01905nas a2200181 4500008004100000022001400041245008400055210006900139260007100208300001200279490000600291520122600297100001801523700003101541700001901572700001801591856011401609 2013 eng d a1554-892900aMolecular-beacon-based screen for small molecule inhibitors of miRNA maturation0 aMolecularbeaconbased screen for small molecule inhibitors of miR a1155 16TH ST, NW, WASHINGTON, DC 20036 USAbAMER CHEMICAL SOCcMAY a930-9380 v83 a

miRNAs are small non-coding RNAs that regulate about 60% of mammalian genes by modulating their transcript levels. Network scale studies of miRNA-mediated regulatory circuits demonstrate the central importance of this class of small RNA in the maintenance of biological robustness. More recently, several reports have described the deregulation of numerous miRNA to be causally associated with many diseases, including cancer. These studies have highlighted the potential for development of therapeutic modalities against miRNA. Previous screening protocols, for small molecules targeting miRNA function, are either costly or technically too complex to be applied in a high-throughput manner in standard chemical laboratories. We describe a simple in vitro screening method using a DNA-based molecular beacon that overcomes the limitations associated with earlier screens. We used this method to identify inhibitors of miR-27a function from a library of 14 aminoglycosides as a pilot study. Inhibitory molecules identified were further scrutinized to identify the validity of screen. With this proof of concept we illustrate the utility of a scalable molecular-beacon-based screening strategy for miRNA inhibitors.

1 aBose, Debojit1 aJayaraj, Gopal, Gunanathan1 aKumar, Santosh1 aMaiti, Souvik uhttps://library.ncl.res.in/content/molecular-beacon-based-screen-small-molecule-inhibitors-mirna-maturation-002196nas a2200217 4500008004100000022001400041245009200055210006900147260007100216300001400287490000700301520139700308100001801705700002701723700001901750700001601769700003101785700002301816700001801839856012101857 2014 eng d a0006-296000aMorphological effects of G-quadruplex stabilization using a small molecule in zebrafish0 aMorphological effects of Gquadruplex stabilization using a small a1155 16TH ST, NW, WASHINGTON, DC 20036 USAbAMER CHEMICAL SOCcFEB a1117-11240 v533 a

Zebrafish (Danio rerio) embryos are transparent and advantageous for studying early developmental changes due to ex utero development, making them an appropriate model for studying gene expression changes as a result of molecular targeting. Zebrafish embryos were injected with a previously reported G-quadruplex selective ligand, and the phenotypic changes were recorded. We report marked discrepancies in the development of intersegmental vessels. In silico analysis determined that the putative G-quadruplex motif occur in the upstream promoter region of the Cdh5 (N-cadherin) gene. A real-time polymerase chain reaction-based investigation indicated that in zebrafish, CDH-2 (ZN-cad) was significantly downregulated in the ligand-treated embryos. Biophysical characterization of the interaction of the ligand with the G-quadruplex motif found in this promoter yielded strong binding and stabilization of the G-quadruplex with this ligand. Hence, we report for the first time the phenotypic impact of G-quadruplex targeting with a ligand in a vertebrate organism. This study has unveiled not only G-quadruplex targeting in non-human animal species but also the potential that G-quadruplexes can provide a ready tool for understanding the phenotypic effects of targeting certain important genes involved in differentiation and developmental processes in a living eukaryotic organism.

1 aAgarwal, Tani1 aLalwani, Mukesh, Kumar1 aKumar, Santosh1 aRoy, Saumya1 aChakraborty, Tushar, Kanti1 aSivasubbu, Sridhar1 aMaiti, Souvik uhttps://library.ncl.res.in/content/morphological-effects-g-quadruplex-stabilization-using-small-molecule-zebrafish-001773nas 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