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 seven and eight base pair recognition sequences are often also called rare-cutter enzymes (six bp recognition sequences are much more common).
For example, rare-cutter enzymes with 7-nucleotide recognition sites cut once every 47 bp (16,384 bp), and those with 8-nucleotide recognition sites cut every 48 bp (65,536 bp) respectively. They are used in top-down mapping to cut a chromosome into chunks of these sizes on average.
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