Cutting the DNA

Genetic engineering has three basic parts.  First, the

Sticky Ends

DNA is cut in the desired place using restriction enzymes.  Each different type of restriction enzyme "seeks out" and cuts DNA at a spot marked by a different sequence of base pairs.  One restriction enzyme may cut the DNA at every "AATC", for example, while another cuts all "ATG" sequences.  The DNA is cut in such a way that one helix is a bit longer than the other because of a few extra base pairs.  These extra base pairs are called the "sticky end", because they will bond easily to another strand of DNA with the corresponding set of genes.  The new genes that will be injected have sticky ends that complement the sticky ends the restriction enzyme leaves.

Inserting New DNA

Once the restriction enzyme has cut the DNA, new DNA is inserted into the cell.  This is difficult, because cells by nature do not allow DNA through the cell wall.  There are many ways around this difficulty, though.  Electroporation involves jolting the cells with a burst of electricity, opening the cell wall pores and allowing DNA to fall into the cell.  Microinjection uses a small glass needle to inject the DNA through the cell wall.  A gene gun can be used, which blasts tiny metal fragments coated with DNA through the cell wall and into the cell.  DNA can also be shrouded in lipids, fatty molecules which the cell will take in; when the lipid is digested, the DNA is released.  These methods work fairly well for prokaryotic cells, which have one chromosome and no nucleus.  However, in order for DNA insertion to work consistently and accurately in multicellular organisms with eukaryotic cells, something better is called for.
To find that something better, science turned to the natural world.  They realized that a retrovirus, a form of a virus, was just what they needed.  Retroviruses enter the cell through the cell wall and implant their DNA into the cell's nucleus.  The retroviral DNA is incorporated into the cell's DNA, causing the disease that the particular retrovirus is associated with.  Scientists reasoned that if they could put a gene into the retrovirus, the retrovirus would deliver that gene to the cell's DNA.  An added bonus is that different retroviruses target different areas of the body, so the scientists could put DNA into a retrovirus for delivery to a specific organ.

Attaching the New DNA

Once the cell's original DNA is cut with the restriction enzyme and the new DNA is in place, the scientists use ligase (another enzyme) to stick the DNA segments together.  The sticky ends of the new and the original DNA merge together, and the cell begins to carry out the instructions of the new DNA along with its own.

Atrition

Of course, this technique does not work on 100% of the cells.  A scientist may start with a lot of cells, and the restriction enzyme may not get to some.  The DNA may not enter some of the cells.  Other cells' DNA will not line up properly with the new DNA, causing the ligase to bond the DNA incorrectly.  The new DNA may find its way to the wrong position along the original DNA.  In others, the ligase may not get to the cell and fuse the DNA at all.  In every "batch" of genetically altered cells, there will be some that do not have the new trait.  The cells are grown in culture, and the cells that do not posses the desired trait are culled out, usually by subjecting all the cells to whatever treatment the new cells were designed to withstand.  The cells that survive have the new DNA properly aligned, and are ready to go to work.

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