siRNA Design Tool: A Functional Genomics Accelerator

Natasha Levenkova1, Qingjuan Gu2, John J. Rux, The Wistar Institute;, The Wistar Institute

Functional genomics applications often use gene silencing to infer the function of a gene by observing the effect caused by loss of that gene. A convenient method for producing targeted gene silencing is the use of RNA interference (RNAi), a natural defense mechanism against molecular parasites. Specific genes are down-regulated by the expression of small interfering RNA (siRNA) that have sequences that correspond to the target gene. An essential step in designing siRNA sequences is to ensure that the siRNA is specific to the gene of interest. We have developed an siRNA design tool to assist researchers in choosing an appropriate siRNA sequence to produce gene-specific silencing. The siRNA design tool scans the target gene for candidate siRNA sequences that satisfy user-adjustable rules. Selected candidates are then screened to identify those siRNA sequences that match only the gene of interest.