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Abstract

Biosensing based on CRISPR-Cas systems is a young but rapidly evolving technology. The unprecedented properties of the CRISPR-Cas system provide an innovative tool for developing new-generation biosensing strategies. To date, a series of nucleic acid and non-nucleic acid detection methods have been developed based on the CRISPR platform. In this review, we first introduce the core biochemical properties underpinning the development of CRISPR bioassays, such as diverse reaction temperatures, programmability in design, high reaction efficiency, and recognition specificity, and highlight recent efforts to improve these parameters. We then introduce the technical developments, including how to improve sensitivity and quantification capabilities, develop multiplex assays, achieve convenient one-pot assays, create advanced sensors, and extend the applications of detection. Finally, we analyze obstacles to the commercial application of CRISPR detection technology and explore development opportunities and directions.

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2023-06-14
2024-04-29
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Literature Cited

  1. 1.
    Niemz A, Ferguson TM, Boyle DS. 2011. Point-of-care nucleic acid testing for infectious diseases. Trends Biotechnol. 29:240–50
    [Google Scholar]
  2. 2.
    Mullis K, Faloona R, Scharf S, Saiki R, Horn G, Erlich H. 1986. Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harb. Symp. Quant. Biol. 51:263–73
    [Google Scholar]
  3. 3.
    Heid CA, Stevens J, Livak KJ, Williams PM. 1996. Real time quantitative PCR. Genome Res. 6:986–94
    [Google Scholar]
  4. 4.
    Hindson BJ, Ness KD, Masquelier DA, Belgrader P, Heredia NJ et al. 2011. High-throughput droplet digital PCR system for absolute quantitation of DNA copy number. Anal. Chem. 83:8604–10
    [Google Scholar]
  5. 5.
    Gautier L, Cope L, Bolstad BM, Irizarry RA. 2004. Affy—analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 20:307–15
    [Google Scholar]
  6. 6.
    Mardis ER. 2013. Next-generation sequencing platforms. Annu. Rev. Anal. Chem. 6:287–303
    [Google Scholar]
  7. 7.
    Mojica FJ, Díez-Villaseñor C, García-Martínez J, Soria E. 2005. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J. Mol. Evol. 60:174–82
    [Google Scholar]
  8. 8.
    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 337:816–21
    [Google Scholar]
  9. 9.
    Cong L, Ran FA, Cox D, Lin S, Barretto R et al. 2013. Multiplex genome engineering using CRISPR/Cas systems. Science 339:819–23
    [Google Scholar]
  10. 10.
    Mali P, Yang L, Esvelt KM, Aach J, Guell M et al. 2013. RNA-guided human genome engineering via Cas9. Science 339:823–26
    [Google Scholar]
  11. 11.
    Pardee K, Green AA, Takahashi MK, Braff D, Lambert G et al. 2016. Rapid, low-cost detection of Zika virus using programmable biomolecular components. Cell 165:1255–66
    [Google Scholar]
  12. 12.
    Makarova KS, Haft DH, Barrangou R, Brouns SJ, Charpentier E et al. 2011. Evolution and classification of the CRISPR–Cas systems. Nat. Rev. Microbiol. 9:467–77
    [Google Scholar]
  13. 13.
    Makarova KS, Wolf YI, Alkhnbashi OS, Costa F, Shah SA et al. 2015. An updated evolutionary classification of CRISPR–Cas systems. Nat. Rev. Microbiol. 13:722–36
    [Google Scholar]
  14. 14.
    Makarova KS, Wolf YI, Iranzo J, Shmakov SA, Alkhnbashi OS et al. 2020. Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants. Nat. Rev. Microbiol. 18:67–83
    [Google Scholar]
  15. 15.
    Chen JS, Ma E, Harrington LB, Da Costa M, Tian X et al. 2018. CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity. Science 360:436–39
    [Google Scholar]
  16. 16.
    Li S-Y, Cheng Q-X, Liu J-K, Nie X-Q, Zhao G-P, Wang J 2018. CRISPR-Cas12a has both cis- and trans-cleavage activities on single-stranded DNA. Cell Res. 28:491–93
    [Google Scholar]
  17. 17.
    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 360:439–44
    [Google Scholar]
  18. 18.
    East-Seletsky A, O'Connell MR, Knight SC, Burstein D, Cate JH et al. 2016. Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection. Nature 538:270–73
    [Google Scholar]
  19. 19.
