Harnessing the power of clustered regularly interspaced short palindromic repeats (CRISPR) based microfluidics for next-generation molecular diagnostics.
Biosensor
CRISPR/Cas
Diagnostic assays
Lab on chip
Microfluidics
Journal
Molecular biology reports
ISSN: 1573-4978
Titre abrégé: Mol Biol Rep
Pays: Netherlands
ID NLM: 0403234
Informations de publication
Date de publication:
08 Aug 2024
08 Aug 2024
Historique:
received:
10
06
2024
accepted:
31
07
2024
medline:
8
8
2024
pubmed:
8
8
2024
entrez:
8
8
2024
Statut:
epublish
Résumé
CRISPR-based (Clustered regularly interspaced short palindromic repeats-based) technologies have revolutionized molecular biology and diagnostics, offering unprecedented precision and versatility. However, challenges remain, such as high costs, demanding technical expertise, and limited quantification capabilities. To overcome these limitations, innovative microfluidic platforms are emerging as powerful tools for enhancing CRISPR diagnostics. This review explores the exciting intersection of CRISPR and microfluidics, highlighting their potential to revolutionize healthcare diagnostics. By integrating CRISPR's specificity with microfluidics' miniaturization and automation, researchers are developing more sensitive and portable diagnostic tools for a range of diseases. These microfluidic devices streamline sample processing, improve diagnostic performance, and enable point-of-care applications, allowing for rapid and accurate detection of pathogens, genetic disorders, and other health conditions. The review discusses various CRISPR/Cas systems, including Cas9, Cas12, and Cas13, and their integration with microfluidic platforms. It also examines the advantages and limitations of these systems, highlighting their potential for detecting DNA and RNA biomarkers. The review also explores the key challenges in developing and implementing CRISPR-driven microfluidic diagnostics, such as ensuring robustness, minimizing cross-contamination, and achieving robust quantification. Finally, it highlights potential future directions for this rapidly evolving field, emphasizing the transformative potential of these technologies for personalized medicine and global health.
Identifiants
pubmed: 39115550
doi: 10.1007/s11033-024-09840-8
pii: 10.1007/s11033-024-09840-8
doi:
Types de publication
Journal Article
Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
896Informations de copyright
© 2024. The Author(s), under exclusive licence to Springer Nature B.V.
Références
Mojica FJ, Díez-Villaseñor CS, García-Martínez J, Soria E (2005) Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J Mol Evol 60:174–182
pubmed: 15791728
doi: 10.1007/s00239-004-0046-3
Anzalone AV, Koblan LW, Liu DR (2020) Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors. Nat Biotechnol 38(7):824–844
pubmed: 32572269
doi: 10.1038/s41587-020-0561-9
Gootenberg JS, Abudayyeh OO, Lee JW, Essletzbichler P, Dy AJ, Joung J, Zhang F (2017) Nucleic acid detection with CRISPR-Cas13a/C2c2. Science 356(6336):438–442
pubmed: 28408723
pmcid: 5526198
doi: 10.1126/science.aam9321
