Strategies to improve the design of gapmer antisense oligonucleotide on allele-specific silencing

Gapmer antisense oligonucleotides (ASOs) hold therapeutic promise for allele-specific silencing but face challenges distinguishing between mutant and wild-type transcripts. This study explores new design strategies to enhance ASO specificity, focusing on a common dominant mutation in COL6A3 gene associated with Ullrich congenital muscular dystrophy. Initial gapmer ASO design exhibited high efficiency but poor specificity for the mutant allele. We then adopted a mixmer design, incorporating additional RNA bases based on computational predictions of secondary structures for both mutant and wild-type alleles, aiming to enhance ASO accessibility to mutant transcripts. The mixmer ASO design demonstrated up to a 3-fold increase in specificity compared to the classical gapmer design. Further refinement involved introducing a nucleotide mismatch as a structural modification, resulting in a 10-fold enhancement in specificity compared to the gapmer design and a 3-fold over the mixmer design. Additionally, we identified for the first time a potential role of the RISC complex, alongside RNase H1, in gapmer-mediated silencing, in contrast to what was observed with mixmer ASOs, where only RNase H1 was involved. In conclusion, this study presents a novel design concept for allele-specific ASOs leveraging mRNA secondary structures and nucleotide mismatching and suggests a potential involvement of RISC complex in gapmer-mediated silencing.