Application of CRISPR/Cas system in molecular detection

doi:10.3969/j.issn.1673-8640.2020.02.020

Abstract

Abstract:

In recent years,clustered regularly interspaced short palindromic repeat（CRISPR）/CRISPR-associated protein（Cas） system has been widely applied in biology,medicine and other research fields,because of its simple and efficient gene editing ability. With the rapid development of CRISPR technology,the CRISPR/Cas system has been developed as a rapid,portable,low-cost and high-sensitive molecular detection tool,and it has made great breakthroughs and progress in pathogen detection,drug resistance analysis,single nucleotide polymorphism（SNP） typing and tumor gene mutation detection. In order to provide a reference and help for researchers engaged in related fields,this review described the latest research progress of different Cas and their further application in molecular detection.

Key words: Clustered regularly interspaced short palindromic repeat, Clustered regularly interspaced short palindromic repeat-associated protein, Collateral cleavage, Molecular detection, Diagnostics

CLC Number:

R446.1

WANG Xueliang, XIAO Yanqun, WANG Hualiang. Application of CRISPR/Cas system in molecular detection[J]. Laboratory Medicine, 2020, 35(2): 181-185.

Figures/Tables 4

References 39

[1]	CALIENDO A M,HODINKA R L.A CRISPR way to diagnose infectious diseases[J]. N Engl J Med,2017,377(17):1685-1687.
[2]	CHERTOW D S.Next-generation diagnostics with CRISPR[J]. Science,2018,360(6387):381-382.
[3]	LI Y,LI S,WANG J,et al.CRISPR/Cas systems towards next-generation biosensing[J]. Trends Biotechnol,2019,37(7):730-743.
[4]	MARRAFFINI LA.CRISPR-Cas immunity in prokaryotes[J]. Nature,2015,526(7571):55-61.
[5]	MOLLA K A,YANG Y.CRISPR/Cas-mediated base editing:technical considerations and practical applications[J]. Trends Biotechnol,2019,37(10):1121-1142.
[6]	WANG H,LA RUSSA M,QI L S.CRISPR/Cas9 in genome editing and beyond[J]. Annu Rev Biochem,2016,85:227-264.
[7]	HATOUM-ASLAN A.CRISPR methods for nucleic acid detection herald the future of molecular diagnostics[J]. Clin Chem,2018,64(12):1681-1683.
[8]	BARRANGOU R,FREMAUX C,DEVEAU H,et al.CRISPR provides acquired resistance against viruses in prokaryotes[J]. Science,2007,315(5819):1709-1712.
[9]	ISHINO Y,SHINAGAWA H,MAKINO K,et al.Nucleotide sequence of the iap gene,responsible for alkaline phosphatase isozyme conversion in Escherichia coli,and identification of the gene product[J]. J Bacteriol,1987,169(12):5429-5433.
[10]	JANSEN R,EMBDEN J D,GAASTRA W,et al.Identification of genes that are associated with DNA repeats in prokaryotes[J]. Mol Microbiol,2002,43(6):1565-1575.
[11]	YOSEF I,GOREN M G,QIMRON U.Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli[J]. Nucleic Acids Res,2012,40(12):5569-5576.
[12]	GASIUNAS G,BARRANGOU R,HORVATH P,et al.Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria[J]. Proc Natl Acad Sci U S A,2012,109(39):E2579-E2586.
[13]	JINEK M,CHYLINSKI K,FONFARA I,et al.A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity[J]. Science,2012,337(6096):816-821.
[14]	MAKAROVA K S,ZHANG F,KOONIN E V.SnapShot:Class 1 CRISPR-Cas systems[J]. Cell,2017,168(5):946-946e1.
[15]	MAKAROVA K S,ZHANG F,KOONIN E V.SnapShot:Class 2 CRISPR-Cas systems[J]. Cell,2017,168(1-2):328-328e1.
[16]	PICKAR-OLIVER A,GERSBACH C A.The next generation of CRISPR-Cas technologies and applications[J]. Nat Rev Mol Cell Biol,2019,20(8):490-507.