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(6387):436–439
pubmed: 29449511
pmcid: 6628903
doi: 10.1126/science.aar6245
Swarts DC, Jinek M (2019) Mechanistic insights into the cis-and trans-acting DNase activities of Cas12a. Mol Cell 73(3):589–600
pubmed: 30639240
pmcid: 6858279
doi: 10.1016/j.molcel.2018.11.021
Kaminski MM, Abudayyeh OO, Gootenberg JS, Zhang F, Collins JJ (2021) CRISPR-based diagnostics. Nat Biomedical Eng 5(7):643–656
doi: 10.1038/s41551-021-00760-7
Liu TY, Knott GJ, Smock DC, Desmarais JJ, Son S, Bhuiya A, Doudna JA (2021) Accelerated RNA detection using tandem CRISPR nucleases. Nat Chem Biol 17(9):982–988
pubmed: 34354262
pmcid: 10184463
doi: 10.1038/s41589-021-00842-2
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(10):2228–2237
pubmed: 31532637
doi: 10.1021/acssynbio.9b00209
Ackerman CM, Myhrvold C, Thakku SG, Freije CA, Metsky HC, Yang DK, Sabeti PC (2020) Massively multiplexed nucleic acid detection with Cas13. Nature 582(7811):277–282
pubmed: 32349121
pmcid: 7332423
doi: 10.1038/s41586-020-2279-8
Li SY, Cheng QX, Wang JM, Li XY, Zhang ZL, Gao S, Wang J (2018) CRISPR-Cas12a-assisted nucleic acid detection. Cell Discovery 4(1):20
pubmed: 29707234
pmcid: 5913299
doi: 10.1038/s41421-018-0028-z
Kellner MJ, Koob JG, Gootenberg JS, Abudayyeh OO, Zhang F (2019) SHERLOCK: nucleic acid detection with CRISPR nucleases. Nat Protoc 14(10):2986–3012
pubmed: 31548639
pmcid: 6956564
doi: 10.1038/s41596-019-0210-2
Pandey S, Gupta S, Bharadwaj A, Rastogi A (2024) Microfluidic systems: recent advances in Chronic Disease diagnosis and their therapeutic management. Indian J Microbiol 1–15
Dong R, Liu Y, Mou L, Deng J, Jiang X (2019) Microfluidics-based biomaterials and biodevices. Adv Mater 31(45):1805033
doi: 10.1002/adma.201805033
Xiong H, Ye X, Li Y, Qi J, Fang X, Kong J (2021) Efficient microfluidic-based air sampling/monitoring platform for detection of aerosol SARS-CoV-2 on-site. Anal Chem 93(9):4270–4276
pubmed: 33635067
doi: 10.1021/acs.analchem.0c05154
Lin Q, Wu J, Fang X, Kong J (2020) Washing-free centrifugal microchip fluorescence immunoassay for rapid and point-of-care detection of protein. Anal Chim Acta 1118:18–25
pubmed: 32418600
doi: 10.1016/j.aca.2020.04.031
Fabiani L, Saroglia M, Galatà G, De Santis R, Fillo S, Luca V, Arduini F (2021) Magnetic beads combined with carbon black-based screen-printed electrodes for COVID-19: a reliable and miniaturized electrochemical immunosensor for SARS-CoV-2 detection in saliva. Biosens Bioelectron 171:112686
pubmed: 33086175
doi: 10.1016/j.bios.2020.112686
Song Q, Sun X, Dai Z, Gao Y, Gong X, Zhou B, Wen W (2021) Point-of-care testing detection methods for COVID-19. Lab Chip 21(9):1634–1660
pubmed: 33705507
doi: 10.1039/D0LC01156H
Nasseri B, Soleimani N, Rabiee N, Kalbasi A, Karimi M, Hamblin MR (2018) Point-of-care microfluidic devices for pathogen detection. Biosens Bioelectron 117:112–128
pubmed: 29890393
pmcid: 6082696
doi: 10.1016/j.bios.2018.05.050
Lefevre F, Chalifour A, Yu L, Chodavarapu V, Juneau P, Izquierdo R (2012) Algal fluorescence sensor integrated into a microfluidic chip for water pollutant detection. Lab Chip 12(4):787–793
