@article { ISI:000263373600066,
	title = {Dendritic effect of ligand-coated nanoparticles: enhanced apoptotic activity of silica-berberine nanoconjugates},
	journal = {Langmuir},
	volume = {25},
	number = {4},
	year = {2009},
	month = {FEB},
	pages = {2339-2347},
	publisher = {AMER CHEMICAL SOC},
	address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
	abstract = {<p>We describe the synthesis and biological characterization of a novel prototype, namely, silica nanoconjugates bearing a covalently linked berberine, a plant alkaloid known to have antiproliferative activity. The effect of synthesized nanoconjugates on cell proliferation, the cell cycle profile, and apoptosis in the human cervical carcinoma cell line (HeLa), human hepatocellular liver carcinoma cell line (HepG2), and human embryonic kidney (HEK) 293T cell line has been studied and compared with the results obtained for free berberine. Our results show that all the nanoconjugates display higher antiproliferative activity than free berberine. The ability of these nanoconjugates to inhibit cellular proliferation is mediated by the cell cycle arrest at the G1 phase. Moreover, silica nanoconugates caused selective apoptotic arrest with a higher efficiency than free berberine followed by apoptotic cell death as shown by quantitative fluorescence-activated cell sorting analyses. Efficiency of the nanoconjugates increases upon an increase in the linker chain length, demonstrating the distinct role of the spacer chain that conjugates nanoparticles and ligands. The actual reason to show enhanced efficiency by the nanoconjugates has not been elucidated in the present study; however, we hypothesize that an increase in local concentration due to the confinement of a ligand on the nanosurface ({\textquoteright}{\textquoteright}dendritic{\textquoteright}{\textquoteright} effect) might have led to the observed effect.</p>},
	issn = {0743-7463},
	doi = {10.1021/la802761b},
	author = {Halimani, Mahantappa and Chandran, S. Prathap and Kashyap, Sudhir and Jadhav, V. M. and Bhagavatula L. V. Prasad and Hotha, Srinivas and Maiti, Souvik}
}
@article {49648,
	title = {Development of an in silico platform (TRIPinRNA) for the identification of novel RNA intramolecular triple helices and their validation using biophysical techniques},
	journal = {Biochemistry},
	volume = {64},
	year = {2024},
	month = {DEC},
	pages = {250-265},
	type = {Article},
	abstract = {<p>
	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 {\textquoteleft} 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.</p>
},
	issn = {0006-2960},
	doi = {10.1021/acs.biochem.4c00334},
	author = {Rakheja, Isha and Bharti, Vishal and Sahana, S. and Das, Prosad Kumar and Ranjan, Gyan and Kumar, Ajit and Jain, Niyati and Maiti, Souvik}
}
