RNAi FAQ

What is the difference between dsRNAs, siRNAs, and shRNAs?

Double-stranded RNA (dsRNA) consists of complementary strands of RNA bound by hydrogen bonds between ribonucleotides. dsRNA can be formed by base-pairing interactions between separate RNA strands or by secondary structural folding within a single RNA strand. In the generalized RNAi pathway, dsRNA acts as a substrate for Dicer, which cleaves it into smaller siRNAs that trigger gene silencing.

Short interfering RNAs (siRNAs) are 21-23 nucleotide (nt), double-stranded RNA fragments with characteristic 2-nt overhangs on the 3’ ends. They are produced when Dicer clips dsRNA into smaller fragments. Each siRNA is subsequently incorporated into a RISC complex, which then targets and cleaves endogenous mRNAs homologous to the siRNA, leading to gene-specific transcript degradation. siRNAs can occur naturally or be introduced by viral infection or experimental manipulation.

Short hairpin shRNAs (shRNAs) are short strands of RNA that fold into stem-loop secondary structures, forming stretches of dsRNA. As such, they are believed to be processed by Dicer or a similar enzyme to form siRNA-like molecules. shRNA can be expressed from an endogenous gene or from an introduced vector (e.g. a plasmid or recombinant virus).