Eight Triplex-Binding Molecules from Four Chemical Classes Broadly Recognize the MALAT1 Triple Helix

TL;DR

This study explores how eight small molecules interact with the MALAT1 RNA triple helix, showing they can stabilize it and reduce MALAT1 levels in cancer cells.

Contribution

The study identifies specific sensitivities of triplex-binding molecules to the structure and composition of the MALAT1 triple helix.

Findings

Five TBMs selectively stabilize the Hoogsteen interface of the MALAT1 triple helix.

Three TBMs are more sensitive to nucleotide composition, while others respond to helix length.

Most TBMs could not outcompete binding proteins, but neomycin and others reduced MALAT1 levels in cancer cells.

Abstract

RNA triple helices are relatively understudied, including their interactions with small molecules. In this study, we evaluated eight previously reported triplex-binding molecules (TBMs) for their functional effects on the premature and mature MALAT1 triple helix. Based on UV thermal denaturation experiments, the TBMs berberine, coralyne, sanguinarine, berenil, and neomycin selectively stabilize the Hoogsteen interface of the MALAT1 triple helix. Moreover, fisetin, luteolin, and quercetin were more sensitive to nucleotide composition, whereas berberine, coralyne, sanguinarine, and berenil were more sensitive to changes in the length of the major-groove triple helix. Most TBMs could not outcompete MALAT1 triple helix-binding proteins, except for neomycin. Surface plasmon resonance experiments demonstrated that berberine and sanguinarine display relatively quick association and dissociation binding profiles. Treating human colorectal carcinoma cells with each of the TBMs reduced MALAT1 levels by ~20–60%. This study demonstrates that TBMs broadly recognize the premature and mature MALAT1 triple helix but exhibit subtle sensitivities, suggesting that TBMs can be designed to selectively bind triple helices based on nucleotide composition, length, and structural context.

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