[17]	WU W Y,LEBBINK J H G,KANAAR R,et al. Genome editing by natural and engineered CRISPR-associated nucleases[J]. Nat Chem Biol,2018,14(7):642-651.
[18]	PARDEE K,GREEN A A,TAKAHASHI M K,et al.Rapid,low-cost detection of zika virus using programmable biomolecular components[J]. Cell,2016,165(5):1255-1266.
[19]	ZHOU W,HU L,YING L,et al.A CRISPR-Cas9-triggered strand displacement amplification method for ultrasensitive DNA detection[J]. Nat Commun,2018,9(1):5012.
[20]	HUANG M,ZHOU X,WANG H,et al.Clustered regularly interspaced short palindromic repeats/Cas9 triggered isothermal amplification for site-specific nucleic acid detection[J]. Anal Chem,2018,90(3):2193-2200.
[21]	WANG Q,ZHANG B,XU X,et al.CRISPR-typing PCR(ctPCR),a new Cas9-based DNA detection method[J]. Sci Rep,2018,8(1):14126.
[22]	ZHANG B,WANG Q,XU X,et al.Detection of target DNA with a novel Cas9/sgRNAs-associated reverse PCR(CARP) technique[J]. Anal Bioanal Chem,2018,410(12):2889-2900.
[23]	ZHANG B,XIA Q,WANG Q,et al. Detecting and typing target DNA with a novel CRISPR-typing PCR(ctPCR) technique[J]. Anal Biochem,2018,561-562:37-46.
[24]	LEE S H,YU J,HWANG G H,et al.CUT-PCR:CRISPR-mediated,ultrasensitive detection of target DNA using PCR[J]. Oncogene,2017,36(49):6823-6829.
[25]	SHMAKOV S,ABUDAYYEH O O,MAKAROVA K S,et al.Discovery and functional characterization of diverse Class 2 CRISPR-Cas systems[J]. Mol Cell,2015,60(3):385-397.
[26]	ABUDAYYEH O O,GOOTENBERG J S,KONERMANN S,et al. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector[J]. Science,2016,353(6299):aaf5573.
[27]	EAST-SELETSKY A,O'CONNELL M R,KNIGHT S C,et al. Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection[J]. Nature,2016,538(7624):270-273.
[28]	GOOTENBERG J S,ABUDAYYEH O O,LEE J W,et al.Nucleic acid detection with CRISPR-Cas13a/C2c2[J]. Science,2017,356(6336):438-442.
[29]	GOOTENBERG J S,ABUDAYYEH O O,KELLNER M J,et al.Multiplexed and portable nucleic acid detection platform with Cas13,Cas12a,and Csm6[J]. Science,2018,360(6387):439-444.
[30]	MYHRVOLD C,FREIJE C A,GOOTENBERG J S,et al.Field-deployable viral diagnostics using CRISPR-Cas13[J]. Science,2018,360(6387):444-448.
[31]	WU Y,LIU S X,WANG F,et al.Room temperature detection of plasma Epstein-Barr virus DNA with CRISPR-Cas13[J]. Clin Chem,2019,65(4):591-592.
[32]	LIU Y,XU H,LIU C,et al.CRISPR-Cas13a nanomachine based simple technology for avian influenza A(H7N9) virus on-site detection[J]. J Biomed Nanotechnol,2019,15(4):790-798.
[33]	QIN P,PARK M,ALFSON K J,et al.Rapid and fully microfluidic Ebola virus detection with CRISPR-Cas13a[J]. ACS Sens,2019,4(4):1048-1054.
[34]	SHAN Y,ZHOU X,HUANG R,et al.High-fidelity and rapid quantification of miRNA combining crRNA programmability and CRISPR/Cas13a trans-cleavage activity[J]. Anal Chem,2019,91(8):5278-5285.
[35]	ZETSCHE B,GOOTENBERG J S,ABUDAYYEH O O,et al.Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system[J]. Cell,2015,163(3):759-771.
[36]	CHEN J S,MA E,HARRINGTON L B,et al.CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity[J]. Science,2018,360(6387):436-439.
[37]	LI S,CHENG Q,WANG J,et al.CRISPR-Cas12a-assisted nucleic acid detection[J]. Cell Discovry,2018,4:20.
[38]	LI L,LI S,WU N,et al.HOLMESv 2:a CRISPR-Cas12b-assisted platform for nucleic acid detection and DNA methylation quantitation[J]. ACS Synth Biol,2019,8:2228-2237.
[39]	HARRINGTON L B,BURSTEIN D,CHEN J S,et al.Programmed DNA destruction by miniature CRISPR-Cas14 enzymes[J]. Science,2018,362(6416):839-842.