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, random printing in vitro recombination, and the staggered extension process.
History
DNA shuffling by molecular breeding was first reported in 1994 by Willem P.C. Stemmer. He started by fragmenting the β-lactamase gene that had been amplified with the polymerase chain reaction by using DNase I, which randomly cleaves DNA. He then completed a modified PCR reaction where primers were not employed which resulted in the annealing of homologous fragments or fragments with similar sequences. Finally, these fragments were amplified by PCR. Stemmer reported that the use of DNA shuffling in combination with backcrossing resulted in the elimination of non-essential mutations and an increase in the production of the antibiotic cefotaxime. He also emphasized the potential for molecular evolution with DNA shuffling. Specifically, he indicated the technique could be used to modify proteins.DNA shuffling has since been applied to generate libraries of hybrid or chimeric genes and has inspired family shuffling which is defined as the use of related genes in DNA shuffling. Additionally, DNA shuffling has been applied to protein and small molecule pharmaceuticals, bioremediation, gene therapy, vaccines, and evolved viruses.
Procedures
Molecular breeding
First, DNase I is used to fragment a set of parent genes into segments of double stranded DNA ranging from 10-50 bp to more than 1 kbp. This is followed by a PCR without primers. In the PCR, DNA fragments with sufficiently overlapping sequences will anneal to each other and then be extended by DNA polymerase. The PCR extension will not occur unless there are DNA sequences of high similarity. The important factors influencing the sequences synthesized in DNA shuffling are the DNA polymerase, salt concentrations, and annealing temperature. For example, the use of Taq polymerase for amplification of a 1 kbp fragment in a PCR of 20 cycles results in 33% to 98% of the products containing one or more mutations.Multiple cycles of PCR extension can be used to amplify the fragments. The addition of primers that are designed to be complementary to the ends of the extended fragments are added to further amplify the sequences with another PCR. Primers may be chosen to have additional sequences added on to their 5' ends, such as sequences for restriction enzyme recognition sites which are needed for ligation into a cloning vector.
It is possible to recombine portions of the parent genes to generate hybrids or chimeric forms with unique properties, hence the term DNA shuffling. The disadvantage of molecular breeding is the requirement for the similarity between the sequences, which has inspired the development of other procedures for DNA shuffling.
Restriction enzymes
Restriction enzymes are employed to fragment the parent genes. The fragments are then joined together through ligation which can be accomplished with DNA ligase. For example, if two parent genes have three restriction sites fourteen different full-length gene hybrids can be created. The number of unique full-length hybrids is determined by the fact that a gene with three restriction sites can be broken up into four fragments. Thus, there are two options for each of the four positions minus the combinations that would recreate the two parent genes yielding 24 - 2 = 14 different full-length hybrid genes.The main difference between DNA shuffling with restriction enzymes and molecular breeding is molecular breeding relies on the homology of the sequences for the annealing of the strands and PCR for extension whereas by using restriction enzymes, fragment ends that can be ligated are created. The main advantages of using restriction enzymes include control over the number of recombination events and lack of PCR amplification requirement. The main disadvantage is the requirement of common restriction enzyme sites.
Nonhomologous random recombination
In order to generate segments ranging from 10-50 bp to more than 1 kb, DNase I is utilized. The ends of the fragments are made blunt by adding T4 DNA polymerase. Blunting the fragments is important for combining the fragments as incompatible sticky-ends, or overhangs, prevent end joining. Hairpins with a specific restriction site are then added to the mixture of fragments. Next, T4 DNA ligase is employed to ligate the fragments to form extended sequences. The ligation of the hairpins to the fragments limits the length of the extended sequences by preventing the addition of more fragments. Finally, in order to remove the hairpin loops, a restriction enzyme is utilized.Nonhomologous random recombination differs from molecular breeding as homology of the ligated sequences is not necessary which is an advantage. However, because this process recombines the fragments randomly it is probable that a large fraction of the recombined DNA sequences will not have the desired characteristics which is a disadvantage. Nonhomologous random recombination also differs from the use of restriction enzymes for DNA shuffling as common restriction enzyme sites on the parent genes are not required and the use of hairpins is necessary which demonstrates an advantage and disadvantage of nonhomologous random recombination over the use of restriction enzymes, respectively.