What are the structures of the siRNA molecules used in RNAi studies?
The nature of the molecules used in RNAi studies fall into two classes. The first is chemically synthesized siRNA. Typically, these are 21 nt dsRNA molecules with phosphorylated 5’ ends and 3’ dinucleotide overhangs, which directly function as templates for RISC formation. These molecules are introduced via chemical or electroporation-based transfection, and mediate a transient suppression of gene expression. The second class of molecules are shRNA (short hairpin RNA). These are typically delivered to the cell as part of a plasmid or viral vector. The shRNA molecules induce an RNAi effect by serving as substrates for the cytoplasmic RNase, Dicer.