科微学术

生物工程学报

2025年5月30日 18:48 星期五
首页 > 过刊浏览>2023年第39卷第1期 >60-73. DOI:10.13345/j.cjb.220317
PDF HTML阅读 XML下载 导出引用 引用提醒
基于CRISPR的快速灵敏便捷分子检测
作者:
基金项目:

国家自然科学基金(82002144);广州实验室应急攻关项目(EKPGL2021018);上海市科委基金(21N31900400)


CRISPR-based molecular diagnostics: a review
Author:
  • 摘要
    • | |
  • 访问统计
    • |
  • 参考文献 [63]
    • |
  • 相似文献 [20]
    • | | |
  • 文章评论
    摘要:

    快速灵敏检测技术对疾病防控必不可少。特别是新冠疫情暴发以来，人们深刻认识到快速灵敏检测技术的重要性。近年来，以CRISPR/Cas为代表的基因编辑技术带来了生物技术革命性的进步。CRISPR的核酸检测技术因其快速、准确、灵敏、经济等特点，正在引发分子诊断革新，并已被成功应用于传染病、遗传病、肿瘤基因突变诊断，以及食品安全等领域。本文归纳了基于CRISPR的多种核酸检测体系及应用，并对未来CRISPR核酸检测发展趋势及结合人工智能的智能化检测进行了展望。

    Abstract:

    Rapid and accurate detection technologies are crucial for disease prevention and control. In particular, the COVID-19 pandemic has posed a great threat to our society, highlighting the importance of rapid and highly sensitive detection techniques. In recent years, CRISPR/Cas-based gene editing technique has brought revolutionary advances in biotechnology. Due to its fast, accurate, sensitive, and cost-effective characteristics, the CRISPR-based nucleic acid detection technology is revolutionizing molecular diagnosis. CRISPR-based diagnostics has been applied in many fields, such as detection of infectious diseases, genetic diseases, cancer mutation, and food safety. This review summarized the advances in CRISPR-based nucleic acid detection systems and its applications. Perspectives on intelligent diagnostics with CRISPR-based nucleic acid detection and artificial intelligence were also provided.

