When performing an investigation, researchers often wish to be able to test the effects of a gene or a protein in an organism. However, living systems are extremely complicated and dense and it can be difficult to observe what one protein or gene is doing in a cell or living creature. To get around this difficulty, you can create a modified organism that is missing one or more genes/proteins. By observing the difference between a modified and a normal organism/cell the purpose of the missing protein can be determined. There are a number of ways to make modified organisms interrupt different parts of the process of converting from DNA to protein. Some researchers choose to observe the effects of a protein by causing it to be over expressed, generating huge excesses of a particular protein and hopefully increasing its effects to highly noticeable levels.
The most permanent way to create a knockout cell is to alter the DNA in such a way that the gene for the protein you are studying is removed. This can be done by cleaving the gene from the cell's DNA and then recombining the DNA with the sequence missing. Without the gene the cell cannot express the protein.
If the researcher is interested in creating an excessive amount of the protein, this can be accomplished by adding new copies of the gene to the cell. With multiple copies of the gene in the cell, more copies of the protein will be created by the cells natural processes. In complex organisms introducing new genes can be difficult, but standalone fragments of DNA can be constructed and added to the cells, to cause over-production of certain proteins.
A more recent development in biotechnology that can be used to control which proteins are expressed in a cell is RNA interference. The interference process works by introducing small interfering RNA(siRNA) into a cell and convincing the cell to hunt down and destroy messenger RNA (mRNA) with a complementary sequence that is carrying the instructions to produce a protein from the nucleus (where the DNA is) to the ribosome, the cellular machinery that creates proteins. The end result of this is that RNA carrying the instructions to produce the "silenced" protein is broken down before it can deliver its message. The DNA of the organism remains unchanged but the message to produce a particular protein is interrupted, and the protein is never produced in the cell. This produced a modified organism for as long as the siRNA remains to instruct the cell to disrupt the communication between DNA and Protein. This technique is especially powerful because the sequence of an siRNA to knockout any protein can be determined for any protein that we know the gene responsible for. By employing RNA interference across multiple experiments, you can determine at least some of the effects of every gene in the genome under the conditions you set up. Determining which genes have interesting effects under the conditions of weak chemotherapy treatment was the first step in the research process .