@article {48351,
	title = {Small molecule quercetin binds MALAT1 triplex and modulates its cellular function},
	journal = {Molecular Therapy-Nucleic Acids},
	volume = {30},
	year = {2022},
	month = {DEC},
	pages = {241-256},
	type = {Article},
	abstract = {<p>
	The triple-helix structure at the 30 end of metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), a long non -cod-ing RNA, has been considered to be a target for modulating the oncogenic functions of MALAT1. This study examines the binding of quercetin-a known triplex binding molecule-to the MALAT1 triplex. By employing UV-visible spectroscopy, circular dichroism spectroscopy, and isothermal titration calo-rimetry, we observed that quercetin binds to the MALAT1 triplex with a stoichiometry of 1:1 and Kd 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 MALAT1 transcript levels in MCF7 cells, and fluorescence in situ hybridization (FISH) experiments showed concomitantly reduced levels of MALAT1 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, tran-scriptome-wide analysis of alternative splicing changes induced by quercetin revealed modulation of MALAT1 downstream genes. Collectively, our study shows that quercetin strongly binds to the MALAT1 triplex and modulates its functions. It can thus be used as a scaffold for further development of ther-apeutics or as a chemical tool to understand MALAT1 func-tions.</p>
},
	issn = {2162-2531},
	doi = {10.1016/j.omtn.2022.09.016},
	author = {Rakheja, Isha and Ansari, Asgar Hussain and Ray, Arjun and Joshi, Dheeraj Chandra and Maiti, Souvi}
}
@article {49559,
	title = {Molecular modeling of non-canonical intramolecular RNA triple helix structures predicted from TRIPinRNA and their in vitro biophysical structure validation},
	journal = {Journal of Physical Chemistry B},
	volume = {129},
	year = {2025},
	month = {APR},
	pages = {4298-4308},
	type = {Article},
	abstract = {<p>
	RNA triple helices have traditionally been characterized by pyrimidine-type UA-U or CG-C triplets, with other base triplets considered to be destabilizing. However, the presence of non-canonical triplets in riboswitches and self-splicing introns suggests that triplexes containing longer stretches of such triplets may exist in the human genome too. Using molecular modeling, we investigated a chimeric triple helix derived from the FLRT2-AS1 lncRNA, confirming its stability over a 500 ns simulation. Biophysical analyses further support the formation of this triplex in vitro. Although these non-canonical structures exhibit less thermal stability compared to traditional UA-U triplets found in lncRNAs like metastasis associated lung adenocarcinoma transcript 1 and NEAT1, they may serve distinct biological functions, suggesting a dynamic and more temporal role in cellular processes. The triplex selected for this study is found in a human long non-coding RNA gene, paving the way for investigating the intriguing roles of these triple helices in cell biology.</p>
},
	issn = {1520-6106},
	doi = {10.1021/acs.jpcb.5c00160},
	author = {Rakheja, Isha and Panda, Gayatri and Maiti, Souvik and Ray, Arjun}
}
