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According to NCBI, type I REases have a specific target sequence but randomly make cuts at sites far from the target sequence.

How does the restriction enzyme travel from the target sequence to the distant site of restriction, and what is the point of having a target sequence if the cuts are random and far away from the target sequence?

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  • $\begingroup$ The enzymes don't need to travel down the DNA to get from their binding site to their cut site, if the sites are far enough apart the DNA can bend back around and the protein could touch both sites at once. I'm not familiar enough with this class of enzymes to be sure. $\endgroup$ – user137 Aug 21 '14 at 22:43
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To answer your last question first: as long as a restriction enzyme recognises a specific sequence then goes on to cut the DNA it really doesn't matter where the cut takes place, as long as the invading DNA is destroyed.

The WP page on restriction enzymes provides a useful summary of the various classes of restriction enzyme, and led me to a review about Type I enzymes here.

Unlike the familiar Type II enzymes, Type I enzymes require ATP, which they use to power their movement along the DNA, once they have been activated by binding their recognition sequence. The HsdR subunit of the enzyme (R, M and S subunits) contains sequence motifs which mark it out as being related to DNA helicases, which, of course, are able to translocate along a duplex and unwind the duplex.

One particularly striking demonstration of the DNA translocation ability of EcoK1 (a Type I enzyme) is described in

Davies et al. (1999) The DNA translocation and ATPase activities of restriction-deficient mutants of EcoKI. J. Molec. Biol. 292: 787-796 doi:10.1006/jmbi.1999.3081

The experiments are based upon the mechanism by which phage T7 injects DNA into E. coli cells. The phage ejects about 850 bp of the 40 kb genome into the host; the entry of the bulk of the DNA is coupled to transcription, first by host RNA polymerase, and subsequently by the phage-specific RNA polymerase, once the corresponding gene has entered the cell. If the drug rifampin is used to block transcription then the whole process stalls. This block is overcome if the initial leader of 850 bp is engineered to contain a recognition sequence for EcoK1 whereupon the restriction enzyme is able to translocate the entire genome into the cell at 100 - 200 bp per second. Mutations in the helicase motifs of the HsdR subunit abolish this activity.

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