    Abudayyeh OO, Gootenberg JS, Konermann S, Joung J, Slaymaker IM et al. 2016. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science 353:aaf5573
    [Google Scholar]
  20. 20.
    Gootenberg JS, Abudayyeh OO, Lee JW, Essletzbichler P, Dy AJ et al. 2017. Nucleic acid detection with CRISPR-Cas13a/C2c2. Science 356:438–42
    [Google Scholar]
  21. 21.
    Aman R, Mahas A, Mahfouz M. 2020. Nucleic acid detection using CRISPR/Cas biosensing technologies. ACS Synth. Biol. 9:1226–33
    [Google Scholar]
  22. 22.
    Kaminski MM, Abudayyeh OO, Gootenberg JS, Zhang F, Collins JJ. 2021. CRISPR-based diagnostics. Nat. Biomed. Eng. 5:643–56
    [Google Scholar]
  23. 23.
    Zuo X, Fan C, Chen H-Y. 2017. Biosensing: CRISPR-powered diagnostics. Nat. Biomed. Eng. 1:0091
    [Google Scholar]
  24. 24.
    Dai Y, Wu Y, Liu G, Gooding JJ. 2020. CRISPR mediated biosensing toward understanding cellular biology and point-of-care diagnosis. Angew. Chem. Int. Ed. 59:20754–66
    [Google Scholar]
  25. 25.
    Chertow DS. 2018. Next-generation diagnostics with CRISPR. Science 360:381–82
    [Google Scholar]
  26. 26.
    English MA, Soenksen LR, Gayet RV, de Puig H, Angenent-Mari NM et al. 2019. Programmable CRISPR-responsive smart materials. Science 365:780–85
    [Google Scholar]
  27. 27.
    Liang M, Li Z, Wang W, Liu J, Liu L et al. 2019. A CRISPR-Cas12a-derived biosensing platform for the highly sensitive detection of diverse small molecules. Nat. Commun. 10:3672
    [Google Scholar]
  28. 28.
    Xiong Y, Zhang J, Yang Z, Mou Q, Ma Y et al. 2019. Functional DNA regulated CRISPR-Cas12a sensors for point-of-care diagnostics of non-nucleic-acid targets. J. Am. Chem. Soc. 142:207–13
    [Google Scholar]
  29. 29.
    Chen Q, Tian T, Xiong E, Wang P, Zhou X. 2019. CRISPR/Cas13a signal amplification linked immunosorbent assay for femtomolar protein detection. Anal. Chem. 92:573–77
    [Google Scholar]
  30. 30.
    Barber KW, Shrock E, Elledge SJ. 2021. CRISPR-based peptide library display and programmable microarray self-assembly for rapid quantitative protein binding assays. Mol. Cell 81:3650–58.e5
    [Google Scholar]
  31. 31.
    Lee I, Kwon S-J, Sorci M, Heeger PS, Dordick JS. 2021. Highly sensitive immuno-CRISPR assay for CXCL9 detection. Anal. Chem. 93:16528–34
    [Google Scholar]
  32. 32.
    Tang Y, Song T, Gao L, Yin S, Ma M et al. 2022. A CRISPR-based ultrasensitive assay detects attomolar concentrations of SARS-CoV-2 antibodies in clinical samples. Nat. Commun. 13:4667
    [Google Scholar]
  33. 33.
    Shen J, Zhou X, Shan Y, Yue H, Huang R et al. 2020. Sensitive detection of a bacterial pathogen using allosteric probe-initiated catalysis and CRISPR-Cas13a amplification reaction. Nat. Commun. 11:267
    [Google Scholar]
  34. 34.
    Li S-Y, Cheng Q-X, Wang J-M, Li X-Y, Zhang Z-L et al. 2018. CRISPR-Cas12a-assisted nucleic acid detection. Cell Discov. 4:20
    [Google Scholar]
  35. 35.
    Liu TY, Knott GJ, Smock DC, Desmarais JJ, Son S et al. 2021. Accelerated RNA detection using tandem CRISPR nucleases. Nat. Chem. Biol. 17:982–88
    [Google Scholar]
  36. 36.
    Santiago-Frangos A, Hall LN, Nemudraia A, Nemudryi A, Krishna P et al. 2021. Intrinsic signal amplification by type III CRISPR-Cas systems provides a sequence-specific SARS-CoV-2 diagnostic. Cell Rep. Med. 2:100319
    [Google Scholar]
  37. 37.
