1. Restriction endonucleases (also called restriction enzymes) are enzymes isolated from bacteria that recognize specific sequences in DNA and cut the DNA at that point. DNAs cut in this fashion can be put back together in new arrangements using DNA ligase. Such a process is very common in biotechnology. Bacteria use restriction enzymes as a primitive immune system to protect against invading viruses (called phages).
2. Paired with restriction enzymes are other enzymes called methylases that recognize the same specific sequence a restriction enzyme recognizes, but instead of cutting it, the methylase puts methyl groups on the sequence. This keeps the restriction enzyme from cutting the DNA. It is in this way that cellular DNA is protected.
3. Cloning is the term relating to the production of multiple identical copies of something. The "something" can be cells, viruses, DNA, etc. The key to cloning viruses or cells is the dilution of these entities to the point where single copies of them can be plated and allowed to replicate. The mound of cells or viruses arising from replication of these entities are clones of the original single cell or virus.
4. Plasmids are circular DNA molecules that can replicate in bacteria, such as E. coli. Plasmids usually carry a "marker" gene that gives them a phenotype (such as antibiotic resistance) that can be used to identify bacteria that get the plasmid. If one starts with a group of bacteria that is normally killed by the antibiotic ampicillin and puts the plasmid pBR 322 into them, the bacteria will not die in the presence of penicillin and can be grown on plates containing penicillin. Bacteria that fail to acquire the plasmid in an experiment will die on the same plates.
5. Having a selectable marker in a plasmid is useful when one is putting DNA into bacteria (called transforming them, or transformation), because the DNA goes into cells with a VERY low efficiency (1 per hundred thousand or so).
6. Plasmids contain DNA sequences recognized by restriction endonucleases (restriction enzymes), allowing them to be cut. If one cuts a foreign DNA (such as human DNA) with the same enzymes, the foreign DNA can be inserted into the plasmid in place of the original piece. DNA ligase helps to link the DNAs together. Whenever one puts together two DNAs that were not originally linked together, one has made a recombinant DNA. If one puts the recombinant DNA into bacteria, it may be possible to get bacteria to use the recombinant DNA to make a protein. Human insulin can be made in bacteria in this way.
7. Blue-white screening allows one to tell whether or not a desired fragment has been inserted into a plasmid in ligation. It relies on the lac-Z gene, which will catalyze a reaction on an artificial substrate called X-Gal. Cuts are made inside of the lac-Z gene. If a fragment gets inserted, the lac-Z gene does not function and cells treated with X-Gal remain white. Plasmids with no insert have an intact lac-Z gene and turn blue. Thus one can distinguish cells that have an insert from those that don't by the color they produce when treated with X-Gal.
8. The Polymerase Chain Reaction (PCR) was invented in the late 1980s. It provides a way to amplify DNA sequences (make more of them) starting with very tiny amounts of a target DNA. The process borrows from the mechanism of DNA replication. It requires a target DNA, two primers (one for each strand), 4 dNTPs, and a DNA polymerase (such as Taq DNA Polymerase) that is resistant to denaturation under high temperatures. A cycle of PCR consists of priming the DNA strands, DNA replication, and denaturation. Each cycle of PCR can double the amount of DNA present. After 30 cycles, a theoretical amplification of over 1 billion fold is possible.
9. Once one has amplified DNA or cut it with a restriction enzyme, it is useful to be able to determine its size. This involves separating DNA fragments by gel electrophoresis.
10. One useful technique for purifying recombinant proteins from cells is called histidine tagging. In this method, the recombinant gene is inserted in a plasmid such that a string of 6 histidine amino acids is linked to the amino end of the recombinant protein. The histidines will bind to a nickel ion on a column. To purify the desired protein, the mixture of proteins from the cell is passed throught he column. Only the recombinant protein will bind to the nickel because it is the only one with the 6 histidines at the end. All other proteins will then pass through the column, leaving the recombinant in a pure form.