Design and chemical modification of synthetic short shRNAs as potent RNAi triggers

Synthetic shRNAs that are too short to be Dicer substrates (short shRNAs or sshRNAs) can be highly potent RNAi effectors when properly designed, with activities similar to or more potent than the more commonly used siRNAs targeting the same sequences. sshRNAs can be designed in two possible orientations: left- or right-hand loop, designated L-sshRNAs and R-sshRNAs, respectively. Because L- and R-sshRNAs are processed by the RNAi machinery in different ways, optimal designs for the two formats diverge in several key aspects. Here, we describe the principles of design and chemical modification of highly effective L- and R-sshRNAs.