    Shmakov S, Abudayyeh OO, Makarova KS, Wolf YI, Gootenberg JS et al. 2015. Discovery and functional characterization of diverse class 2 CRISPR-Cas systems. Mol. Cell 60:385–97
    [Google Scholar]
  38. 38.
    Liu L, Li X, Wang J, Wang M, Chen P et al. 2017. Two distant catalytic sites are responsible for C2c2 RNase activities. Cell 168:121–34.e12
    [Google Scholar]
  39. 39.
    Gu W, Crawford ED, O'Donovan B, Wilson MR, Chow ED et al. 2016. Depletion of Abundant Sequences by Hybridization (DASH): using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications. Genome Biol. 17:41
    [Google Scholar]
  40. 40.
    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. 90:2193–200
    [Google Scholar]
  41. 41.
    Lee J, Lim H, Jang H, Hwang B, Lee JH et al. 2019. CRISPR-Cap: multiplexed double-stranded DNA enrichment based on the CRISPR system. Nucleic Acids Res. 47:e1
    [Google Scholar]
  42. 42.
    Quan J, Langelier C, Kuchta A, Batson J, Teyssier N et al. 2019. FLASH: a next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences. Nucleic Acids Res. 47:e83
    [Google Scholar]
  43. 43.
    Zhang B, Wang Q, Xu X, Xia Q, Long F et al. 2018. Detection of target DNA with a novel Cas9/sgRNAs-associated reverse PCR (CARP) technique. Anal. Bioanal. Chem. 410:2889–900
    [Google Scholar]
  44. 44.
    Zhang Y, Qian L, Wei W, Wang Y, Wang B et al. 2017. Paired design of dCas9 as a systematic platform for the detection of featured nucleic acid sequences in pathogenic strains. ACS Synth. Biol. 6:211–16
    [Google Scholar]
  45. 45.
    Qiu X-Y, Zhu L-Y, Zhu C-S, Ma J-X, Hou T et al. 2018. Highly effective and low-cost microRNA detection with CRISPR-Cas9. ACS Synth. Biol. 7:807–13
    [Google Scholar]
  46. 46.
    Yang W, Restrepo-Pérez L, Bengtson M, Heerema SJ, Birnie A et al. 2018. Detection of CRISPR-dCas9 on DNA with solid-state nanopores. Nano Lett. 18:6469–74
    [Google Scholar]
  47. 47.
    Hajian R, Balderston S, Tran T, DeBoer T, Etienne J et al. 2019. Detection of unamplified target genes via CRISPR–Cas9 immobilized on a graphene field-effect transistor. Nat. Biomed. Eng. 3:427–37
    [Google Scholar]
  48. 48.
    Balderston S, Taulbee JJ, Celaya E, Fung K, Jiao A et al. 2021. Discrimination of single-point mutations in unamplified genomic DNA via Cas9 immobilized on a graphene field-effect transistor. Nat. Biomed. Eng. 5:713–25
    [Google Scholar]
  49. 49.
    Wang X, Xiong E, Tian T, Cheng M, Lin W et al. 2020. Clustered regularly interspaced short palindromic repeats/Cas9-mediated lateral flow nucleic acid assay. ACS Nano 14:2497–508
    [Google Scholar]
  50. 50.
    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
    [Google Scholar]
  51. 51.
    Wang T, Liu Y, Sun HH, Yin BC, Ye BC. 2019. An RNA-guided Cas9 nickase-based method for universal isothermal DNA amplification. Angew. Chem. Int. Ed. 131:5436–40
    [Google Scholar]
  52. 52.
    Mahony JB, Blackhouse G, Babwah J, Smieja M, Buracond S et al. 2009. Cost analysis of multiplex PCR testing for diagnosing respiratory virus infections. J. Clin. Microbiol. 47:2812–17
    [Google Scholar]
  53. 53.
    Mougiakos I, Mohanraju P, Bosma EF, Vrouwe V, Finger Bou M et al. 2017. Characterizing a thermostable Cas9 for bacterial genome editing and silencing. Nat. Commun. 8:1647
    [Google Scholar]
  54. 54.
    Li L, Li S, Wu N, Wu J, Wang G et al. 2019. HOLMESv2: a CRISPR-Cas12b-assisted platform for nucleic acid detection and DNA methylation quantitation. ACS Synth. Biol. 8:2228–37
    [Google Scholar]
  55. 55.
    Teng F, Guo L, Cui T, Wang X-G, Xu K et al. 2019. CDetection: CRISPR-Cas12b-based DNA detection with sub-attomolar sensitivity and single-base specificity. Genome Biol. 20:132
    [Google Scholar]
  56. 56.
