DNA cleavage site selection by type III restriction enzymes provides evidence for head-on protein collisions following 1D bidirectional motion

FW Schwarz, K van Aelst, J Toth, R Seidel, MD Szczelkun

Research output: Contribution to journalArticle (Academic Journal)peer-review

8 Citations (Scopus)

Abstract

DNA cleavage by the Type III Restriction–Modification enzymes requires communication in 1D between two distant indirectly-repeated recognitions sites, yet results in non-specific dsDNA cleavage close to only one of the two sites. To test a recently proposed ATP-triggered DNA sliding model, we addressed why one site is selected over another during cleavage. We examined the relative cleavage of a pair of identical sites on DNA substrates with different distances to a free or protein blocked end, and on a DNA substrate using different relative concentrations of protein. Under these conditions a bias can be induced in the cleavage of one site over the other. Monte-Carlo simulations based on the sliding model reproduce the experimentally observed behaviour. This suggests that cleavage site selection simply reflects the dynamics of the preceding stochastic enzyme events that are consistent with bidirectional motion in 1D and DNA cleavage following head-on protein collision.
Translated title of the contributionDNA cleavage site selection by type III restriction enzymes provides evidence for head-on protein collisions following 1D bidirectional motion
Original languageEnglish
Pages (from-to)8042 - 8051
Number of pages10
JournalNucleic Acids Research
Volume39 (18)
DOIs
Publication statusPublished - Oct 2011

Bibliographical note

Other: First published on line 30th June 2011

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