The kanamycin resistance gene (nptII or nptIII) is a string of DNA that allows an organism to produce a protein, conferring resistance to the common antibiotic kanamycin. This gene is often used as a selective marker for exogenous plasmids — plasmids that aren't naturally occurring — in organisms such as bacteria or yeast. This selection agent is also used in plants. Scientists who study genetics or proteomics can select for bacterial colonies that include an inserted gene of interest based on applying kanamycin. Kanamycin will kill every cellular colony that doesn't include cells transcribing and translating the associated resistance gene.
The kanamycin resistance gene has natural origins and is found in Streptomyces kanamyceticus, a bacteria that is able to produce an enzyme that breaks down the kanamycin antibiotic before the antibiotic can destroy the bacteria. Any cell that can read this gene and transcribe the resultant enzyme will have a resistance to kanamycin. This gene was isolated from the resistant bacterial strain and copied into other plasmids. Through the use of enzymes, scientists can design plasmids that incorporate resistances against selection agents such as kanamycin.
There are many pathways through which resistance to aminoglycosides, such as kanamycin, take effect. Genetic resistance to kanamycin can be a result of decreased cell permeability or cellular inactivation of the kanamycin enzyme. It's also possible for a cell to exhibit resistance to kanamycin by a chromosomal change leading to an alteration of that cell's ribosomes. This last resistance, however, isn't as useful for geneticists as the other pathways, because it relies on chromosomal DNA and not designed plasmids. In other words, this resistance is a naturally occurring one and can't be inserted.
The kanamycin resistance gene has some resistance crossover to other antibiotics and selection agents such as gentamycin and neomycin. This trait makes the kanamycin resistance gene less useful because broad selection agents prevent specific selection of bacterial strains. In other words, if a scientist wanted to study the interaction of two plasmids, inserting them both into a single-celled organism such as yeast, the scientist couldn't use neomycin or gentamycin resistance as a selection marker if kanamycin resistance is already being relied upon.
Kanamycin resistance typically is used in laboratories, and it has become a common selection agent for use in genetically modified organisms. As one of the most common antibiotics, kanamycin is assumed to exist in abundance. Consequently, there are few restrictions on the use of kanamycin in plant transgenics and genetic modifications of plants for large-scale industrial agricultural production.