    Nguyen LT, Macaluso NC, Pizzano BL, Cash MN, Spacek J et al. 2022. A thermostable Cas12b from Brevibacillus leverages one-pot discrimination of SARS-CoV-2 variants of concern. EBioMedicine 77:103926
    [Google Scholar]
  57. 57.
    Guo L, Sun X, Wang X, Liang C, Jiang H et al. 2020. SARS-CoV-2 detection with CRISPR diagnostics. Cell Discov. 6:34
    [Google Scholar]
  58. 58.
    Joung J, Ladha A, Saito M, Kim N-G, Woolley AE et al. 2020. Detection of SARS-CoV-2 with SHERLOCK one-pot testing. N. Engl. J. Med. 383:1492–94
    [Google Scholar]
  59. 59.
    Mahas A, Marsic T, Lopez-Portillo Masson M, Wang Q, Aman R et al. 2022. Characterization of a thermostable Cas13 enzyme for one-pot detection of SARS-CoV-2. PNAS 119:e2118260119
    [Google Scholar]
  60. 60.
    Marsic T, Ali Z, Tehseen M, Mahas A, Hamdan S, Mahfouz M. 2021. Vigilant: an engineered VirD2-Cas9 complex for lateral flow assay-based detection of SARS-CoV2. Nano Lett. 21:3596–603
    [Google Scholar]
  61. 61.
    Xiong E, Jiang L, Tian T, Hu M, Yue H et al. 2021. Simultaneous dual-gene diagnosis of SARS-CoV-2 based on CRISPR/Cas9-mediated lateral flow assay. Angew. Chem. Int. Ed. 60:5307–15
    [Google Scholar]
  62. 62.
    Dai Y, Xu W, Somoza RA, Welter JF, Caplan AI, Liu CC. 2020. An integrated multi-function heterogeneous biochemical circuit for high-resolution electrochemistry-based genetic analysis. Angew. Chem. Int. Ed. 132:20726–32
    [Google Scholar]
  63. 63.
    Liu L, Li X, Ma J, Li Z, You L et al. 2017. The molecular architecture for RNA-guided RNA cleavage by Cas13a. Cell 170:714–26.e10
    [Google Scholar]
  64. 64.
    East-Seletsky A, O'Connell MR, Burstein D, Knott GJ, Doudna JA 2017. RNA targeting by functionally orthogonal type VI-A CRISPR-Cas enzymes. Mol. Cell 66:373–83.e3
    [Google Scholar]
  65. 65.
    O'Connell MR. 2019. Molecular mechanisms of RNA targeting by Cas13-containing type VI CRISPR–Cas systems. J. Mol. Biol. 431:66–87
    [Google Scholar]
  66. 66.
    Swarts DC, Jinek M. 2019. Mechanistic insights into the cis- and trans-acting DNase activities of Cas12a. Mol. Cell 73:589–600.e4
    [Google Scholar]
  67. 67.
    Huyke DA, Ramachandran A, Bashkirov VI, Kotseroglou EK, Kotseroglou T, Santiago JG. 2022. Enzyme kinetics and detector sensitivity determine limits of detection of amplification-free CRISPR-Cas12 and CRISPR-Cas13 diagnostics. Anal. Chem. 94:9826–34
    [Google Scholar]
  68. 68.
    Ramachandran A, Santiago JG. 2021. CRISPR enzyme kinetics for molecular diagnostics. Anal. Chem. 93:7456–64
    [Google Scholar]
  69. 69.
    Hsieh K, Zhao G, Wang T-H. 2020. Applying biosensor development concepts to improve preamplification-free CRISPR/Cas12a-Dx. Analyst 145:4880–88
    [Google Scholar]
  70. 70.
    Yue H, Shu B, Tian T, Xiong E, Huang M et al. 2021. Droplet Cas12a assay enables DNA quantification from unamplified samples at the single-molecule level. Nano Lett. 21:4643–53
    [Google Scholar]
  71. 71.
    Li Z, Zhao W, Ma S, Li Z, Yao Y, Fei T. 2021. A chemical-enhanced system for CRISPR-based nucleic acid detection. Biosens. Bioelectron. 192:113493
    [Google Scholar]
  72. 72.
    Nguyen LT, Smith BM, Jain PK. 2020. Enhancement of trans-cleavage activity of Cas12a with engineered crRNA enables amplified nucleic acid detection. Nat. Commun. 11:4906
    [Google Scholar]
  73. 73.
