02321nas a2200181 4500008004100000022001400041245010600055210006900161260007100230300001400301490000700315520160500322100002101927700002501948700001701973700001801990856013102008 2013 eng d a0006-296000aG-quadruplex augments translation in the 5 ` untranslated region of transforming growth factor beta 20 aGquadruplex augments translation in the 5 untranslated region of a1155 16TH ST, NW, WASHINGTON, DC 20036 USAbAMER CHEMICAL SOCcMAR a1528-15380 v523 a

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' 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' UTR sequence interestingly enhances gene expression. Mutation or removal of the G-quadruplex sequence from the 5' 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.

1 aAgarwala, Prachi1 aPandey, Satyaprakash1 aMapa, Koyeli1 aMaiti, Souvik uhttps://library.ncl.res.in/content/g-quadruplex-augments-translation-5-untranslated-region-transforming-growth-factor-beta-2-001528nas a2200229 4500008004100000022001400041245005000055210004900105260007700154300001400231490000700245520082100252653001901073653001401092653002201106653001301128653001301141100002101154700002501175700001801200856008001218 2013 eng d a1439-422700aG-Quadruplexes as tools for synthetic biology0 aGQuadruplexes as tools for synthetic biology aBOSCHSTRASSE 12, D-69469 WEINHEIM, GERMANYbWILEY-V C H VERLAG GMBHcNOV a2077-20810 v143 a

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.

10aG-quadruplexes10aribozymes10asynthetic biology10atopology10azipcodes1 aAgarwala, Prachi1 aPandey, Satyaprakash1 aMaiti, Souvik uhttps://library.ncl.res.in/content/g-quadruplexes-tools-synthetic-biology-001757nas a2200229 4500008004100000022001400041245010000055210006900155260000800224300001400232490000700246520099300253100001701246700001801263700002001281700001601301700001801317700002301335700002701358700001801385856012401403 2018 eng d a1359-734500aG-quadruplex motif at the 3' end of sgRNAs improves CRISPR-Cas9 based genome editing efficiency0 aGquadruplex motif at the 3 end of sgRNAs improves CRISPRCas9 bas cMAR a2377-23800 v543 aOriginating 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.1 aNahar, Smita1 aSehgal, Paras1 aAzhar, Mohammad1 aRai, Manish1 aSingh, Amrita1 aSivasubbu, Sridhar1 aChakraborty, Debojyoti1 aMaiti, Souvik uhttps://library.ncl.res.in/content/g-quadruplex-motif-3-end-sgrnas-improves-crispr-cas9-based-genome-editing-efficiency02519nas a2200385 4500008004100000245010900041210006900150260000900219300001200228490000700240520127600247653002001523653002301543653003101566653003001597653002101627100002501648700001801673700002601691700002101717700001701738700001901755700001801774700002001792700002801812700001801840700001801858700001801876700002301894700001801917700002601935700001801961700002401979856013002003 2023 eng d00aG4-binding drugs, chlorpromazine and prochlorperazine, repurposed against COVID-19 infection in hamsters0 aG4binding drugs chlorpromazine and prochlorperazine repurposed a cMAR  a11331230 v103 a

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.

10aConserved motif10aFDA-approved drugs10aG-quadruplex binding drugs10ahamster model of COVID-1910aRNA G-quadruplex1 aRoy, Shuvra, Shekhar1 aSharma, Shalu1 aRizvi, Zaigham, Abbas1 aSinha, Dipanjali1 aGupta, Divya1 aRophina, Mercy1 aSehgal, Paras1 aSadhu, Srikanth1 aTripathy, Manas, Ranjan1 aSamal, Sweety1 aMaiti, Souvik1 aScaria, Vinod1 aSivasubbu, Sridhar1 aAwasthi, Amit1 aHarshan, Krishnan, H.1 aJain, Sanjeev1 aChowdhury, Shantanu uhttps://library.ncl.res.in/content/g4-binding-drugs-chlorpromazine-and-prochlorperazine-repurposed-against-covid-19-infection