The expanded development and application of CRISPR system for sensitive nucleotide detection

References

[1] Abudayyeh OO, Gootenberg JS, Konermann S, Joung J, Slaymaker IM, Cox DB, Shmakov S, Makarova KS, Semenova E, Minakhin L (2016) C2c2 is a single-component programmable RNAguided RNA-targeting CRISPR effector. Science 353:aaf5573

[2] Abudayyeh OO, Gootenberg JS, Kellner MJ, Zhang F (2019) Nucleic acid detection of plant genes using CRISPR-Cas13. CRISPR J 2:165–171

[3] Anzalone AV, Randolph PB, Davis JR, Sousa AA, Koblan LW, Levy JM, Chen PJ, Wilson C, Newby GA, Raguram A (2019) Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576:149–157

[4] Barrangou R, Marraffini Luciano A (2014) CRISPR-Cas systems: prokaryotes upgrade to adaptive immunity. Mol Cell 54:234–244

[5] Chang W, Liu W, Liu Y, Zhan F, Chen H, Lei H,Liu Y (2019) Colorimetric detection of nucleic acid sequences in plant pathogens based on CRISPR/Cas9 triggered signal amplification. Microchim Acta 186:243

[6] Chen JS, Ma E, Harrington LB, Da Costa M, Tian X, Palefsky JM, Doudna JA (2018) CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity. Science 360:436–439

[7] East-Seletsky A, O’Connell MR, Knight SC, Burstein D, Cate JH, Tjian R, Doudna JA (2016) Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection. Nature 538:270–273

[8] Field AE, Robertson N, Wang T, Havas A, Ideker T, Adams PD (2018) DNA methylation clocks in aging: categories, causes, and consequences. Mol Cell 71:882–895

[9] Gootenberg JS, Abudayyeh OO, Kellner MJ, Joung J, Collins JJ, Zhang F (2018) Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6. Science 360:439–444

[10] Freije CA, Myhrvold C, Boehm CK, Lin AE, Welch NL, Carter A, Metsky HC, Luo CY, Abudayyeh OO, Gootenberg JS (2019) Programmable inhibition and detection of RNA viruses using Cas13. Mol Cell 76:826–837.e811

[11] Gootenberg JS, Abudayyeh OO, Lee JW, Essletzbichler P, Dy AJ, Joung J, Verdine V, Donghia N, Daringer NM, Freije CA (2017) Nucleic acid detection with CRISPR-Cas13a/C2c2. Science 356:438–442

[12] Harrington LB, Burstein D, Chen JS, Paez-Espino D, Ma E, Witte IP, Cofsky JC, Kyrpides NC, Banfield JF, Doudna JA (2018) Programmed DNA destruction by miniature CRISPR-Cas14 enzymes. Science 362:839–842

[13] Horvath P, Barrangou R (2010) CRISPR/Cas, the immune system of bacteria and archaea. Science 327:167–170

[14] Huang M, Zhou X, Wang H, Xing D (2018) Clustered regularly interspaced short palindromic repeats/Cas9 triggered isothermal amplification for site-specific nucleic acid detection. Anal Chem 90:2193–2200

[15] Ishino Y, Shinagawa H, Makino K,Amemura M, Nakata A (1987) Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. J Bacteriol 169:5429–5433

[16] Jansen R, Embden JD, Gaastra W, Schouls LM (2002) Identification of genes that are associated with DNA repeats in prokaryotes. Mol Microbiol 43:1565–1575

[17] Jenkins S, Yang JC, Ramalingam SS, Yu K, Patel S, Weston S, Hodge R, Cantarini M, Janne PA, Mitsudomi T (2017) Plasma ctDNA analysis for detection of the EGFR T790M mutation in patients with advanced non-small cell lung cancer. J Thorac Oncol 12:1061–1070

[18] Jia C, Huai C, Ding J,Hu L, Su B, Chen H, Lu D (2018) New applications of CRISPR/Cas9 system on mutant DNA detection. Gene 641:55–62

[19] Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E (2012) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337:816–821

[20] Kebed YGCM (2015) Review article: genetically modified crops and food security. Food Sci Qual Manage 42:41–49

[21] Konermann S, Lotfy P, Brideau NJ, Oki J, Shokhirev MN, Hsu PD (2018) Transcriptome engineering with RNA-targeting type VI-D CRISPR effectors. Cell 173:665–676.e614

