Trbp Binding Preferences for siRNA

Joseph A. Gredell1, Michael J. Dittmer1, and S. Patrick Walton2. (1) Department of Chemical Engineering and Materials Science, Michigan State University, 2527 Engineering Building, East Lansing, MI 48824, (2) Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824

RNA interference (RNAi) is a natural phenomenon resulting in potent and primarily specific gene silencing that occurs in most eukaryotes. It is initiated in cells by the presence of short interfering RNAs (siRNAs), which are double-stranded, non-coding RNA molecules ~21 nucleotides long. siRNAs guide the active enzyme complex of RNAi, the RNA induced silencing complex (RISC), to mRNAs possessing regions of sequence complementarity, leading to degradation of the target message. TAR RNA binding protein (TRBP), historically associated with binding the TAR structure present on all HIV-1 transcripts, was recently discovered to be a component of RISC. It has been proposed that TRBP facilitates the production of siRNAs by sensing the thermodynamic asymmetry of the siRNA, thus leading to incorporation of the guide strand into RISC, analogous to the role of R2D2 in the Drosophila silencing pathway. We will present our results detailing the precise structural and sequence requirements for TRBP recognition of siRNAs. The contributions of these features to the sensing of duplex asymmetry will also be described.