A NEW CLASS OF GENOME RARE CUTTERS

Although significant efforts have been directed at developing efficien t techniques for rare and super rare genome cutting, only limited succ ess has been achieved, Here we propose a new approach to solve this pr oblem, We demonstrate that peptide nucleic acid 'clamps' (bis-PNAs) bi nd strongly and sequence specifically to short homopyrimidine sites on lambda and yeast genomic DNAs, Such binding efficiently shields methy lation/restriction sites which overlap with the bis-PNA binding sites from enzymatic methylation, After removing the bis-PNA, the genomic DN As are quantitatively cleaved by restriction enzymes into a limited nu mber of pieces of lengths from several hundred kbp to several Mbp, By combining various bis-PNAs with different methylation/restriction enzy me pairs, a huge new class of genome rare cutters can be created, Thes e cutters cover the range of recognition specificities where very few, if any, cutters are now available.