pubmed: 22193420
doi: 10.1039/C2LC20998E
Yang K, Zong S, Zhang Y, Qian Z, Liu Y, Zhu K, Cui Y (2019) Array-assisted SERS microfluidic chips for highly sensitive and multiplex gas sensing. ACS Appl Mater Interfaces 12(1):1395–1403
pubmed: 31820638
doi: 10.1021/acsami.9b19358
Zeming KK, Vernekar R, Chua MT, Quek KY, Sutton G, Krüger T, Han J (2021) Label-Free Biophysical Markers from Whole Blood Microfluidic Immune Profiling Reveal Severe Immune Response Signatures. Small 17(12): 2006123
Mohan JM, Amreen K, Javed A, Dubey SK, Goel S (2022) Emerging trends in miniaturized and microfluidic electrochemical sensing platforms. Curr Opin Electrochem 33:100930
doi: 10.1016/j.coelec.2021.100930
Li P, Zhang J, Lin Q, Kong J, Fang X (2021) Rapid differential diagnosis of the B. 1.617. 2 (delta) variant of SARS-CoV-2 using an automated Cas12a–microfluidic system. Chem Commun 57(92):12270–12272
doi: 10.1039/D1CC04874K
Liu FX, Cui JQ, Wu Z, Yao S (2023) Recent progress in nucleic acid detection with CRISPR. Lab Chip 23(6):1467–1492
pubmed: 36723235
doi: 10.1039/D2LC00928E
Kulkarni MB, Vyas R (2024) A role of integrated microheaters in a microfluidics-based point-of-care-testing and beyond for healthcare applications. Appl Mater Today 38:102225
doi: 10.1016/j.apmt.2024.102225
Nordin AN, Abd Manaf A (2023) Design and fabrication technologies for microfluidic sensors. Microfluidic biosensors. Academic, pp 41–85
Waldbaur A, Rapp H, Länge K, Rapp BE (2011) Let there be chip—towards rapid prototyping of microfluidic devices: one-step manufacturing processes. Anal Methods 3(12):2681–2716
doi: 10.1039/c1ay05253e
Jothimuthu P (2008) Photodefinable Polydimethylsiloxane (PDMS) Thin Films (Master’s thesis, University of Cincinnati)
Morbioli GG, Speller NC, Stockton AM (2020) A practical guide to rapid-prototyping of PDMS-based microfluidic devices: a tutorial. Anal Chim Acta 1135:150–174
pubmed: 33070852
doi: 10.1016/j.aca.2020.09.013
Xie Y, Li H, Chen F, Udayakumar S, Arora K, Chen H, Yin K (2022) Clustered regularly interspaced short palindromic repeats-based Microfluidic System in Infectious diseases diagnosis: current status, challenges, and perspectives. Adv Sci 9(34):2204172
doi: 10.1002/advs.202204172
Yigci D, Atçeken N, Yetisen AK, Tasoglu S (2023) Loop-mediated isothermal amplification-integrated CRISPR methods for infectious disease diagnosis at point of care. ACS Omega 8(46):43357–43373
pubmed: 38027359
pmcid: 10666231
doi: 10.1021/acsomega.3c04422
Liu Y, Kumblathan T, Tao J, Xu J, Feng W, Xiao H, Le XC (2023) Recent advances in RNA sample preparation techniques for the detection of SARS-CoV-2 in saliva and gargle. TRAC Trends Anal Chem 165:117107
doi: 10.1016/j.trac.2023.117107
Myhrvold C, Freije CA, Gootenberg JS, Abudayyeh OO, Metsky HC, Durbin AF et al (2018) Field-deployable viral diagnostics using CRISPR-Cas13. Science 360:444–448. https://doi.org/10.1126/science.aas8836
doi: 10.1126/science.aas8836
pubmed: 29700266
pmcid: 6197056
Mohammad N, Katkam SS, Wei Q (2022) Recent advances in CRISPR-based biosensors for point-of-care pathogen detection. CRISPR J 5(4):500–516