    参考文献
    [1] PARDEE K, GREEN AA, TAKAHASHI MK, BRAFF D, LAMBERT G, LEE JW, FERRANTE T, MA D, DONGHIA N, FAN M, DARINGER NM, BOSCH I, DUDLEY DM, O'CONNOR DH, GEHRKE L, COLLINS JJ. Rapid, low-cost detection of zika virus using programmable biomolecular components[J]. Cell, 2016, 165(5):1255-1266.
    [2] ZHOU WH, HU L, YING LM, ZHAO Z, CHU PK, YU XF. A CRISPR-Cas9-triggered strand displacement amplification method for ultrasensitive DNA detection[J]. Nature Communications, 2018, 9:5012.
    [3] HAJIAN R, BALDERSTON S, TRAN T, DEBOER T, ETIENNE J, SANDHU M, WAUFORD NA, CHUNG JY, NOKES J, ATHAIYA M, PAREDES J, PEYTAVI R, GOLDSMITH B, MURTHY N, CONBOY IM, ARAN K. Detection of unamplified target genes via CRISPR-Cas9 immobilized on a graphene field-effect transistor[J]. Nature Biomedical Engineering, 2019, 3(6):427-437.
    [4] CHEN JS, MA EB, HARRINGTON LB, da COSTA M, TIAN XR, PALEFSKY JM, DOUDNA JA. CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity[J]. Science, 2018, 360(6387):436-439.
    [5] LI SY, CHENG QX, WANG JM, LI XY, ZHANG ZL, GAO S, CAO RB, ZHAO GP, WANG J. CRISPR-Cas12a-assisted nucleic acid detection[J]. Cell Discovery, 2018, 4:20.
    [6] TENG F, GUO L, CUI TT, WANG XG, XU K, GAO QQ, ZHOU Q, LI W. CDetection:CRISPR- Cas12b-based DNA detection with sub-attomolar sensitivity and single-base specificity[J]. Genome Biology, 2019, 20(1):132.
    [7] HARRINGTON LB, BURSTEIN D, CHEN JS, PAEZ-ESPINO D, MA EB, WITTE IP, COFSKY JC, KYRPIDES NC, BANFIELD JF, DOUDNA JA. Programmed DNA destruction by miniature CRISPR-Cas14 enzymes[J]. Science, 2018, 362(6416):839-842.
    [8] GOOTENBERG JS, ABUDAYYEH OO, LEE JW, ESSLETZBICHLER P, DY AJ, JOUNG J, VERDINE V, DONGHIA N, DARINGER NM, FREIJE CA, MYHRVOLD C, BHATTACHARYYA RP, LIVNY J, REGEV A, KOONIN EV, HUNG DT, SABETI PC, COLLINS JJ, ZHANG F. Nucleic acid detection with CRISPR-Cas13a/C2c2[J]. Science, 2017, 356(6336):438-442.
    [9] ZHAO YX, CHEN F, LI Q, WANG LH, FAN CH. Isothermal amplification of nucleic acids[J]. Chemical Reviews, 2015, 115(22):12491-12545.
    [10] SINGH D, MALLON J, PODDAR A, WANG YB, TIPPANA R, YANG O, BAILEY S, HA T. Real-time observation of DNA target interrogation and product release by the RNA-guided endonuclease CRISPR Cpf1(Cas12a)[J]. Proceedings of the National Academy of Sciences of the United States of America, 2018, 115(21):5444-5449.
    [11] GOOTENBERG JS, ABUDAYYEH OO, KELLNER MJ, JOUNG J, COLLINS JJ, ZHANG F. Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6[J]. Science, 2018, 360(6387):439-444.
    [12] MA PX, MENG QZ, SUN BQ, ZHAO B, DANG L, ZHONG MT, LIU SY, XU HT, MEI H, LIU J, CHI T, YANG G, LIU M, HUANG XX, WANG XJ. MeCas12a, a highly sensitive and specific system for COVID-19 detection[J]. Advanced Science:Weinheim, Baden- Wurttemberg, Germany, 2020, 7(20):2001300.
    [13] LI LX, LI SY, WU N, WU JC, WANG G, ZHAO GP, WANG J. HOLMESv2:a CRISPR-Cas12b-assisted platform for nucleic acid detection and DNA methylation quantitation[J]. ACS Synthetic Biology, 2019, 8(10):2228-2237.
