siRNA shearing during light sonication? - (Mar/25/2011 )
I am working on novel biomaterials for delivery of siRNA, and the synthesis conditions involve a 5 minute period of sonication, alternating every 30s between duty cycles of 1 and 4 (max on the machine is 10) on ice using a tip. All soluble agents to be loaded into the vehicles (ie- siRNA) must be encapsulated prior to the sonication.
I know that sonication is commonly used to create a smear from large nucleic acids such as gDNA, but since siRNAs are already small, and my sonication power is relatively low, I am wondering if I will get significant amounts of degradation? Anyone have experience with this?
You can run a simple agarose gel to check whether the siRNA has been sheared using un-sonicated samples as control. Probably that is the easiest way of answering your question.