@article {46331, title = {Francisella novicida Cas9 interrogates genomic DNA with very high specificity and can be used for mammalian genome editing}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, year = {2019}, month = {OCT}, pages = {20959-20968}, type = {Article}, abstract = {

Genome editing using the CRISPR/Cas9 system has been used to make precise heritable changes in the DNA of organisms. Although the widely used Streptococcus pyogenes Cas9 (SpCas9) and its engineered variants have been efficiently harnessed for numerous gene-editing applications across different platforms, concerns remain regarding their putative off-targeting at multiple loci across the genome. Here we report that Francisella novicida Cas9 (FnCas9) shows a very high specificity of binding to its intended targets and negligible binding to off-target loci. The specificity is determined by its minimal binding affinity with DNA when mismatches to the target single-guide RNA (sgRNA) are present in the sgRNA:DNA heteroduplex. FnCas9 produces staggered cleavage, higher homology-directed repair rates, and very low nonspecific genome editing compared to SpCas9. We demonstrate FnCas9-mediated correction of the sickle cell mutation in patient-derived induced pluripotent stem cells and propose that it can be used for precise therapeutic genome editing for a wide variety of genetic disorders.

}, keywords = {CRISPR Cas9, gene therapy, Genome editing, iPSCs, sickle cell anemia}, issn = {0027-8424}, doi = {10.1073/pnas.1818461116}, author = {Acharya, Sundaram and Mishra, Arpit and Paul, Deepanjan and Ansari, Asgar Hussain and Azhar, Mohd and Kumar, Manoj and Rauthan, Riya and Sharma, Namrata and Aich, Meghali and Sinha, Dipanjali and Sharma, Saumya and Jain, Shivani and Ray, Arjun and Jain, Suman and Ramalingam, Sivaprakash and Maiti, Souvik and Chakraborty, Debojyoti} } @article {46741, title = {Terminal uridylyl transferase mediated site-directed access to clickable chromatin employing CRISPR-dCas9}, journal = {Journal of the American Chemical Society}, volume = {142}, year = {2020}, month = {AUG}, pages = {13954-13965}, type = {Article}, abstract = {

Locus-specific interrogation of target genes employing functional probes such as proteins and small molecules is paramount in decoding the molecular basis of gene function and designing tools to modulate its downstream effects. In this context, CRISPR-based gene editing and targeting technologies have proved tremendously useful, as they can be programmed to target any gene of interest by simply changing the sequence of the single guide RNA (sgRNA). Although these technologies are widely utilized in recruiting genetically encoded functional proteins, display of small molecules using CRISPR system is not well developed due to the lack of adequate techniques. Here, we have devised an innovative technology called sgRNA-Click (sgR-CLK) that harnesses the power of bioorthogonal click chemistry for remodeling guide RNA to display synthetic molecules on target genes. sgR-CLK employs a novel posttranscriptional chemoenzymatic labeling platform wherein a terminal uridylyl transferase (TUTase) was repurposed to generate clickable sgRNA of choice by site-specific tailoring of multiple azide-modified nucleotide analogues at the 3{\textquoteright} end. The presence of a minimally invasive azide handle assured that the sgRNAs are indeed functional. Notably, an azide-tailed sgRNA targeting the telomeric repeat served as a Trojan horse on the CRISPR-dCas9 system to guide synthetic tags (biotin) site-specifically on chromatin employing copper-catalyzed or strain-promoted click reactions. Taken together, sgR-CLK presents a significant advancement on the utility of bioorthogonal chemistry, TUTase, and the CRISPR toolbox, which could offer a simplified solution for site-directed display of small molecule probes and diagnostic tools on target genes.

}, issn = {0002-7863}, doi = {10.1021/jacs.0c06541}, author = {George, Jerrin Thomas and Azhar, Mohd and Aich, Meghali and Sinha, Dipanjali and Ambi, Uddhav B. and Maiti, Souvik and Chakraborty, Debojyoti and Srivatsan, Seergazhi G.} } @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 {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} }