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 an...

Restriction mapping involves cleaving DNA clones at specific sites with enzymes to produce a set of fragments. These fragments have characteristic lengths which together constitute a multiset (a set allowing repeated elements) called the “fingerprint” of the clone. Clones that overlap with each other share common restriction fragments as long as the region of overlap contains at least two enzym...