Res., June 1, 2008; 36(11): 3522 - 3530. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. Jesudason, L. Black, A. Majumdar, P. Stone, and B. Suki Differential effects of static and cyclic stretching during elastase digestion on the mechanical properties of extracellular matrices J Appl Physiol, September 1, 2007; 103(3): 803 - 811. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. M. Reinhard, S. Sheikholeslami, A. Mastroianni, A. P. Alivisatos, and J. Liphardt Use of plasmon coupling to reveal the dynamics of DNA bending and cleavage by single EcoRV restriction enzymes PNAS, February 20, 2007; 104(8): 2667 - 2672. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. J. Gemmen, R. Millin, and D. E. Smith Tension-dependent DNA cleavage by restriction endonucleases: Two-site enzymes are "switched off" at low force PNAS, August 1, 2006; 103(31): 11555 - 11560. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. v. d. Broek, F. Vanzi, D. Normanno, F. S. Pavone, and G. J.L. Wuite Real-time observation of DNA looping dynamics of Type IIE restriction enzymes NaeI and NarI Nucleic Acids Res., January 10, 2006; 34(1): 167 - 174. [Abstract] [Full Text] [PDF]
|
|