    [14] YUE HH, SHU BW, TIAN T, XIONG EH, HUANG MQ, ZHU DB, SUN J, LIU Q, WANG SC, LI YR, ZHOU XM. Droplet Cas12a assay enables DNA quantification from unamplified samples at the single-molecule level[J]. Nano Letters, 2021, 21(11):4643-4653.
    [15] LI ZH, ZHAO WC, MA SX, LI ZX, YAO YJ, FEI T. A chemical-enhanced system for CRISPR-Based nucleic acid detection[J]. Biosensors and Bioelectronics, 2021, 192:113493.
    [16] OOI KH, LIU MM, TAY JWD, TEO SY, KAEWSAPSAK P, JIN SY, LEE CK, HOU JW, MAURER-STROH S, LIN WS, YAN B, YAN G, GAO YG, TAN MH. An engineered CRISPR-Cas12a variant and DNA-RNA hybrid guides enable robust and rapid COVID-19 testing[J]. Nature Communications, 2021, 12:1739.
    [17] NGUYEN LT, SMITH BM, JAIN PK. Enhancement of trans-cleavage activity of Cas12a with engineered crRNA enables amplified nucleic acid detection[J]. Nature Communications, 2020, 11:4906.
    [18] DAI YF, SOMOZA RA, WANG L, WELTER JF, LI Y, CAPLAN AI, LIU CC. Exploring the trans-cleavage activity of CRISPR-Cas12a (cpf1) for the development of a universal electrochemical biosensor[J]. Angewandte Chemie:International Ed in English, 2019, 58(48):17399-17405.
    [19] SETHI K, DAILEY GP, ZAHID OK, TAYLOR EW, RUZICKA JA, HALL AR. Direct detection of conserved viral sequences and other nucleic acid motifs with solid-state nanopores[J]. ACS Nano, 2021, 15(5):8474-8483.
    [20] NOURI R, JIANG YQ, TANG ZF, LIAN XL, GUAN WH. Detection of SARS-CoV-2 with solid-state CRISPR-Cas12a-assisted nanopores[J]. Nano Letters, 2021, 21(19):8393-8400.
    [21] HEO W, LEE K, PARK S, HYUN KA, JUNG HI. Electrochemical biosensor for nucleic acid amplification-free and sensitive detection of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) RNA via CRISPR/Cas13a trans- cleavage reaction[J]. Biosensors and Bioelectronics, 2022, 201:113960.
    [22] MYHRVOLD C, FREIJE CA, GOOTENBERG JS, ABUDAYYEH OO, METSKY HC, DURBIN AF, KELLNER MJ, TAN AL, PAUL LM, PARHAM LA, GARCIA KF, BARNES KG, CHAK B, MONDINI A, NOGUEIRA ML, ISERN S, MICHAEL SF, LORENZANA I, YOZWIAK NL, MACINNIS BL, et al. Field-deployable viral diagnostics using CRISPR- Cas13[J]. Science, 2018, 360(6387):444-448.
    [23] JIANG YZ, HU ML, LIU AN, LIN Y, LIU LL, YU B, ZHOU XM, PANG DW. Detection of SARS-CoV-2 by CRISPR/Cas12a-enhanced colorimetry[J]. ACS Sensors, 2021, 6(3):1086-1093.
    [24] HU ML, YUAN CQ, TIAN T, WANG XS, SUN J, XIONG EH, ZHOU XM. Single-step, salt-aging-free, and thiol-free freezing construction of AuNP-based bioprobes for advancing CRISPR-based diagnostics[J]. Journal of the American Chemical Society, 2020, 142(16):7506-7513.
    [25] JOUNG J, LADHA A, SAITO M, KIM NG, WOOLLEY AE, SEGEL M, BARRETTO RPJ, RANU A, MACRAE RK, FAURE G, IOANNIDI EI, KRAJESKI RN, BRUNEAU R, HUANG ML W, YU XG, LI JZ, WALKER BD, HUNG DT, GRENINGER AL, JEROME KR, et al. Detection of SARS-CoV-2 with SHERLOCK one-pot testing[J]. The New England Journal of Medicine, 2020, 383(15):1492-1494.
    [26] CHEN Y, MEI YX, ZHAO XH, JIANG XY. Reagents-loaded, automated assay that integrates recombinase-aided amplification and Cas12a nucleic acid detection for a point-of-care test[J]. Analytical Chemistry, 2020, 92(21):14846-14852.
