@article { ISI:000315844500003, title = {G-quadruplex augments translation in the 5 {\textquoteleft} untranslated region of transforming growth factor beta 2}, journal = {Biochemistry}, volume = {52}, number = {9}, year = {2013}, month = {MAR}, pages = {1528-1538}, publisher = {AMER CHEMICAL SOC}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

Transforming growth factor beta 2 (TGF beta 2) is a versatile cytokine with a prominent role in cell migration, invasion, cellular development, and immunomodulation. TGF beta 2 promotes the malignancy of tumors by inducing epithelial-mesenchymal transition, angiogenesis, and immunosuppression. As it is well-documented that nucleic acid secondary structure can regulate gene expression, we assessed whether any secondary motif regulates its expression at the post-transcriptional level. Bioinformatics analysis predicts an existence of a 23-nucleotide putative G-quadruplex sequence (PG4) in the 5{\textquoteright} untranslated region (UTR) of TGF beta 2 mRNA. The ability of this stretch of sequence to form a highly stable, intramolecular parallel quadruplex was demonstrated using ultraviolet and circular dichroism spectroscopy. Footprinting studies further validated its existence in the presence of a neighboring nucleotide sequence. Following structural characterization, we evaluated the biological relevance of this secondary motif using a dual luciferase assay. Although PG4 inhibits the expression of the reporter gene, its presence in the context of the entire 5{\textquoteright} UTR sequence interestingly enhances gene expression. Mutation or removal of the G-quadruplex sequence from the 5{\textquoteright} UTR of the gene diminished the level of expression of this gene at the translational level. Thus, here we highlight an activating role of the G-quadruplex in modulating gene expression of TGF beta 2 at the translational level and its potential to be used as a target for the development of therapeutics against cancer.

}, issn = {0006-2960}, doi = {10.1021/bi301365g}, author = {Agarwala, Prachi and Pandey, Satyaprakash and Mapa, Koyeli and Maiti, Souvik} } @article { ISI:000326292100005, title = {G-Quadruplexes as tools for synthetic biology}, journal = {Chembiochem}, volume = {14}, number = {16}, year = {2013}, month = {NOV}, pages = {2077-2081}, publisher = {WILEY-V C H VERLAG GMBH}, address = {BOSCHSTRASSE 12, D-69469 WEINHEIM, GERMANY}, abstract = {

With the potential to engineer biological systems, synthetic biology is an emerging field that combines various disciplines of sciences. It encompasses combinations of DNA, RNA and protein modules for constructing desired systems and the rewiring of existing signalling networks. Despite recent advances, this field still lags behind in the artificial reconstruction of cellular processes, and thus demands new modules and switches to create genetic circuits. The widely characterised noncanonical nucleic acid secondary structures, G-quadruplexes are promising candidates to be used as biological modules in synthetic biology. Structural plasticity and functional versatility are significant G-quadruplex traits for its integration into a biological system and for diverse applications in synthetic circuits.

}, keywords = {G-quadruplexes, ribozymes, synthetic biology, topology, zipcodes}, issn = {1439-4227}, doi = {10.1002/cbic.201300456}, author = {Agarwala, Prachi and Pandey, Satyaprakash and Maiti, Souvik} } @article {44489, title = {G-quadruplex motif at the 3{\textquoteright} end of sgRNAs improves CRISPR-Cas9 based genome editing efficiency}, journal = {Chemical Communications}, volume = {54}, year = {2018}, month = {MAR}, pages = {2377-2380}, abstract = {Originating as a component of prokaryotic adaptive immunity, the type II CRISPR/Cas9 system has been repurposed for targeted genome editing in various organisms. Although Cas9 can bind and cleave DNA efficiently under in vitro conditions, its activity inside a cell can vary dramatically between targets owing to differences between genomic loci and availability of enough Cas9/sgRNA (single guide RNA) complex molecules for cleavage. Most methods to improve CRISPR/Cas9 activity have so far relied on Cas9 protein engineering or base modifications in the sgRNA sequence. Here we demonstrate that a structure based rational design of sgRNAs can enhance the efficiency of Cas9 cleavage in vivo. By appending a naturally forming RNA G-quadruplex motif to the 3' end of sgRNAs we can improve its stability and target cleavage efficiency in zebrafish embryos without inducing off-target activity, thereby underscoring its value in the design of better and optimized genome editing triggers.}, issn = {1359-7345}, doi = {10.1039/C7CC08893K}, author = {Nahar, Smita and Sehgal, Paras and Azhar, Mohammad and Rai, Manish and Singh, Amrita and Sivasubbu, Sridhar and Chakraborty, Debojyoti and Maiti, Souvik} } @article {48338, title = {G4-binding drugs, chlorpromazine and prochlorperazine, repurposed against COVID-19 infection in hamsters}, journal = {Frontiers in Molecular Biosciences}, volume = {10}, year = {2023}, month = {MAR }, pages = {1133123}, type = {Article}, abstract = {

The COVID-19 pandemic caused by SARS-CoV-2 has caused millions of infections and deaths worldwide. Limited treatment options and the threat from emerging variants underline the need for novel and widely accessible therapeutics. G-quadruplexes (G4s) are nucleic acid secondary structures known to affect many cellular processes including viral replication and transcription. We identified heretofore not reported G4s with remarkably low mutation frequency across \>5 million SARS-CoV-2 genomes. The G4 structure was targeted using FDA-approved drugs that can bind G4s - Chlorpromazine (CPZ) and Prochlorperazine (PCZ). We found significant inhibition in lung pathology and lung viral load of SARS-CoV-2 challenged hamsters when treated with CPZ or PCZ that was comparable to the widely used antiviral drug Remdesivir. In support, in vitro G4 binding, inhibition of reverse transcription from RNA isolated from COVID-infected humans, and attenuated viral replication and infectivity in Vero cell cultures were clear in case of both CPZ and PCZ. Apart from the wide accessibility of CPZ/PCZ, targeting relatively invariant nucleic acid structures poses an attractive strategy against viruses like SARS-CoV-2, which spread fast and accumulate mutations quickly.

}, keywords = {Conserved motif, FDA-approved drugs, G-quadruplex binding drugs, hamster model of COVID-19, RNA G-quadruplex}, doi = {10.3389/fmolb.2023.1133123}, author = {Roy, Shuvra Shekhar and Sharma, Shalu and Rizvi, Zaigham Abbas and Sinha, Dipanjali and Gupta, Divya and Rophina, Mercy and Sehgal, Paras and Sadhu, Srikanth and Tripathy, Manas Ranjan and Samal, Sweety and Maiti, Souvik and Scaria, Vinod and Sivasubbu, Sridhar and Awasthi, Amit and Harshan, Krishnan H. and Jain, Sanjeev and Chowdhury, Shantanu} }