LONG-RANGE MAPPING OF GAPS AND TELOMERES WITH RECA-ASSISTED RESTRICTION-ENDONUCLEASE (RARE) CLEAVAGE

RecA-assisted restriction endonuclease (RARE) cleavage is a method to perform sequence-specific cleavage of genomic DNA, and is useful in ph ysical mapping studies. After making two modifications, we have applie d this method to mapping targe regions of DNA in several cell types, i ncluding a notorious gap near the Huntington disease (HD) locus on chr omosome 4. RARE cleavage fragments were analysed by pulsed field gel e lectrophoresis and Southern blotting and the distances between cleavag e sites determined with accuracy. Using RARE cleavage, the gap measure d was less than 60 kilobases in length. RARE cleavage is also a straig htforward technique to map the distance from a marker to a telomere. T he terminal 1.7 megabases of several HD and control cell lines were ma pped with no large differences between cell lines in this region.