    [27] FENG W, PENG HY, XU JY, LIU YM, PABBARAJU K, TIPPLES G, JOYCE MA, SAFFRAN HA, TYRRELL DL, BABIUK S, ZHANG HQ, LE XC. Integrating reverse transcription recombinase polymerase amplification with CRISPR technology for the one-tube assay of RNA[J]. Analytical Chemistry, 2021, 93(37):12808-12816.
    [28] de PUIG H, LEE RA, NAJJAR D, TAN X, SOEKNSEN LR, ANGENENT-MARI NM, DONGHIA NM, WECKMAN NE, ORY A, NG CF, NGUYEN PQ, MAO AS, FERRANTE TC, LANSBERRY G, SALLUM H, NIEMI J, COLLINS JJ. Minimally instrumented SHERLOCK (miSHERLOCK) for CRISPR-based point-of-care diagnosis of SARS-CoV-2 and emerging variants[J]. Science Advances, 2021, 7(32):eabh2944.
    [29] DING X, YIN K, LI ZY, LALLA RV, BALLESTEROS E, SFEIR MM, LIU CC. Ultrasensitive and visual detection of SARS-CoV-2 using all-in-one dual CRISPR-Cas12a assay[J]. Nature Communications, 2020, 11:4711.
    [30] LU SH, TONG XH, HAN Y, ZHANG K, ZHANG YZ, CHEN QB, DUAN JY, LEI XL, HUANG MH, QIU Y, ZHANG DY, ZHOU X, ZHANG Y, YIN H. Fast and sensitive detection of SARS-CoV-2 RNA using suboptimal protospacer adjacent motifs for Cas12a[J]. Nature Biomedical Engineering, 2022, 6(3):286-297.
    [31] WU H, HE JS, ZHANG F, PING JF, WU J. Contamination-free visual detection of CaMV35S promoter amplicon using CRISPR/Cas12a coupled with a designed reaction vessel:rapid, specific and sensitive[J]. Analytica Chimica Acta, 2020, 1096:130-137.
    [32] CHEN YJ, SHI Y, CHEN Y, YANG ZN, WU H, ZHOU ZH, LI J, PING JF, HE LP, SHEN H, CHEN ZX, WU J, YU YS, ZHANG YJ, CHEN H. Contamination-free visual detection of SARS-CoV-2 with CRISPR/Cas12a:a promising method in the point-of-care detection[J]. Biosensors & Bioelectronics, 2020, 169:112642.
    [33] WANG B, WANG R, WANG DQ, WU J, LI JX, WANG J, LIU HH, WANG YM. Cas12aVDet:a CRISPR/Cas12a-based platform for rapid and visual nucleic acid detection[J]. Analytical Chemistry, 2019, 91(19):12156-12161.
    [34] YIN K, DING X, LI ZY, ZHAO H, COOPER K, LIU CC. Dynamic aqueous multiphase reaction system for one-pot CRISPR-Cas12a-based ultrasensitive and quantitative molecular diagnosis[J]. Analytical Chemistry, 2020, 92(12):8561-8568.
    [35] KAMINSKI MM, ABUDAYYEH OO, GOOTENBERG JS, ZHANG F, COLLINS JJ. CRISPR-based diagnostics[J]. Nature Biomedical Engineering, 2021, 5(7):643-656.
    [36] ACKERMAN CM, MYHRVOLD C, THAKKU SG, FREIJE CA, METSKY HC, YANG DK, YE SH, BOEHM CK, KOSOKO-THORODDSEN TS F, KEHE J, NGUYEN TG, CARTER A, KULESA A, BARNES JR, DUGAN VG, HUNG DT, BLAINEY PC, SABETI PC. Massively multiplexed nucleic acid detection with Cas13[J]. Nature, 2020, 582(7811):277-282.
    [37] HUANG MQ, LIU SH, XU YN, LI AQ, WU W, LIANG MF, NIU GY, WANG ZY, WANG T. CRISPR/Cas12a technology combined with RPA for rapid and portable SFTSV detection[J]. Frontiers in Microbiology, 2022, 13:754995.
    [38] ZHANG BB, XIA Q, WANG Q, XIA XY, WANG JK. Detecting and typing target DNA with a novel CRISPR-typing PCR (ctPCR) technique[J]. Analytical Biochemistry, 2018, 561/562:37-46.
    [39] ZHANG BB, WANG Q, XU XH, XIA Q, LONG FF, LI WW, SHUI YC, XIA XY, WANG JK. Detection of target DNA with a novel Cas9/sgRNAs-associated reverse PCR (CARP) technique[J]. Analytical and Bioanalytical Chemistry, 2018, 410(12):2889-2900.
