DNA shuffling is a way to rapidly propagate beneficial mutation

Mutation

In molecular biology and genetics, mutations are changes in a genomic sequence: the DNA sequence of a cell's genome or the DNA or RNA sequence of a virus. They can be defined as sudden and spontaneous changes in the cell. Mutations are caused by radiation, viruses, transposons and mutagenic...

s in a directed evolution

Directed evolution

thumb|250px|right|An example of a possible round to evolve a protein based fluorescent sensor for a specific analyte using two consecutive FACS sortings...

 experiment. It is used to rapidly increase DNA library size.

Procedure

DNAse I is first used to fragment a set of parent gene

Gene

A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...

s into pieces of 50-100 bp

Base pair

In molecular biology and genetics, the linking between two nitrogenous bases on opposite complementary DNA or certain types of RNA strands that are connected via hydrogen bonds is called a base pair...

 in length. This is then followed by a polymerase chain reaction

Polymerase chain reaction

The polymerase chain reaction is a scientific technique in molecular biology to amplify a single or a few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence....

 (PCR) without primers- DNA fragments with sufficient overlapping homologous sequence will anneal to each other and are then extended by DNA polymerase

DNA polymerase

A DNA polymerase is an enzyme that helps catalyze in the polymerization of deoxyribonucleotides into a DNA strand. DNA polymerases are best known for their feedback role in DNA replication, in which the polymerase "reads" an intact DNA strand as a template and uses it to synthesize the new strand....

.

Several rounds of this PCR extension are allowed to occur, after some of the DNA

DNA

Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...

 molecules reach the size of the parental genes. These genes can then be amplified with another PCR, this time with the addition of primers

Primer (molecular biology)

A primer is a strand of nucleic acid that serves as a starting point for DNA synthesis. They are required for DNA replication because the enzymes that catalyze this process, DNA polymerases, can only add new nucleotides to an existing strand of DNA...

 that are designed to complement the ends of the strands. The primers may have additional sequences added to their 5' ends, such as sequences for restriction enzyme

Restriction enzyme

A Restriction Enzyme is an enzyme that cuts double-stranded DNA at specific recognition nucleotide sequences known as restriction sites. Such enzymes, found in bacteria and archaea, are thought to have evolved to provide a defense mechanism against invading viruses...

 recognition sites needed for ligation into a cloning vector.

It is possible to recombine

Recombination

Recombination may refer to:* Recombination , the process by which genetic material is broken and joined to other genetic material* Recombination , in semiconductors, the elimination of mobile charge carriers...

 portion of these genes to generate hybrids or chimeric forms

Chimera (genetics)

A chimera or chimaera is a single organism that is composed of two or more different populations of genetically distinct cells that originated from different zygotes involved in sexual reproduction. If the different cells have emerged from the same zygote, the organism is called a mosaic...

 with unique properties, this is called DNA shuffling.

Restriction enzymes

1. Restriction enzyme
   Enzyme
   Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...
   
   s that cut in similar places are used to digest members of the gene family
2. DNA fragments are joined together with DNA ligase
   DNA ligase
   In molecular biology, DNA ligase is a specific type of enzyme, a ligase, that repairs single-stranded discontinuities in double stranded DNA molecules, in simple words strands that have double-strand break . Purified DNA ligase is used in gene cloning to join DNA molecules together...
   
   
3. Large numbers of hybrids are produced which can be tested for unique properties

DNase 1

1. Different members of the gene family are fragmented using DNase 1 followed by PCR
2. During PCR different members of the family are cross-primed, DNA fragments with high homology
   Homology (biology)
   Homology forms the basis of organization for comparative biology. In 1843, Richard Owen defined homology as "the same organ in different animals under every variety of form and function". Organs as different as a bat's wing, a seal's flipper, a cat's paw and a human hand have a common underlying...
   
    will anneal to each other
3. The hybrids generated are then used generate a library of mutants which are tested for unique properties