    Rossetti M, Merlo R, Bagheri N, Moscone D, Valenti A et al. 2022. Enhancement of CRISPR/Cas12a trans-cleavage activity using hairpin DNA reporters. Nucleic Acids Res. 50:8377–91
    [Google Scholar]
  74. 74.
    Xia X, Ma B, Zhang T, Lu Y, Khan MR et al. 2021. G-quadruplex-probing CRISPR-Cas12 assay for label-free analysis of foodborne pathogens and their colonization in vivo. ACS Sens. 6:3295–302
    [Google Scholar]
  75. 75.
    Li T, Hu R, Xia J, Xu Z, Chen D et al. 2021. G-triplex: a new type of CRISPR-Cas12a reporter enabling highly sensitive nucleic acid detection. Biosens. Bioelectron. 187:113292
    [Google Scholar]
  76. 76.
    Huang M, Xiong E, Wang Y, Hu M, Yue H et al. 2022. Fast microwave heating-based one-step synthesis of DNA and RNA modified gold nanoparticles. Nat. Commun. 13:968
    [Google Scholar]
  77. 77.
    Ryan DE, Taussig D, Steinfeld I, Phadnis SM, Lunstad BD et al. 2018. Improving CRISPR–Cas specificity with chemical modifications in single-guide RNAs. Nucleic Acids Res. 46:792–803
    [Google Scholar]
  78. 78.
    Ke Y, Huang S, Ghalandari B, Li S, Warden AR et al. 2021. Hairpin-spacer crRNA-enhanced CRISPR/Cas13a system promotes the specificity of single nucleotide polymorphism (SNP) identification. Adv. Sci. 8:2003611
    [Google Scholar]
  79. 79.
    Hendel A, Bak RO, Clark JT, Kennedy AB, Ryan DE et al. 2015. Chemically modified guide RNAs enhance CRISPR-Cas genome editing in human primary cells. Nat. Biotechnol. 33:985–89
    [Google Scholar]
  80. 80.
    Ooi KH, Liu MM, Tay JWD, Teo SY, Kaewsapsak P et al. 2021. An engineered CRISPR-Cas12a variant and DNA-RNA hybrid guides enable robust and rapid COVID-19 testing. Nat. Commun. 12:1739
    [Google Scholar]
  81. 81.
    Boyle EA, Andreasson JO, Chircus LM, Sternberg SH, Wu MJ et al. 2017. High-throughput biochemical profiling reveals sequence determinants of dCas9 off-target binding and unbinding. PNAS 114:5461–66
    [Google Scholar]
  82. 82.
    Singh D, Mallon J, Poddar A, Wang Y, Tippana R et al. 2018. Real-time observation of DNA target interrogation and product release by the RNA-guided endonuclease CRISPR Cpf1 (Cas12a). PNAS 115:5444–49
    [Google Scholar]
  83. 83.
    Yuan C, Tian T, Sun J, Hu M, Wang X et al. 2020. Universal and naked-eye gene detection platform based on the clustered regularly interspaced short palindromic repeats/Cas12a/13a system. Anal. Chem. 92:4029–37
    [Google Scholar]
  84. 84.
    de Puig H, Lee RA, Najjar D, Tan X, Soenksen LR et al. 2021. Minimally instrumented SHERLOCK (miSHERLOCK) for CRISPR-based point-of-care diagnosis of SARS-CoV-2 and emerging variants. Sci. Adv. 7:eabh2944
    [Google Scholar]
  85. 85.
    Jiao C, Sharma S, Dugar G, Peeck NL, Bischler T et al. 2021. Noncanonical crRNAs derived from host transcripts enable multiplexable RNA detection by Cas9. Science 372:941–48
    [Google Scholar]
  86. 86.
    Welch NL, Zhu M, Hua C, Weller J, Mirhashemi ME et al. 2022. Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants. Nat. Med. 28:1083–94
    [Google Scholar]
  87. 87.
    Arizti-Sanz J, Bradley AD, Zhang YB, Boehm CK, Freije CA et al. 2022. Simplified Cas13-based assays for the fast identification of SARS-CoV-2 and its variants. Nat. Biomed. Eng. 6:932–43
    [Google Scholar]
  88. 88.
    Chandrasekaran SS, Agrawal S, Fanton A, Jangid AR, Charrez B et al. 2022. Rapid detection of SARS-CoV-2 RNA in saliva via Cas13. Nat. Biomed. Eng. 6:944–56
    [Google Scholar]
  89. 89.
