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Eight Triplex-Binding Molecules from Four Chemical Classes Broadly Recognize the MALAT1 Triple Helix
Madeline M Mousseau1, Krishna M Shivakumar1, Jaesang Yoo1
1Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
Small molecules called triplex-binding molecules (TBMs) can interact with the MALAT1 triple helix. These TBMs show potential for targeting cancer cells by reducing MALAT1 levels.
Area of Science:
- Molecular Biology
- Biochemistry
- Drug Discovery
Background:
- RNA triple helices are understudied structures with potential therapeutic applications.
- The MALAT1 triple helix is a key target for small molecule interactions.
Purpose of the Study:
- To evaluate eight triplex-binding molecules (TBMs) for their effects on the MALAT1 triple helix.
- To understand how TBMs interact with different structural features of the MALAT1 triple helix.
Main Methods:
- UV thermal denaturation experiments to assess helix stabilization.
- Surface plasmon resonance to analyze binding kinetics.
- Cell-based assays to determine the effect on MALAT1 levels in cancer cells.
Main Results:
- Several TBMs, including berberine and sanguinarine, selectively stabilize the MALAT1 triple helix.
- TBMs showed varying sensitivities to nucleotide composition and helix length.
- Neomycin was the only TBM that could outcompete MALAT1-binding proteins.
- TBM treatment reduced MALAT1 levels in colorectal carcinoma cells by 20-60%.
Conclusions:
- TBMs broadly recognize the MALAT1 triple helix.
- TBMs can be designed for selective binding based on specific structural features.
- This study provides insights for developing novel therapeutics targeting RNA structures.
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