RNA-Protein Interaction Protocols pp 367-381
Designing and Utilization of siRNAs Targeting RNA Binding Proteins
Small interfering RNA (siRNA)-mediated RNA interference (RNAi) is a very powerful tool for triggering posttranscriptional gene silencing in several organisms. We discuss the improvement of two different sources of siRNAs synthesized either chemically or by an enzymatic method. When the siRNAs are synthesized by in vitro transcription using a phage polymerase, the initiating triphosphates trigger a potent interferon induction that can lead to misinterpretation of the data. A novel method is presented to minimize the nonspecific effect of enzymatic siRNAs while maintaining the advantages of lower cost and less turnaround time. When chemical siRNAs are used, the expense and long turnaround time can be a problem, especially if the selected siR-NAs are not highly functional in triggering RNAi. The new format for making double-stranded RNAs (dsRNAs) is described to achieve more efficient suppression. The format has been tested by creating siRNAs targeting two RNA binding proteins, La and hnRNP (heterogeneous nuclear ribonucleoprotein) H, and has shown better potency at lower concentrations than the conventional 21-mer siRNA.