    Kellner MJ, Koob JG, Gootenberg JS, Abudayyeh OO, Zhang F. 2019. SHERLOCK: nucleic acid detection with CRISPR nucleases. Nat. Protoc. 14:2986–3012
    [Google Scholar]
  90. 90.
    Shan Y, Zhou X, Huang R, Xing D. 2019. High-fidelity and rapid quantification of miRNA combining crRNA programmability and CRISPR/Cas13a trans-cleavage activity. Anal. Chem. 91:5278–85
    [Google Scholar]
  91. 91.
    Zhang W, Shi R, Dong K, Hu H, Shu W et al. 2022. The off-target effect of CRISPR-Cas12a system toward insertions and deletions between target DNA and crRNA sequences. Anal. Chem. 94:8596–604
    [Google Scholar]
  92. 92.
    Zetsche B, Gootenberg JS, Abudayyeh OO, Slaymaker IM, Makarova KS et al. 2015. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell 163:759–71
    [Google Scholar]
  93. 93.
    Cox DB, Gootenberg JS, Abudayyeh OO, Franklin B, Kellner MJ et al. 2017. RNA editing with CRISPR-Cas13. Science 358:1019–27
    [Google Scholar]
  94. 94.
    Harrington LB, Burstein D, Chen JS, Paez-Espino D, Ma E et al. 2018. Programmed DNA destruction by miniature CRISPR-Cas14 enzymes. Science 362:839–42
    [Google Scholar]
  95. 95.
    Wang B, Wang R, Wang D, Wu J, Li J et al. 2019. Cas12aVDet: a CRISPR/Cas12a-based platform for rapid and visual nucleic acid detection. Anal. Chem. 91:12156–61
    [Google Scholar]
  96. 96.
    Pang B, Xu J, Liu Y, Peng H, Feng W et al. 2020. Isothermal amplification and ambient visualization in a single tube for the detection of SARS-CoV-2 using loop-mediated amplification and CRISPR technology. Anal. Chem. 92:16204–12
    [Google Scholar]
  97. 97.
    Wang R, Qian C, Pang Y, Li M, Yang Y et al. 2021. opvCRISPR: one-pot visual RT-LAMP-CRISPR platform for SARS-cov-2 detection. Biosens. Bioelectron. 172:112766
    [Google Scholar]
  98. 98.
    Yin K, Ding X, Li Z, Zhao H, Cooper K, Liu C. 2020. Dynamic aqueous multiphase reaction system for one-pot CRISPR-Cas12a-based ultrasensitive and quantitative molecular diagnosis. Anal. Chem. 92:8561–68
    [Google Scholar]
  99. 99.
    Lin M, Yue H, Tian T, Xiong E, Zhu D et al. 2022. Glycerol additive boosts 100-fold sensitivity enhancement for one-pot RPA-CRISPR/Cas12a assay. Anal. Chem. 94:8277–84
    [Google Scholar]
  100. 100.
    Chen Y, Mei Y, Zhao X, Jiang X. 2020. Reagents-loaded, automated assay that integrates recombinase-aided amplification and Cas12a nucleic acid detection for a point-of-care test. Anal. Chem. 92:14846–52
    [Google Scholar]
  101. 101.
    Ding X, Yin K, Li Z, Lalla RV, Ballesteros E et al. 2020. Ultrasensitive and visual detection of SARS-CoV-2 using all-in-one dual CRISPR-Cas12a assay. Nat. Commun. 11:4711
    [Google Scholar]
  102. 102.
    Lu S, Tong X, Han Y, Zhang K, Zhang Y et al. 2022. Fast and sensitive detection of SARS-CoV-2 RNA using suboptimal protospacer adjacent motifs for Cas12a. Nat. Biomed. Eng. 6:286–97
    [Google Scholar]
  103. 103.
    Hu M, Qiu Z, Bi Z, Tian T, Jiang Y, Zhou X. 2022. Photocontrolled crRNA activation enables robust CRISPR-Cas12a diagnostics. PNAS 119:e2202034119
    [Google Scholar]
  104. 104.
    Huang Q, Chen D, Du C, Liu Q, Lin S et al. 2022. Highly multiplex PCR assays by coupling the 5′-flap endonuclease activity of Taq DNA polymerase and molecular beacon reporters. PNAS 119:e2110672119
    [Google Scholar]
  105. 105.
