Figure 3.

Comparison of RARE-cleavage fragments from two overlapping YACs. Two yeast colonies containing YAC y901a10 (lanes 1–3 and 10–12) were analyzed by RARE cleavage at the EcoRI site defining the right end of YAC y935a8. Lanes 4–9 contain samples from two different DNA preparations of YAC y935a8 that were cleaved at the EcoRI site at the right end of YAC 901a10. The leftmost lane within each group of three contained undigested DNA. The cleavage reactions contained 40 μg RecA protein and either 1.32 μg (middle) or 0.66 μg (right lanes) of oligonucleotide. The products were separated on a PFG, which was run for 24 h at 6 V/cm, and a switching time ramped from 35 to 70 s. The hybridization probe was a mixture of pBR322 and λ DNA to visualize the λ-concatemer size markers. The positions of YACs and of RARE-cleavage fragments are indicated on the right. y935a8 is 2.3 Mbp in size. Both full length and deleted y935a8 as well as the right-vector-arm containing fragments thereof migrate in the unresolved limiting-mobility band. The right end-fragment of the deleted y901a10 clone (DEL-y901a10-R; lanes 2 and 3) is smaller than the right end-fragment from the intact version (y901a10-R; lanes 11 and 12), which in turn has the same size as the left end-fragment from y935a8 (y935a8-L; lanes 8 and 9). DEL-y935a8-L is a deleted fragment that was observed in one particular y935a8 preparation. The hybridization signal at the bottom of lanes 11 and 12 is due to a spill-over from the λ ladder.