Allele-Specific Silencing by RNA Interference

Allele-specific gene silencing by RNA interference (RNAi) is therapeutically useful for specifically inhibiting the expression of disease-associated alleles without suppressing the expression of corresponding wild-type alleles. To realize such allele-specific RNAi (ASP-RNAi), the design and assessment of small interfering RNA (siRNA) duplexes conferring ASP-RNAi is vital; however, it is also difficult. We have developed an assay system with reporter alleles that encode the Photinus and Renilla luciferase genes carrying mutant and wild-type allelic sequences in their 3′-untranslated regions. The assay system allows us to evaluate designed siRNAs and also short hairpin RNAs for allele-specific silencing against target mutant alleles as well as off-target silencing against corresponding wild-type alleles simultaneously in a qualitative and quantitative manner.