Reproducible Computational Framework for Precision RNA Targeting in Myotonic Dystrophy Type 1: Balancing ASO Specificity and Cas13 Potency at the DMPK Locus

Myotonic dystrophy type 1 (DM1) is caused by toxic CTG repeat expansions in the 3′UTR of the DMPK gene, leading to pathogenic RNA gain-of-function effects and widespread splicing abnormalities. RNA-targeting strategies such as antisense oligonucleotides (ASOs) and CRISPR-Cas13 hold strong therapeutic promise, but require reproducible design frameworks that balance specificity with potency. Here, we present a transparent computational pipeline for candidate identification and evaluation at the DMPK locus. The pipeline integrates off-target searches, RNA structure predictions, and composite scoring metrics to generate 50 ASO and 50 Cas13 candidates. ASOs achieved absolute specificity with zero off-targets, clustering tightly around moderate composite scores (mean 57.71), while Cas13 guides consistently carried a single off-target that mapped uniquely to the DMPK gene, with no additional genes affected yet delivered superior thermodynamic properties and higher corrected scores (62.12 vs. 57.71). By anchoring design to the pathogenic 3′UTR region and releasing complete candidate listings, this framework ensures methodological rigor, reproducibility, and translational relevance. Overall, it advances readiness for DM1 therapy by combining ASO safety with Cas13 potency, and establishes a reproducible foundation for precision RNA therapeutics across both monogenic and complex diseases.