The activity of siRNA in mammalian cells is related to the kinetics of siRNA-target recognition in vitro: mechanistic implications

The specificity of siRNA-mediated suppression of gene expression involves base-base recognition between siRNA and its single-stranded RNA target. We investigated the kinetics of this process in vitro by using full-length ICAM-1 target RNA and biologically active and inactive ICAM-1-directed siRNA, respectively. To mimic the situation in living cells we used the well-characterised facilitator of RNA-RNA annealing and strand exchange cetyltrimethylammonium bromide, which increases strongly the kinetics of RNA-RNA interactions at conditions that do not affect RNA structure nor the presumed structure-function relationship. For the biologically active siRNA si2B, we find faster binding, i.e. recognition of the target and a slower backward reaction when compared with the biologically inactive siRNA si1. This is reflected by an approximately 400-fold more favorable equilibrium constant of si2B. Kinetic evidence favors an associative mechanism of recognition of the target strand by the double-stranded siRNA. The minimal model for siRNA-target recognition described here is consistent with the high biological activity of si2B only if one assumes a step subsequent to target recognition, which might be degradation of the target RNA when complexed with the antisense strand of siRNA or when considering rapid destruction of the released sense strand of siRNA.