DNA shuffling

DNA shuffling, also known as molecular breeding, is an in vitro random recombination method to generate mutant genes for directed evolution and to enable a rapid increase in DNA library size. Three procedures for accomplishing DNA shuffling are molecular breeding which relies on homologous recombination or the similarity of the DNA sequences, restriction enzymes which rely on common restriction sites, and nonhomologous random recombination which requires the use of hairpins. In all of these techniques, the parent genes are fragmented and then recombined.

DNA shuffling utilizes random recombination as opposed to site-directed mutagenesis in order to generate proteins with unique attributes or combinations of desirable characteristics encoded in the parent genes such as thermostability and high activity. The potential for DNA shuffling to produce novel proteins is exemplified by the figure shown on the right which demonstrates the difference between point mutations, insertions and deletions, and DNA shuffling. Specifically, this figure shows the use of DNA shuffling on two parent genes which enables the generation of recombinant proteins that have a random combination of sequences from each parent gene. This is distinct from point mutations in which one nucleotide has been changed, inserted, or deleted and insertions or deletions where a sequence of nucleotides has been added or removed, respectively. As a result of the random recombination, DNA shuffling is able to produce proteins with new qualities or multiple advantageous features derived from the parent genes.

In 1994, Willem P.C. Stemmer published the first paper on DNA shuffling. Since the introduction of the technique, DNA shuffling has been applied to protein and small molecule pharmaceuticals, bioremediation, vaccines, gene therapy, and evolved viruses. Other techniques which yield similar results to DNA shuffling include random chimeragenesis on transient templates (RACHITT), random printing in vitro recombination (RPR), and the staggered extension process (StEP).