02061nas a2200193 4500008004100000022001400041245008600055210006900141260000800210300001200218490000700230520140400237100001801641700002701659700001501686700002801701700001701729856012101746 2022 eng d a2162-253100aSmall molecule quercetin binds MALAT1 triplex and modulates its cellular function0 aSmall molecule quercetin binds MALAT1 triplex and modulates its  cDEC a241-2560 v303 a

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.

1 aRakheja, Isha1 aAnsari, Asgar, Hussain1 aRay, Arjun1 aJoshi, Dheeraj, Chandra1 aMaiti, Souvi uhttps://library.ncl.res.in/content/small-molecule-quercetin-binds-malat1-triplex-and-modulates-its-cellular-function02100nas a2200229 4500008004100000022001400041245016900055210006900224260000800293300001200301490000700313520127500320100001801595700001901613700001501632700002301647700001701670700001601687700001701703700001801720856013201738 2024 eng d a0006-296000aDevelopment of an in silico platform (TRIPinRNA) for the identification of novel RNA intramolecular triple helices and their validation using biophysical techniques0 aDevelopment of an in silico platform TRIPinRNA for the identific cDEC a250-2650 v643 a

There are surprisingly few RNA intramolecular triple helices known in the human transcriptome. The structure has been most well-studied as a stability-element at the 3 ` end of lncRNAs such as MALAT1 and NEAT1, but the intrigue remains whether it is indeed as rare as it is understood to be or just waiting for a closer look from a new vantage point. TRIPinRNA, our Python-based in silico platform, allows for a comprehensive sequence-pattern search for potential triplex formation in the human transcriptome-noncoding as well as coding. Using this tool, we report the putative occurrence of homopyrimidine type (canonical) triple helices as well as heteropurine-pyrimidine strand type (noncanonical) triple helices in the human transcriptome and validate the formation of both types of triplexes using biophysical approaches. We find that the occurrence of triplex structures has a strong correlation with local GC content, which might be influencing their formation. By employing a search that encompasses both canonical and noncanonical triplex structures across the human transcriptome, this study enriches the understanding of RNA biology. Lastly, TRIPinRNA can be utilized in finding triplex structures for any organism with an annotated transcriptome.

1 aRakheja, Isha1 aBharti, Vishal1 aSahana, S.1 aDas, Prosad, Kumar1 aRanjan, Gyan1 aKumar, Ajit1 aJain, Niyati1 aMaiti, Souvik uhttps://library.ncl.res.in/content/development-silico-platform-tripinrna-identification-novel-rna-intramolecular-triple-helices01773nas a2200181 4500008004100000022001400041245016000055210006900215260000800284300001400292490000800306520108200314100001801396700001901414700001801433700001501451856012501466 2025 eng d a1520-610600aMolecular modeling of non-canonical intramolecular RNA triple helix structures predicted from TRIPinRNA and their in vitro biophysical structure validation0 aMolecular modeling of noncanonical intramolecular RNA triple hel cAPR a4298-43080 v1293 a

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.

1 aRakheja, Isha1 aPanda, Gayatri1 aMaiti, Souvik1 aRay, Arjun uhttps://library.ncl.res.in/content/molecular-modeling-non-canonical-intramolecular-rna-triple-helix-structures-predicted