Rapid mapping of NotI linking clones with differential hybridization and Alu-PCR

For construction of a NotI restriction map of the human genome, the isolation and mapping of unique NotI linking clones represent important and critical steps. Recently we have shown that an Alu-PCR approach can be used for isolation of NotI linking clones from defined regions of the chromosomes. This represents a useful method for isolating and analyzing a small number of clones, but it would be laborious to use it for mapping many NotI linking clones simultaneously. Here we suggest another modification of Alu-PCR for rapid concurrent mapping of many NotI linking clones. The results clearly demonstrate the utility of this approach. Seventy-one random NotI linking clones were analyzed. Among them, 65 clones (91.5%) were correctly selected and mapped using this approach. With differential hybridization and Alu-PCR, a significant portion of all human NotI linking clones (> 30%) can be rapidly mapped to particular chromosomes or to defined regions of these chromosomes.