Fine control

Since the discovery of small RNAs, RNA interference (RNAi) has become a popular alternative to technologies such as gene disruption and chemical inhibition. RNAi is an extremely powerful tool for repressing gene expression; indeed, effects other than the desired one are often seen.

Because short interfering RNAs (siRNAs) don't require perfect complementarity to suppress a target gene's transcription, they could affect genes that you haven't targeted. Small RNAs can also influence cell metabolism, including triggering innate immune responses in mammalian cells. Depending on the experimental system, such off-target effects can easily throw off results. "There are many insidious different ways to get misled by these kinds of experiments," says Mark Behlke of Integrated DNA Technologies in Coralville, Iowa.

So what can be done about these unwanted side effects? You run controls, of course. By using the right combination of siRNA controls, you can be confident that your results are due solely to suppression of your target gene. In general, the more controls you perform, the more certain you can be of your conclusions. Some controls are more informative than others, however, and different controls present different technical challenges. To help you determine the combination of siRNA controls that will best support your experiments, The Scientist talked with researchers who have successfully navigated this tricky field.