pubmed: 35856644
doi: 10.1089/crispr.2021.0146
De Puig H, Lee RA, Najjar D, Tan X, Soenksen LR, Angenent-Mari NM, Collins JJ (2021) Minimally instrumented SHERLOCK (miSHERLOCK) for CRISPR-based point-of-care diagnosis of SARS-CoV-2 and emerging variants. Sci Adv 7(32):eabh2944
pubmed: 34362739
pmcid: 8346217
doi: 10.1126/sciadv.abh2944
Rossetti M, Merlo R, Bagheri N, Moscone D, Valenti A, Saha A, Porchetta A (2022) Enhancement of CRISPR/Cas12a trans-cleavage activity using hairpin DNA reporters. Nucleic Acids Res 50(14):8377–8391
pubmed: 35822842
pmcid: 9371913
doi: 10.1093/nar/gkac578
Horvath P, Barrangou R (2010) CRISPR/Cas, the immune system of bacteria and archaea. Science 327(5962):167–170
pubmed: 20056882
doi: 10.1126/science.1179555
Wright AV, Nuñez JK, Doudna JA (2016) Biology and applications of CRISPR systems: harnessing nature’s toolbox for genome engineering. Cell 164(1):29–44
pubmed: 26771484
doi: 10.1016/j.cell.2015.12.035
Zhou W, Hu L, Ying L, Zhao Z, Chu PK, Yu XF (2018) A CRISPR–Cas9-triggered strand displacement amplification method for ultrasensitive DNA detection. Nat Commun 9(1):5012
pubmed: 30479331
pmcid: 6258682
doi: 10.1038/s41467-018-07324-5
Chhipa AS, Radadiya E, Patel S (2024) CRISPR-Cas based diagnostic tools: bringing diagnosis out of labs. Diagn Microbiol Infect Dis 116252
Makarova KS, Haft DH, Barrangou R, Brouns SJ, Charpentier E, Horvath P, Koonin EV (2011) Evolution and classification of the CRISPR–Cas systems. Nat Rev Microbiol 9(6):467–477
pubmed: 21552286
doi: 10.1038/nrmicro2577
Freije CA, Sabeti PC (2021) Detect and destroy: CRISPR-based technologies for the response against viruses. Cell Host Microbe 29(5):689–703
pubmed: 33915112
pmcid: 8080417
doi: 10.1016/j.chom.2021.04.003
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(6096): 816–821
Cai Y, Zhuang L, Yu J, He L, Wang Z, Hu T, Huang X (2024) A dual-chamber one-pot CRISPR/Cas12a-based portable and self-testing system for rapid HPV diagnostics. Sens Actuators B 405:135295
doi: 10.1016/j.snb.2024.135295
Yan WX, Hunnewell P, Alfonse LE, Carte JM, Keston-Smith E, Sothiselvam S, Scott DA (2019) Functionally diverse type V CRISPR-Cas systems. Science 363(6422):88–91
pubmed: 30523077
doi: 10.1126/science.aav7271
Wang X, Xiong E, Tian T, Cheng M, Lin W, Wang H, Zhou X (2020) Clustered regularly interspaced short palindromic repeats/Cas9-mediated lateral flow nucleic acid assay. ACS Nano 14(2):2497–2508
pubmed: 32045522
doi: 10.1021/acsnano.0c00022
Bharadwaj A, Kaur R, Gupta S (2024) Emerging treatment approaches for COVID-19 infection: a critical review. Curr Mol Med
Zhou H, Xu Z, He L, Wang Z, Zhang T, Hu T, Huang X (2023) Coupling CRISPR/Cas12a and recombinase polymerase amplification on a stand-alone microfluidics platform for fast and parallel nucleic acid detection. Anal Chem 95(6):3379–3389
pubmed: 36735954
doi: 10.1021/acs.analchem.2c04713
Li J, Macdonald J, Von Stetten F (2019) A comprehensive summary of a decade development of the recombinase polymerase amplification. Analyst 144(1):31–67
doi: 10.1039/C8AN01621F
