@article { ISI:000343847000023, title = {Role of G-quadruplex located at 5 end of mRNAs}, journal = {Biochimica Et Biophysica Acta-General Subjects}, volume = {1840}, number = {12}, year = {2014}, month = {DEC}, pages = {3503-3510}, publisher = {ELSEVIER SCIENCE BV}, address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS}, abstract = {

Background: Secondary structures in 5{\textquoteright} UTR of mRNAs play a critical role in regulating protein synthesis. Though studies have indicated the role of secondary structure G-quadruplex in translational regulation, position-specific effect of G-quadruplex in naturally occurring mRNAs is still not understood. As a pre-initiation complex recognises 5{\textquoteright} cap of the mRNA and scans along the untranslated region (UTR) before initiating translation, the presence of G-quadruplex in 5{\textquoteright} region may have a significant contribution in regulating translation. Here, we investigate the role of G-quadruplex located at the 5{\textquoteright} end of an mRNA. Methods: Biophysical characterisation of putative G-quadruplexes was performed using UV and CD spectroscopy. Functional implication of G-quadruplex in the context of their location was assessed in cellulo using gRT-PCR and dual luciferase assay system. Results: PG4 sequences in 5{\textquoteright} UTR of AICT interacting protein (AKTIP), cathepsin B (CTSB) and forkhead box E3 (FOXE3) mRNAs form G-quadruplex whereas it is unable to form G-quadruplex in apolipoprotein A-I binding protein (APOA1BP). Our results demonstrated diverse roles of G-quadruplex located at 5{\textquoteright} end of mRNAs. Though G-quadruplex in AKTIP and CTSB mRNA act as inhibitory modules, it activates translation in FOXE3 mRNA. Conclusions: Our works suggests that G-quadruplex present at the 5{\textquoteright} terminal of an mRNA behaves differently in a different gene context. It can activate or inhibit gene expression. General significance: This study demonstrated that it is difficult to predict the role of G-quadruplex on the basis of its position in 5{\textquoteright} UTR. The neighbouring nucleotide sequence, the intracellular milieu and the interacting partners might render diverse functions to this secondary structure. (C) 2014 Elsevier B.V. All rights reserved.

}, keywords = {AKTIP, APOA1BP, CTSB, FOXE3, G-quadruplex, UTR}, issn = {0304-4165}, doi = {10.1016/j.bbagen.2014.08.017}, author = {Agarwala, Prachi and Pandey, Satyaprakash and Maiti, Souvik} } @article { ISI:000366339300003, title = {RNA stem-loop to G-quadruplex equilibrium controls mature MicroRNA production inside the cell}, journal = {Biochemistry}, volume = {54}, number = {48}, year = {2015}, month = {DEC}, pages = {7067-7078}, publisher = {AMER CHEMICAL SOC}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

The biological role of the existence of overlapping structures in RNA is possible yet remains very unexplored. G-Rich tracts of RNA form G-quadruplexes, while GC-rich sequences prefer stem-loop structures. The equilibrium between alternate structures within RNA may occur and influence its functionality. We tested the equilibrium between G-quadruplex and stem-loop structure in RNA and its effect on biological processes using pre-miRNA as a model system. Dicer enzyme recognizes canonical stem-loop structures in pre-miRNA to produce mature miRNAs. Deviation from stem-loop leads to deregulated mature miRNA levels, providing readout of the existence of an alternate structure per se G-quadruplex-mediated structural interference in miRNA maturation. In vitro analysis using beacon and Dicer cleavage assays indicated that mature miRNA levels depend on relative amounts of K+: and Mg2+ ions, suggesting an ion-dependent structural shift. Further in cellulo studies with and without TmPyP4 (RNA G-quadruplex destabilizer) demonstrated that miRNA biogenesis is modulated by G-quadruplex to stem-loop equilibrium in a subset of pre-miRNAs. Our combined analysis thus provides evidence of the formation of noncanonical G-quaciruplexes in competition with canonical stem-loop structure inside the cell and its effect on miRNA maturation in a comprehensive manner.

}, issn = {0006-2960}, doi = {10.1021/acs.biochem.5b00574}, author = {Pandey, Satyaprakash and Agarwala, Prachi and Jayaraj, Gopal Gunanathan and Gargallo, Raimundo and Maiti, Souvik} } @article {47346, title = {Rapid and accurate nucleobase detection using FnCas9 and its application in COVID-19 diagnosis}, journal = {Biosensors \& Bioelectronics}, volume = {183}, year = {2021}, month = {JUL }, pages = {113207}, type = {Article}, abstract = {

Rapid detection of DNA/RNA pathogenic sequences or variants through point-of-care diagnostics is valuable for accelerated clinical prognosis, as witnessed during the recent COVID-19 outbreak. Traditional methods relying on qPCR or sequencing are tough to implement with limited resources, necessitating the development of accurate and robust alternative strategies. Here, we report FnCas9 Editor Linked Uniform Detection Assay (FELUDA) that utilizes a direct Cas9 based enzymatic readout for detecting nucleobase and nucleotide sequences without transcleavage of reporter molecules. We also demonstrate that FELUDA is 100\% accurate in detecting single nucleotide variants (SNVs), including heterozygous carriers, and present a simple web-tool JATAYU to aid end-users. FELUDA is semi-quantitative, can adapt to multiple signal detection platforms, and deploy for versatile applications such as molecular diagnosis during infectious disease outbreaks like COVID-19. Employing a lateral flow readout, FELUDA shows 100\% sensitivity and 97\% specificity across all ranges of viral loads in clinical samples within 1hr. In combination with RT-RPA and a smartphone application True Outcome Predicted via Strip Evaluation (TOPSE), we present a prototype for FELUDA for CoV-2 detection closer to home.

}, keywords = {CRISPRDx, FELUDA, FnCas9, LFA, SARS-CoV2, SNV detection}, issn = {0956-5663}, doi = {10.1016/j.bios.2021.113207}, author = {Azhar, Mohd and Phutela, Rhythm and Kumar, Manoj and Ansari, Asgar Hussain and Rauthan, Riya and Gulati, Sneha and Sharma, Namrata and Sinha, Dipanjali and Sharma, Saumya and Singh, Sunaina and Acharya, Sundaram and Sarkar, Sajal and Paul, Deepanjan and Kathpalia, Poorti and Aich, Meghali and Sehgal, Paras and Ranjan, Gyan and Bhoyar, Rahul C. and Singhal, Khushboo and Lad, Harsha and Patra, Pradeep Kumar and Makharia, Govind and Chandak, Giriraj Ratan and Pesala, Bala and Chakraborty, Debojyoti and Maiti, Souvik and Indian CoV2 Genomics Genetic Epide} } @article {47401, title = {Rapid identification and tracking of SARS-CoV-2 variants of concern}, journal = {Lancet}, volume = {397}, year = {2021}, month = {APR}, pages = {1346-1347}, type = {Letter}, issn = {0140-6736}, doi = {10.1016/S0140-6736(21)00470-0}, author = {Chakraborty, Debojyoti and Agrawal, Anurag and Maiti, Souvik} }