    [40] WANG Q, ZHANG BB, XU XH, LONG FF, WANG JK. CRISPR-typing PCR (ctPCR), a new Cas9-based DNA detection method[J]. Scientific Reports, 2018, 8:14126.
    [41] BROUGHTON JP, DENG XD, YU GX, FASCHING CL, SERVELLITA V, SINGH J, MIAO X, STREITHORST JA, GRANADOS A, SOTOMAYOR- GONZALEZ A, ZORN K, GOPEZ A, HSU E, GU W, MILLER S, PAN CY, GUEVARA H, WADFORD DA, CHEN JS, et al. CRISPR-Cas12-based detection of SARS-CoV-2[J]. Nature Biotechnology, 2020, 38(7):870-874.
    [42] WANG XJ, ZHONG MT, LIU Y, MA PX, DANG L, MENG QZ, WAN WW, MA XD, LIU J, YANG G, YANG ZF, HUANG XX, LIU M. Rapid and sensitive detection of COVID-19 using CRISPR/Cas12a-based detection with naked eye readout, CRISPR/Cas12a- NER[J]. Science Bulletin, 2020, 65(17):1436-1439.
    [43] MENG QZ, WANG XJ, WANG YQ, DANG L, LIU XY, MA XD, CHI T, WANG X, ZHAO Q, YANG G, LIU M, HUANG XX, MA PX. Detection of the SARS-CoV-2 D614G mutation using engineered Cas12a guide RNA[J]. Biotechnology Journal, 2021, 16(6):e2100040.
    [44] NIU MW, HAN Y, DONG X, YANG L, LI F, ZHANG YC, HU Q, XIA XS, LI H, SUN YS. Highly sensitive detection method for HV69-70del in SARS-CoV-2 alpha and Omicron variants based on CRISPR/Cas13a[J]. Frontiers in Bioengineering and Biotechnology, 2022, 10:831332.
    [45] LIANG YH, ZOU LR, LIN HQ, LI BS, ZHAO JH, WANG HY, SUN JF, CHEN JD, MO YL, YANG XF, DENG XL, TANG SX. Detection of major SARS-CoV-2 variants of concern in clinical samples via CRISPR-Cas12a-mediated mutation-specific assay[J]. ACS Synthetic Biology, 2022, 11(5):1811-1823.
    [46] LIANG YH, LIN HQ, ZOU LR, DENG XL, TANG SX. Rapid detection and tracking of Omicron variant of SARS-CoV-2 using CRISPR-Cas12a-based assay[J]. Biosensors and Bioelectronics, 2022, 205:114098.
    [47] FOZOUNI P, SON S, de LEóN DERBY MD, KNOTT GJ, GRAY CN, D'AMBROSIO MV, ZHAO CY, SWITZ NA, KUMAR GR, STEPHENS SI, BOEHM D, TSOU CL, SHU J, BHUIYA A, ARMSTRONG M, HARRIS AR, CHEN PY, OSTERLOH JM, MEYER- FRANKE A, JOEHNK B, et al. Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy[J]. Cell, 2021, 184(2):323-333.e9.
    [48] HUANG CH, LEE KC, DOUDNA JA. Applications of CRISPR-cas enzymes in cancer therapeutics and detection[J]. Trends in Cancer, 2018, 4(7):499-512.
    [49] LIU Y, CHEN YL, DANG L, LIU YX, HUANG SS, WU SY, MA PX, JIANG HQ, LI Y, PAN YB, WEI YC, MA XD, LIU M, JI QJ, CHI T, HUANG XX, WANG XJ, ZHOU FL. EasyCatch, a convenient, sensitive and specific CRISPR detection system for cancer gene mutations[J]. Molecular Cancer, 2021, 20(1):157.
    [50] LIANG MD, LI ZL, WANG WS, LIU JK, LIU LS, ZHU GL, KARTHIK L, WANG M, WANG KF, WANG Z, YU J, SHUAI YT, YU JM, ZHANG L, YANG ZH, LI C, ZHANG Q, SHI T, ZHOU LM, XIE F, et al. A CRISPR-Cas12a-derived biosensing platform for the highly sensitive detection of diverse small molecules[J]. Nature Communications, 2019, 10:3672.
    [51] XIONG Y, ZHANG JJ, YANG ZL, MOU QB, MA Y, XIONG YH, LU Y. Functional DNA regulated CRISPR-Cas12a sensors for point-of-care diagnostics of non-nucleic-acid targets[J]. Journal of the American Chemical Society, 2020, 142(1):207-213.
