Agarose gel elelectrophoresis
The standard method used to separate, identify, and purify DNA fragments is electrophoresis through agarose gels. If an electric field is applied to a solution containing DNA, the negatively charged DNA will migrate towards the + terminal (anode). In gel electrophoresis the solution is replaces by a gel such as agarose . The dense network of the polymeric agarose reduce the rate of migration of DNA molecules in an electric field. Larger molecules experience more friction and migrate more slowly, whereas smaller molecules can travel more freely, i.e. faster. After a given period of time, the distance a DNA molecule has moved is proportional to the inverse log of its molecular weight. In addition to molecular size and charge the rate of migration depends on the gel concentration and voltage applied. The location of DNA within the gel can be determined directly. Bands of DNA in the gel are stained with low concentrations of the fluorescent, intercalating dye ethidium bromide. As little as 1 ng of DNA can then be detected by direct examination of the gel in ultraviolet light. DNA standard

Plasmid
Bacterial plasmids as vectors for recombinant DNA
Prokaryotic DNA exists in form of one single double stranded DNA molecule. In most, but not all bacteria this dsDNA assumes a circular form. In addition to the chromosomal DNA some bacteria have plasmid dsDNA, which is a much smaller circular DNA in the range from a few 1000 bases to 100 kbases. Plasmids are also found in certain unicellular eukaryotes such as yeast. Plasmid replicate independently of chromosomal DNA and therefore bacterial cells may contain several copies of a plasmid. Naturally occurring plasmids contain genes that provide some benefit for the host organism, e.g. some plasmid genes code for enzymes that can deactivate antibiotics. The same bacterium, which does not contain the plasmid is killed by the antibiotic. Such drug resistance has become a major problem in the treatment against common pathogens. Many plasmids also contain transfer genes, that encode for proteins which cause a copy of plasmid DNA to be transferred to another host cell. Such transfer expands the number of drug resistant organisms. Plasmids are commonly used in recombinant DNA technology, and they have been engineered to optimize their use as cloning vectors

Recombinant DNA
DNA technology began with the invention of preparing recombinant DNA from plasmid DNA. The key to this method are so called restriction enzymes, which can cleave DNA strands at very specific sites or base sequences. The figure shows the action of an restriction enzyme on a plasmid and chromosomal DNA sequence. The clevage produces DNA fragments with " sticky ends " . These fragments can recombine in either the original combination or they can form a new recombinant DNA. The final joining is accomplished by DNA ligase recombinant DNA

Using restriction enzymes and DNA ligase, DNA segments of can be inserted into a plasmid ( which is then called a cloning factor) . If the recombinant plasmid is reintroduced into the bacterium, millions of copies of the recombinant plasmid will be obtained as the bacterium grows and replicates in a cultural medium. To insure that only bacteria with recombinant plasmids replicate, certain protocols have to be implemented.

(Some of the images below are taken from "Biology, Raven and Johnson, 2. Ed.")
pBR322
Clone libraries are often employed if a particular gene is to be replicated and isolated.
Finding genes
Which genes are expressed     microarray

Examples of cloning
agrobacterium , somatotropin     Dolly     Cloning protocol     Stem cells

Polymerase chain reaction
PCR animation     VNTR     VNTR by PCR     VNTR of a family;     additional example