    Elnifro EM, Ashshi AM, Cooper RJ, Klapper PE. 2000. Multiplex PCR: optimization and application in diagnostic virology. Clin. Microbiol. Rev. 13:559–70
    [Google Scholar]
  106. 106.
    Smith AM, Heisler LE, St. Onge RP, Farias-Hesson E, Wallace IM et al. 2010. Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples. Nucleic Acids Res. 38:e142
    [Google Scholar]
  107. 107.
    Tian T, Qiu Z, Jiang Y, Zhu D, Zhou X. 2022. Exploiting the orthogonal CRISPR-Cas12a/Cas13a trans-cleavage for dual-gene virus detection using a handheld device. Biosens. Bioelectron. 196:113701
    [Google Scholar]
  108. 108.
    Ackerman CM, Myhrvold C, Thakku SG, Freije CA, Metsky HC et al. 2020. Massively multiplexed nucleic acid detection with Cas13. Nature 582:277–82
    [Google Scholar]
  109. 109.
    Patchsung M, Jantarug K, Pattama A, Aphicho K, Suraritdechachai S et al. 2020. Clinical validation of a Cas13-based assay for the detection of SARS-CoV-2 RNA. Nat. Biomed. Eng. 4:1140–49
    [Google Scholar]
  110. 110.
    Broughton JP, Deng X, Yu G, Fasching CL, Servellita V et al. 2020. CRISPR–Cas12-based detection of SARS-CoV-2. Nat. Biotechnol. 38:870–74
    [Google Scholar]
  111. 111.
    Arizti-Sanz J, Freije CA, Stanton AC, Petros BA, Boehm CK et al. 2020. Streamlined inactivation, amplification, and Cas13-based detection of SARS-CoV-2. Nat. Commun. 11:5921
    [Google Scholar]
  112. 112.
    Ramachandran A, Huyke DA, Sharma E, Sahoo MK, Huang C et al. 2020. Electric field-driven microfluidics for rapid CRISPR-based diagnostics and its application to detection of SARS-CoV-2. PNAS 117:29518–25
    [Google Scholar]
  113. 113.
    Najjar D, Rainbow J, Sharma Timilsina S, Jolly P, de Puig H et al. 2022. A lab-on-a-chip for the concurrent electrochemical detection of SARS-CoV-2 RNA and anti-SARS-CoV-2 antibodies in saliva and plasma. Nat. Biomed. Eng. 6:968–78
    [Google Scholar]
  114. 114.
    Chen W, Luo H, Zeng L, Pan Y, Parr JB et al. 2022. A suite of PCR-LwCas13a assays for detection and genotyping of Treponema pallidum in clinical samples. Nat. Commun. 13:4671
    [Google Scholar]
  115. 115.
    Fozouni P, Son S, de León Derby MD, Knott GJ, Gray CN et al. 2021. Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy. Cell 184:323–33.e9
    [Google Scholar]
  116. 116.
    Niewoehner O, Garcia-Doval C, Rostøl JT, Berk C, Schwede F et al. 2017. Type III CRISPR–Cas systems produce cyclic oligoadenylate second messengers. Nature 548:543–48
    [Google Scholar]
  117. 117.
    Shi K, Xie S, Tian R, Wang S, Lu Q et al. 2021. A CRISPR-Cas autocatalysis-driven feedback amplification network for supersensitive DNA diagnostics. Sci. Adv. 7:eabc7802
    [Google Scholar]
  118. 118.
    Tian T, Shu B, Jiang Y, Ye M, Liu L et al. 2020. An ultralocalized Cas13a assay enables universal and nucleic acid amplification-free single-molecule RNA diagnostics. ACS Nano 15:1167–78
    [Google Scholar]
  119. 119.
    Tian T, Shu B, Liu L, Zhou X. 2019. Droplet-digital Cas13a assay enables direct single-molecule microRNA quantification. bioRxiv 748939. https://doi.org/10.1101/748939
  120. 120.
    Shinoda H, Taguchi Y, Nakagawa R, Makino A, Okazaki S et al. 2021. Amplification-free RNA detection with CRISPR–Cas13. Commun. Biol. 4:476
    [Google Scholar]
  121. 121.
    Yu T, Zhang S, Matei R, Marx W, Beisel CL, Wei Q. 2021. Coupling smartphone and CRISPR–Cas12a for digital and multiplexed nucleic acid detection. AIChE J. 67:e17365
    [Google Scholar]
  122. 122.
