The triple-helix structure at the 3' end of metastasis-associated lung adenocarcinoma transcript 1 (), a long non-coding RNA, has been considered to be a target for modulating the oncogenic functions of . This study examines the binding of quercetin-a known triplex binding molecule-to the triplex. By employing UV-visible spectroscopy, circular dichroism spectroscopy, and isothermal titration calorimetry, we observed that quercetin binds to the triplex with a stoichiometry of 1:1 and of 495 ± 61 nM, along with a negative change in free energy, indicating a spontaneous interaction. Employing real-time PCR measurements, we observed around 50% downregulation of transcript levels in MCF7 cells, and fluorescence hybridization (FISH) experiments showed concomitantly reduced levels of in nuclear speckles. This interaction is likely a result of a direct interaction between the molecule and the RNA, as indicated by a transcription-stop experiment. Further, transcriptome-wide analysis of alternative splicing changes induced by quercetin revealed modulation of downstream genes. Collectively, our study shows that quercetin strongly binds to the triplex and modulates its functions. It can thus be used as a scaffold for further development of therapeutics or as a chemical tool to understand functions.