263: Bifacial γPNA triplets target rCUG repeats and displace MBNL1 in Myotonic Dystrophy type 1

Perera J et al., Proc. Natl. Acad. Sci. U.S.A. 2026.123:e2507065123 - Gamma-PNA triplet ligands with Janus bases selectively bind expanded rCUG repeats, displace MBNL1, and show length-dependent cooperativity with partial splicing rescue. Key terms: rCUG repeats, gamma PNA, Janus bases, MBNL1 displacement, myotonic dystrophy type 1.

Study Highlights:
The authors designed compact three-unit bifacial nucleic acid ligands (Janus bases on a γPNA backbone) and evaluated them against rCUG repeat duplexes and DM1 patient-derived myotubes using molecular dynamics, EMSA, SPR, AFM, and cellular splicing assays. MD and EMSA/SPR show cooperative, length-dependent binding with Kd values decreasing to ~0.56 µM for rCUG98 and Hill coefficients rising to ~5, driven by enhanced hydrogen-bonding and π–π stacking between adjacent ligands. AFM revealed a 0.348 nm increase in RNA helix contour height on binding, consistent with a pothole-filling insertion mechanism that selectively recognizes hairpin duplexes over single-stranded RNA. Functionally, a cell-permeable LG2c analog reduced nuclear foci and partially restored mis-splicing of Serca1, cTNT, and IR in DM1 myotubes, though cellular uptake remains limiting.

Conclusion:
Short bifacial γPNA triplet ligands selectively recognize pathogenic rCUG hairpins via a pothole-filling mechanism, displace MBNL1, and can partially restore splicing in DM1 myotubes while cellular delivery requires further optimization.

Music:
Enjoy the music based on this article at the end of the episode.

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

First author:
Perera J

Journal:
Proc. Natl. Acad. Sci. U.S.A. 2026.123:e2507065123

DOI:
10.1073/pnas.2507065123

Reference:
Perera J. D. R., Thadke S. A., Thrikawala S. W., Wilson W. D., Tan K. W. R., Chand N. Z. W., Phan A. T., Ly D. H., et al. A pothole-filling strategy for selective targeting of rCUG-repeats associated with myotonic dystrophy type 1. Proc. Natl. Acad. Sci. U.S.A. 2026;123:e2507065123. https://doi.org/10.1073/pnas.2507065123

License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) - https://creativecommons.org/licenses/by/4.0/

Support:
Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00

Official website https://basebybase.com

On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics.

Episode link: https://basebybase.com/episodes/pothole-filling-rcug-gamma-pna

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-01-18.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited the transcript portions describing (a) design of bifacial Janus bases on a gammaPNA backbone, (b) pothole-filling mechanism and cooperative binding to rCUG repeats, (c) selectivity for long pathogenic repeats vs. short normal repeats, (d) displacement of MBNL1, (e) splicing rescue in DM1 patient-derived myotube
- transcript topics: Janus bases and gammaPNA backbone design; Pothole-filling mechanism and RNA hairpin targeting; Cooperativity and length-dependent binding to rCUG repeats; Pathogenic vs normal repeat selectivity (rCUG98 vs rCUG33); MBNL1 displacement by LG2b; LG2c: cell uptake and rescue of splicing in DM1 myotubes

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 6
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- DM1 is driven by expanded rCUG repeats that sequester MBNL1 and disrupt splicing
- Bifacial Janus base ligands on a gammaPNA backbone enable targeted RNA recognition via hydrogen-bonding on two faces
- LG2b binds longer pathogenic rCUG repeats with cooperativity (N ~ 5) and shows length-dependent binding (Kd decreases with longer repeats; e.g., rCUG98 ~0.56 µM)
- LG2b selectively binds pathogenic repeats (rCUG98) and ignores normal repeats (rCUG33)
- AFM evidence shows a 0.348 nm height increase upon LG2b binding, supporting a pothole-filling mechanism
- LG2b can displace MBNL1 from rCUG98 and can prevent binding in competitive formats

QC result: Pass.