A technique designed for directed evolution
, that involves - as the name suggests - shuffling DNA
like a pack of cards. However, as ever, Nature got there first
. Bacteria and Archaea regularly shuffle genes to produce new functions, and it has sometimes been suggested that exon
s are modules for this purpose
. Your immune system does this to provide a random selection of binding sites for antigens, although in a much more controlled way (controlled randomness?:).
Also called in vitro recombination, achieving this in the lab involves PCR and restriction enzymes. The gene is cut into fragments by the restriction enzyme (its specificity determining the fragment size) and the bits are stuck back together again with a ligase. Since the patching together is sequence independant, the reassembled gene is shuffled intrinsically.
A potentially more powerful technique is to use a family of genes for the shuffling. This means recombining fragments from several related genes, each with point mutations. The same effect can be achieved by error-prone PCR before ligation, but naturally arising mutants have already been selected for fitness.