Locked Nucleic Acid Oligonucleotides Facilitate RNA•LNA-RNA Triple-Helix Formation and Reduce MALAT1 Levels

Area of Science:

• Molecular Biology
• RNA Therapeutics
• Cancer Research

Background:

• Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) and multiple endocrine neoplasia-β (MENβ) are long noncoding RNAs overexpressed in various cancers.
• These RNAs are recognized as potential therapeutic targets due to their oncogenic roles.
• Traditional therapeutic strategies include small-molecule and antisense-based approaches.

Purpose of the Study:

• To investigate a novel locked nucleic acid (LNA)-based approach for targeting MALAT1 and MENβ.
• To evaluate the efficacy of LNA oligonucleotides in forming triple helices with MALAT1 and MENβ.
• To assess the therapeutic potential of LNAs in reducing cancer-associated lncRNA expression.

Main Methods:

• Design and synthesis of two LNA oligonucleotides (L15 and PS-L15) targeting the A-rich tract of MALAT1 and MENβ.
• Assessment of LNA binding affinity and triple-helix formation using UV thermal denaturation assays.
• Evaluation of LNA-mediated displacement of RNA and protein (METTL16) from RNA complexes.
• Quantification of MALAT1 and MENβ levels in human colorectal carcinoma (HCT116) cells transfected with LNAs.

Main Results:

• Both L15 and PS-L15 effectively formed RNA•LNA•RNA triple helices with MALAT1 and MENβ stem loops.
• LNAs selectively stabilized the Hoogsteen interface over the Watson-Crick interface.
• L15 and PS-L15 displaced the A-rich tract and METTL16 from relevant RNA complexes.
• Transfection with LNAs resulted in a significant 2-fold reduction in MALAT1 and MENβ levels in HCT116 cells.

Conclusions:

• LNA-based oligonucleotides represent a promising strategy for targeting MALAT1 and MENβ.
• This approach demonstrates effective disruption of lncRNA structures and associated protein interactions.
• The dual targeting of MALAT1 and MENβ using LNAs holds potential for cancer therapy.