An algorithm for selection of functional siRNA sequences.

By M. Amarzguioui, H. Prydz. Biochemical and Biophysical Research Communications - BBRC, 2004

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Design of a genome-wide siRNA library using an artificial neural network (2005, background): “Finally, strong internal structures, an absence of G/C stretches and a prevalence of certain nucleotides at positions 4, 7, 9, 14 and at the 3′-end are also characteristic of active siRNA”
Perspective: machines for RNAi. (2005, background): “…and we implore readers to explore these “design rules” before synthesizing siRNAs to reduce expression of a favorite gene (Khvorova et al. 2003; Amarzguioui and Prydz 2004; Hohjoh 2004; Naito et al. 2004; Reynolds et al. 2004; Ui-Tei et al. 2004; Yiu et al. 2005). siRNAs designed to load one…”
RNAi therapeutics: principles, prospects and challenges. (2007, background): “include thermodynamic end stability [6], target mRNA accessibility [14], structural features [15] and additional position specific determinants [16,17].”
Synthetic dsRNA Dicer substrates enhance RNAi potency and efficacy (2005, methodology): “, necessitating complex design algorithms to predict effective site”