Structural diversity repertoire of gene silencing small interfering RNAs

Abstract

Since the discovery of double-stranded (ds) RNA-mediated RNA interference (RNAi) phenomenon in Caenorhabditis elegans, specific gene silencing based upon RNAi mechanism has become a novel biomedical tool that has extended our understanding of cell biology and opened the door to an innovative class of therapeutic agents. To silence genes in mammalian cells, short dsRNA referred to as small interfering RNA (siRNA) is used as an RNAi trigger to avoid nonspecific interferon responses induced by long dsRNAs. An early structure-activity relationship study performed in Drosophila melanogaster embryonic extract suggested the existence of strict siRNA structural design rules to achieve optimal gene silencing. These rules include the presence of a 3' overhang, a fixed duplex length, and structural symmetry, which defined the structure of a classical siRNA. However, several recent studies performed in mammalian cells have hinted that the gene silencing siRNA structure could be much more flexible than that originally proposed. Moreover, many of the nonclassical siRNA structural variants reported improved features over the classical siRNAs, including increased potency, reduced nonspecific responses, and enhanced cellular delivery. In this review, we summarize the recent progress in the development of gene silencing siRNA structural variants and discuss these in light of the flexibility of the RNAi machinery in mammalian cells.

FIG. 1.

Structures of siRNA structural variants. Top strand: sense (passenger) strand; bottom strand: antisense (guide) strand; ellipsoid: RNA; square box: DNA. (a) Classical 19 + 2 siRNA; (b) Dicer-substrate siRNA (R 25/27D form); (c) Dicer-noncleavable long siRNA (25 bp); (d) 38-bp-long dual-target siRNA; (e, f) asymmetric short siRNAs; (e) aiRNA; (f) asiRNA; (g) sisiRNA; (h) immunostimulatory siRNA; (i) ssiRNA.