[22] Li S-Y, Cheng Q-X, Wang J-M, Li X-Y, Zhang Z-L, Gao S,Cao R-B, Zhao G-P, Wang J(2018) CRISPR-Cas12a-assisted nucleic acid detection. Cell Discov 4:20

[23] Li L, Li S, Wu N, Wu J, Wang G,Zhao G,Wang J (2019) HOLMESv2: a CRISPR-Cas12b-assisted platform for nucleic acid detection and DNA methylation quantitation. ACS Synth Biol 8:2228–2237

[24] Liang M,Li Z, Wang W, Liu J, Liu L, Zhu G, Karthik L,Wang M, Wang K-F,Wang Z et al (2019) A CRISPR-Cas12a-derived biosensing platform for the highly sensitive detection of diverse small molecules. Nat Commun 10:3672

[25] Metsky HC, Freije CA, Kosoko-Thoroddsen T-SF, Sabeti PC, Myhrvold C (2020) CRISPR-based COVID-19 surveillance using a genomically-comprehensive machine learning approach. bioRxiv.https://doi.org/10.1101/2020.02.26.967026

[26] Myhrvold C, Freije CA, Gootenberg JS, Abudayyeh OO, Metsky HC, Durbin AF, Kellner MJ, Tan AL, Paul LM, Parham LA (2018) Field-deployable viral diagnostics using CRISPR-Cas13. Science 360:444–448

[27] Pardee K, Green AA, Takahashi MK, Braff D, Lambert G, Lee JW, Ferrante T, Ma D, Donghia N, Fan M (2016) Rapid, low-cost detection of Zika virus using programmable biomolecular components. Cell 165:1255–1266

[28] Shmakov S, Abudayyeh Omar O, Makarova Kira S, Wolf Yuri I, Gootenberg Jonathan S, Semenova E, Minakhin L, Joung J, Konermann S, Severinov K et al (2015) Discovery and functional characterization of diverse class 2 CRISPR-Cas systems. Mol Cell 60:385–397

[29] Sorek R, Lawrence CM, Wiedenheft B (2013) CRISPR-mediated adaptive immune systems in bacteria and archaea. Annu Rev Biochem 82:237–266

[30] Strecker J, Jones S, Koopal B, Schmid-Burgk J, Zetsche B, Gao L, Makarova KS, Koonin EV, Zhang F (2019) Engineering of CRISPR-Cas12b for human genome editing. Nat Commun 10:212

[31] Teng F, Cui T, Feng G, Guo L, Xu K, Gao Q, Li T, Li J, Zhou Q, Li W (2018) Repurposing CRISPR-Cas12b for mammalian genome engineering. Cell Discov 4:63

[32] Teng F, Cui T, Gao Q, Guo L, Wan H, Li W (2019) Artificial sgRNAs engineered for genome editing with new Cas12b orthologs. Cell Discov 5:23

[33] Wang X-W, Hu L-F, Hao J, Liao L-Q, Chiu Y-T, Shi M, Wang Y (2019) A microRNA-inducible CRISPR–Cas9 platform serves as a microRNA sensor and cell-type-specific genome regulation tool. Nat Cell Biol 21:522–530

[34] Yan WX, Chong S, Zhang H, Makarova KS, Koonin EV, Cheng DR, Scott DA (2018) Cas13d is a compact RNA-targeting type VI CRISPR effector positively modulated by a WYL-domain-containing accessory protein. Mol Cell 70:327–339.e325

[35] Yan WX, Hunnewell P, Alfonse LE, Carte JM, Keston-Smith E, Sothiselvam S, Garrity AJ, Chong S, Makarova KS, Koonin EV (2019) Functionally diverse type V CRISPR-Cas systems. Science 363:88

[36] Zetsche B, Gootenberg Jonathan S, Abudayyeh Omar O, Slaymaker Ian M, Makarova Kira S, Essletzbichler P, Volz Sara E,Joung J, van der Oost J, Regev A (2015) Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell 163:759–771

[37] Zhang K, Deng R, Teng X, Li Y, Sun Y,Ren X, Li J (2018) Direct visualization of single-nucleotide variation in mtDNA using a CRISPR/Cas9-mediated proximity ligation assay. J Am Chem Soc 140:11293–11301

[38] Zhou W, Hu L, Ying L, Zhao Z, Chu PK, Yu X-F (2018) A CRISPR–Cas9-triggered strand displacement amplification method for ultrasensitive DNA detection. Nat Commun 9:5012

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