    Son S, Lyden A, Shu J, Stephens SI, Fozouni P et al. 2021. Sensitive and multiplexed RNA detection with Cas13 droplets and kinetic barcoding. MedRxiv 21261509. https://doi.org/10.1101/2021.08.02.21261509
    [Crossref]
  123. 123.
    Kim H, Lee S, Seo HW, Kang B, Moon J et al. 2020. Clustered regularly interspaced short palindromic repeats-mediated surface-enhanced Raman scattering assay for multidrug-resistant bacteria. ACS Nano 14:17241–53
    [Google Scholar]
  124. 124.
    Bruch R, Baaske J, Chatelle C, Meirich M, Madlener S et al. 2019. CRISPR/Cas13a-powered electrochemical microfluidic biosensor for nucleic acid amplification-free miRNA diagnostics. Adv. Mater. 31:1905311
    [Google Scholar]
  125. 125.
    Hu M, Yuan C, Tian T, Wang X, Sun J et al. 2020. Single-step, salt-aging-free, and thiol-free freezing construction of AuNP-based bioprobes for advancing CRISPR-based diagnostics. J. Am. Chem. Soc. 142:7506–13
    [Google Scholar]
  126. 126.
    Broto M, Kaminski MM, Adrianus C, Kim N, Greensmith R et al. 2022. Nanozyme-catalysed CRISPR assay for preamplification-free detection of non-coding RNAs. Nat. Nanotechnol. 17:1120–26
    [Google Scholar]
  127. 127.
    Li Y, Mansour H, Wang T, Poojari S, Li F. 2019. Naked-eye detection of grapevine red-blotch viral infection using a plasmonic CRISPR Cas12a assay. Anal. Chem. 91:11510–13
    [Google Scholar]
  128. 128.
    Jiang Y, Hu M, Liu A-A, Lin Y, Liu L et al. 2021. Detection of SARS-CoV-2 by CRISPR/Cas12a-enhanced colorimetry. ACS Sens. 6:1086–93
    [Google Scholar]
  129. 129.
    Cheng X, Li Y, Jun K, Liao D, Zhang W et al. 2022. Novel non-nucleic acid targets detection strategies based on CRISPR/Cas toolboxes: a review. Biosens. Bioelectron. 215:114559
    [Google Scholar]
  130. 130.
    Watzinger F, Ebner K, Lion T. 2006. Detection and monitoring of virus infections by real-time PCR. Mol. Aspects Med. 27:254–98
    [Google Scholar]
  131. 131.
    Li Y, Li S, Wang J, Liu G 2019. CRISPR/Cas systems towards next-generation biosensing. Trends Biotechnol. 37:730–43
    [Google Scholar]
  132. 132.
    Yue H, Huang M, Tian T, Xiong E, Zhou X. 2021. Advances in clustered, regularly interspaced short palindromic repeats (CRISPR)-based diagnostic assays assisted by micro/nanotechnologies. ACS Nano 15:7848–59
    [Google Scholar]
  133. 133.
    Doench JG, Fusi N, Sullender M, Hegde M, Vaimberg EW et al. 2016. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat. Biotechnol. 34:184–91
    [Google Scholar]
  134. 134.
    Cui Y, Xu J, Cheng M, Liao X, Peng S. 2018. Review of CRISPR/Cas9 sgRNA design tools. Interdiscip. Sci. 10:455–65
    [Google Scholar]
  135. 135.
    Gong J, Kan L, Zhang X, He Y, Pan J et al. 2021. An enhanced method for nucleic acid detection with CRISPR-Cas12a using phosphorothioate modified primers and optimized gold-nanoparticle strip. Bioact. Mater. 6:4580–90
    [Google Scholar]
  136. 136.
    Myhrvold C, Freije CA, Gootenberg JS, Abudayyeh OO, Metsky HC et al. 2018. Field-deployable viral diagnostics using CRISPR-Cas13. Science 360:444–48
    [Google Scholar]
  137. 137.
    Lee RA, Puig HD, Nguyen PQ, Angenent-Mari NM, Donghia NM et al. 2020. Ultrasensitive CRISPR-based diagnostic for field-applicable detection of Plasmodium species in symptomatic and asymptomatic malaria. PNAS 117:25722–31
    [Google Scholar]
  138. 138.
    Nguyen PQ, Soenksen LR, Donghia NM, Angenent-Mari NM, de Puig H et al. 2021. Wearable materials with embedded synthetic biology sensors for biomolecule detection. Nat. Biotechnol. 39:1366–74
    [Google Scholar]
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