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  • Title: DNA looping and translocation provide an optimal cleavage mechanism for the type III restriction enzymes.
    Author: Crampton N, Roes S, Dryden DT, Rao DN, Edwardson JM, Henderson RM.
    Journal: EMBO J; 2007 Aug 22; 26(16):3815-25. PubMed ID: 17660745.
    Abstract:
    EcoP15I is a type III restriction enzyme that requires two recognition sites in a defined orientation separated by up to 3.5 kbp to efficiently cleave DNA. The mechanism through which site-bound EcoP15I enzymes communicate between the two sites is unclear. Here, we use atomic force microscopy to study EcoP15I-DNA pre-cleavage complexes. From the number and size distribution of loops formed, we conclude that the loops observed do not result from translocation, but are instead formed by a contact between site-bound EcoP15I and a nonspecific region of DNA. This conclusion is confirmed by a theoretical polymer model. It is further shown that translocation must play some role, because when translocation is blocked by a Lac repressor protein, DNA cleavage is similarly blocked. On the basis of these results, we present a model for restriction by type III restriction enzymes and highlight the similarities between this and other classes of restriction enzymes.
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