ArticleMethods in molecular biology (Clifton, N.J.)2025
siRMSD: A Structural Parameter to Reduce Sequence-Dependent Off-Target Effects for siRNA Design with Chemical Modifications.
Article in Methods in molecular biology (Clifton, N.J.), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
RNA interference (RNAi) is a mechanism for regulating gene expression through small interfering RNAs (siRNAs), double-stranded RNA molecules approximately 20-23 nucleotides in length. The RNAi holds significant therapeutic potential for suppressing disease-related genes in a sequence-specific manner. Most commercially available siRNAs are extensively chemically modified to enhance stability or reduce immunogenicity. These chemical modifications also play a crucial role in mitigating off-target effects, which primarily arise from unintended interactions between the siRNA seed region (positions 2-8) and non-target mRNAs. Here, we introduce small interfering RNA root-mean-square deviation (siRMSD), a novel parameter that quantifies structural distortions induced by chemical modifications in siRNAs. We demonstrate a strong correlation between deviations from the canonical A-form RNA structure and the reduction in siRNA off-target effect. This approach provides a predictive framework for rational siRNA design, facilitating the development of chemically modified siRNAs with minimized off-target interactions.Our findings contribute to the advancement of more precise and effective RNAi-based therapeutics by elucidating the position-dependent effects of chemical modifications on siRNA off-target effects.
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