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RNA interference (RNAi), a process through which small interfering RNAs (siRNAs) induce sequence-specific post-transcriptional gene silencing, is commonly recognized as a powerful tool not only for functional genomics but also for therapeutic applications. To achieve accurate target gene function and successful therapeutic applications, it is necessary to select an efficient and target genespecific siRNA with minimal off-target effects. We found that the ability to induce off-target effects on unintended genes is strongly correlated to the thermodynamic stability of the duplex formed between the seed region (positions 2-8 from the 5\' end of the siRNA guide strand) and target mRNA. Consistent with this property, we found that DNA-RNA chimeric siRNA (chiRNA) with deoxyribonucleotides in the 5\' proximal eight nucleotides of the guide strand and the complementary nucleotides in the passenger strand exerted virtually no off-target effect due to low stability of the DNA-RNA duplex in seed-target base-pairing. However, the corresponding RNAi activities for primary target genes were also decreased to one-tenth on average by the DNA substitutions. Here, we report that siRNAs with seven deoxyribonucleotides exclusively in the seed region (sdRNA) may exhibit efficient target-specificity, but off-target effect-reduced RNAi activity.

sdRNA: siRNA with a DNA Seed for an Efficient and Target-gene Specific RNA Interference