Rare-cutter enzyme

A rare-cutter enzyme is a restriction enzyme with a recognition sequence which occurs only rarely in a genome. An example is NotI, which cuts after the first GC of a 5'-GCGGCCGC-3' sequence; restriction enzymes with six-base recognition sequences are often also called rare-cutter enzymes.

They are used in top-down mapping to cut a chromosome into chunks large enough to be handled by other means but small enough that there are not too many to keep track of.