Slide 2: Map-based Cloning: Jumping-Linking Chromosome walks can be interrupted if a segment of the region to be walked through is non-clonable (for example if it is toxic to the host cell).
Chromosome walks can be detoured in many directions if one of the clone end probes (filled box) is a repeated sequence.
The jumping-linking strategy was invented to overcome the problems of unclonable segments and repeated sequences and to enable larger regions of the genome to be scanned. Use is made of a restriction enzyme that recognizes few sites in the DNA (large thick bars) and an enzyme that cuts frequently (small thin bars).
The jumping library contains clones in which the two double digestion fragments at either end of a large fragment are cloned in the same plasmid in the library (segments connected by dotted lines).
The linking library consists of plasmids containing the fragments generated by the frequent cutter that also contain a recognition site for the rare cutter.
The two libraries are used in alternation to hop down the molecular chromosome. © A.K. Chhabra