    [52] QIAO B, XU JK, YIN WH, XIN WM, MA LX, QIAO J, LIU Y. "Aptamer-locker" DNA coupling with CRISPR/Cas12a-guided biosensing for high-efficiency melamine analysis[J]. Biosensors and Bioelectronics, 2021, 183:113233.
    [53] IWASAKI RS, BATEY RT. SPRINT:a Cas13a-based platform for detection of small molecules[J]. Nucleic Acids Research, 2020, 48(17):e101.
    [54] CHEN YJ, WU H, QIAN S, YU XP, CHEN H, WU J. Applying CRISPR/Cas system as a signal enhancer for DNAzyme-based lead ion detection[J]. Analytica Chimica Acta, 2022, 1192:339356.
    [55] SUN X, WANG Y, ZHANG L, LIU S, ZHANG M, WANG J, NING BA, PENG Y, HE J, HU YG, GAO ZX. CRISPR-Cas9 triggered two-step isothermal amplification method for E. coli O157:H7 detection based on a metal-organic framework platform[J]. Analytical Chemistry, 2020, 92(4):3032-3041.
    [56] LEE SY, OH SW. Filtration-based LAMP-CRISPR/Cas12a system for the rapid, sensitive and visualized detection of Escherichia coli O157:H7[J]. Talanta, 2022, 241:123186.
    [57] LIU H, WANG JB, ZENG HJ, LIU XF, JIANG W, WANG Y, OUYANG WB, TANG XM. RPA-Cas12a-FS:a frontline nucleic acid rapid detection system for food safety based on CRISPR-Cas12a combined with recombinase polymerase amplification[J]. Food Chemistry, 2021, 334:127608.
    [58] ZHUANG JW, ZHAO ZY, LIAN K, YIN LJ, WANG JJ, MAN SL, LIU GZ, MA L. SERS-based CRISPR/Cas assay on microfluidic paper analytical devices for supersensitive detection of pathogenic bacteria in foods[J]. Biosensors and Bioelectronics, 2022, 207:114167.
    [59] LI C, CHEN X, WEN RQ, MA P, GU K, LI C, ZHOU CY, LEI CW, TANG YZ, WANG HN. Immunocapture magnetic beads enhanced the LAMP-CRISPR/Cas12a method for the sensitive, specific, and visual detection of Campylobacter jejuni[J]. Biosensors, 2022, 12(3):154.
    [60] ZHOU J, YIN LJ, DONG YN, PENG L, LIU GZ, MAN SL, MA L. CRISPR-Cas13a based bacterial detection platform:sensing pathogen Staphylococcus aureus in food samples[J]. Analytica Chimica Acta, 2020, 1127:225-233.
    [61] SHEN JJ, ZHOU XM, SHAN YY, YUE HH, HUANG R, HU JM, XING D. Sensitive detection of a bacterial pathogen using allosteric probe-initiated catalysis and CRISPR-Cas13a amplification reaction[J]. Nature Communications, 2020, 11:267.
    [62] ZHANG T, ZHOU WH, LIN XY, KHAN MR, DENG S, ZHOU M, HE GP, WU CY, DENG RJ, HE Q. Light-up RNA aptamer signaling-CRISPR-Cas13a-based mix- and-read assays for profiling viable pathogenic bacteria[J]. Biosensors and Bioelectronics, 2021, 176:112906.
    [63] METSKY HC, WELCH NL, PILLAI PP, HARADHVALA NJ, RUMKER L, MANTENA S, ZHANG YB, YANG DK, ACKERMAN CM, WELLER J, BLAINEY PC, MYHRVOLD C, MITZENMACHER M, SABETI PC. Designing sensitive viral diagnostics with machine learning[J]. Nature Biotechnology, 2022, 40(7):1123-1131.
    引证文献
引用本文

孙雯君,黄行许,王鑫杰. 基于CRISPR的快速灵敏便捷分子检测[J]. 生物工程学报, 2023, 39(1): 60-73

复制
分享
文章指标
  • 点击次数:
  • 下载次数:
  • HTML阅读次数:
  • 引用次数:
历史
  • 收稿日期:2022-04-18
  • 最后修改日期:2022-08-02
  • 在线发布日期: 2023-02-01
  • 出版日期: 2023-01-25
文章二维码
您是第位访问者
生物工程学报 ® 2025 版权所有

通信地址：中国科学院微生物研究所    邮编：100101

电话：010-64807509   E-mail：cjb@im.ac.cn

技术支持：北京勤云科技发展有限公司