BAC trimming: Minimizing clone overlaps

Bacterial vectors containing large inserts of genomic DNA are now the stand ard substrates for large-scale genomic sequencing. Long overlaps between so me clones lead to considerable redundant effort. A method for deleting defi ned regions from bacterial artificial chromosome (BAC) inserts, using homol ogous recombination, was applied to minimize the overlap between successive BAC clones. This procedure, called trimming, was carried out in the recA(- ) BAC host. We have precisely deleted up to 70 kb of DNA from BACs that wer e to be sequenced. This method requires minimal prior characterization of t he clones: collections of BAC end sequences or STS-based maps will accelera te the process. BAC trimming will be useful in both small and large genome sequencing projects and will be of particular utility for gap closure in fi nishing phases. (C) 2000 Academic Press.