shRNA (short hairpin RNAs) are artificial constructs that can be expressed endogenously. These expressed hairpins fold to form dsRNA, and Drosha and Dicer then act on these hairpins to create mature sequence, used by the RISC complex to target genes.
Besides intended gene down-regulation, shRNAs can introduce off-target gene silencing. Our program design shRNA with higher on-target potency, and less off-target effect. Unlike many traditional design programs, which focus on seed complementarity, we systematically study the influence of different nucleotides in each shRNA guide strand position on unintended gene silencing, and finally assign a score matrix for determining the degree of off-target effect. When scanning a target sequence, This program calculates the score for every possible shRNA, and ranks them from highest to lowest score. Ranked top shRNAs are then selected for on-target potency, and less off-target effect.
The algorithm can be accessed via siRNA/shRNA/Oligo Optimal Design