The first technique of genetic engineering, the plasmid method, is the most familiar technique of the three, and is generally used for altering microorganisms such as bacteria. In the plasmid method, a small ring of DNA called a plasmid (generally found in bacteria) is placed in a container with special restriction enzymes that cut the DNA at a certain recognizable sequence. The same enzyme is then used to treat the DNA sequence to be engineered into the bacteria; this procedure creates "sticky ends" that will fuse together if given the opportunity. Next, the two separate cut-up DNA sequences are introduced into the same container, where the sticky ends allow them to fuse, thus forming a ring of DNA with additional content. new enzymes are added to help cement the new linkages, and the culture is then separated by molecular weight. Those molecules that weigh the most have successfully incorporated the new DNA, and they are to be preserved. The next step involves adding the newly formed plasmids to a culture of live bacteria with known genomes, some of which will take up the free-floating plasmids and begin to express them. In general, the DNA introduced into the plasmid will include not only instructions for making a protein, but also antibiotic-resistance genes. These resistance genes can then be used to separate the bacteria which have taken up the plasmid from those that have not. The scientist simply adds the appropriate antibiotic, and the survivors are virtually guaranteed (barring spontaneous mutations) to possess the new genes.

Next, the scientist allows the successfully altered bacteria to grow and reproduce. They can now be used in experiments or put to work in industry. Furthermore, the bacteria can be allowed to evolve on their own, with a "selection pressure" provided by the scientist for producing more protein. Because of the power of natural selection, the bacteria produced after many generations will outperform the best of the early generations. Many people strongly object to the plasmid method of genetic engineering because they fear that the engineered plasmids will be transferred into other bacteria which would cause problems if they expressed the gene. Lateral gene transfer of this type is indeed quite common in bacteria, but in general the bacteria engineered by this method do not come in contact with natural bacteria except in controlled laboratory conditions. Those bacteria that will be used in the wild - for example, those that could clean up oil spills - are generally released for a specific purpose and in a specific area, and they are carefully supervised by scientists.