# A pothole-filling strategy for selective targeting of rCUG-repeats associated with myotonic dystrophy type 1

## TL;DR

Researchers developed a new type of molecule that can selectively target harmful RNA repeats linked to myotonic dystrophy type 1, combining the best features of small molecules and antisense drugs.

## Contribution

A novel class of compact nucleic acid ligands with bifacial recognition and a preorganized backbone for selective targeting of RNA repeats.

## Key findings

- The ligands show high specificity and selectivity for pathogenic over normal-length CUG-RNA repeats.
- The 'pothole-filling' mechanism enhances recognition by avoiding RNA unfolding penalties.
- The design offers potential for targeting other disease-related RNA structures in neuromuscular disorders.

## Abstract

This work presents a class of triplet nucleic acid ligands that combine the targeting precision of antisense oligonucleotides with the compactness of small molecules to selectively engage expanded CUG-RNA repeats implicated in Myotonic Dystrophy type 1. Featuring bifacial (Janus) recognition elements and a conformationally preorganized gamma peptide nucleic acid backbone, these ligands exhibit unusually high binding cooperativity, specificity, and selectivity for pathogenic over normal-length repeats. While cellular uptake remains an area for improvement, the design shows broad potential for targeting both RNA triplet-repeat expansions and other native RNA structures with essential physiological functions.

We present an alternative approach to conventional small-molecule and antisense strategies for selectively targeting expanded CUG-RNA repeats associated with Myotonic Dystrophy type 1. Our alternatively designed nucleic acid ligands uniquely integrate advantageous features from both existing methods: They are compact (only three units in length), structurally resembling small molecules, yet recognize RNA targets through directional hydrogen-bonding similar to antisense oligonucleotides. Notably, these ligands exhibit greater specificity and selectivity than either approach alone. This enhanced specificity results from their bifacial recognition mechanism, wherein mismatches on one binding interface are reciprocally mirrored on the complementary face. Additionally, their short length significantly amplifies specificity, as even a single mismatch substantially reduces the overall binding free energy, effectively minimizing off-target interactions. Unlike conventional oligonucleotides, these ligands avoid binding single-stranded RNA and only recognize defined hairpin motifs via a “pothole-filling” mechanism. This method amplifies recognition specificity and selectivity, circumventing the thermodynamic penalties associated with RNA unfolding. This proof-of-concept study thus lays a foundation for developing versatile nucleic acid ligands capable of selectively targeting not only pathogenic CUG-RNA repeats in Myotonic Dystrophy type 1 but also other disease-associated triplet-repeat expansions prevalent in various neuromuscular disorders.