Wang B, Wang R, Wang D, Wu J, Li J, Wang J, Wang Y (2019) Cas12aVDet: a CRISPR/Cas12a-based platform for rapid and visual nucleic acid detection. Anal Chem 91(19):12156–12161
pubmed: 31460749
doi: 10.1021/acs.analchem.9b01526
Bu S, Liu X, Wang Z, Wei H, Yu S, Li Z, Wan J (2021) Ultrasensitive detection of pathogenic bacteria by CRISPR/Cas12a coupling with a primer exchange reaction. Sens Actuators B 347:130630
doi: 10.1016/j.snb.2021.130630
Joung J, Ladha A, Saito M, Kim NG, Woolley AE, Segel M, Zhang F (2020) Detection of SARS-CoV-2 with SHERLOCK one-pot testing. N Engl J Med 383(15):1492–1494
pubmed: 32937062
doi: 10.1056/NEJMc2026172
Choi JH, Shin M, Yang L, Conley B, Yoon J, Lee SN, Choi JW (2021) Clustered regularly interspaced short palindromic repeats-mediated amplification-free detection of viral DNAs using surface-enhanced Raman spectroscopy-active nanoarray. ACS Nano 15(8):13475–13485
pubmed: 34369760
doi: 10.1021/acsnano.1c03975
Kaur R, Mishra A, Saha S (2023) An overview of phyto-assisted fabrication of metallic nanoparticles. Biocatal Agric Biotechnol 102723
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(6387): 439–444
Myhrvold C, Freije CA, Gootenberg JS, Abudayyeh OO, Metsky HC, Durbin AF, Sabeti PC (2018) Field-deployable viral diagnostics using CRISPR-Cas13. Science 360(6387):444–448
pubmed: 29700266
pmcid: 6197056
doi: 10.1126/science.aas8836
Arizti-Sanz J, Freije CA, Stanton AC, Petros BA, Boehm CK, Siddiqui S, Myhrvold C (2020) Streamlined inactivation, amplification, and Cas13-based detection of SARS-CoV-2. Nat Commun 11(1):5921
pubmed: 33219225
pmcid: 7680145
doi: 10.1038/s41467-020-19097-x
Qing M, Chen SL, Sun Z, Fan Y, Luo HQ, Li NB (2021) Universal and programmable rolling circle amplification-CRISPR/Cas12a-mediated immobilization-free electrochemical biosensor. Anal Chem 93(20):7499–7507
pubmed: 33980009
doi: 10.1021/acs.analchem.1c00805
Pardee K, Green AA, Takahashi MK, Braff D, Lambert G, Lee JW, Collins JJ (2016) Rapid, low-cost detection of Zika virus using programmable biomolecular components. Cell 165(5):1255–1266
pubmed: 27160350
doi: 10.1016/j.cell.2016.04.059
Mukama O, Wu J, Li Z, Liang Q, Yi Z, Lu X, Zeng L (2020) An ultrasensitive and specific point-of-care CRISPR/Cas12 based lateral flow biosensor for the rapid detection of nucleic acids. Biosens Bioelectron 159:112143
pubmed: 32364943
doi: 10.1016/j.bios.2020.112143
Pujadas E, Chaudhry F, McBride R, Richter F, Zhao S, Wajnberg A, Cordon-Cardo C (2020) SARS-CoV-2 viral load predicts COVID-19 mortality. Lancet Respiratory Med 8(9):e70
doi: 10.1016/S2213-2600(20)30354-4
Welch NL, Zhu M, Hua C, Weller J, Mirhashemi ME, Nguyen TG, Myhrvold C (2022) Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants. Nat Med 28(5):1083–1094
pubmed: 35130561
pmcid: 9117129
doi: 10.1038/s41591-022-01734-1
Fozouni P, Son S, de León Derby MD, Knott GJ, Gray CN, D’Ambrosio MV, Ott M (2021) Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy. Cell 184(2):323–333
pubmed: 33306959
doi: 10.1016/j.cell.2020.12.001
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 132(46):20726–20732
doi: 10.1002/ange.202010648
Shinoda H, Taguchi Y, Nakagawa R, Makino A, Okazaki S, Nakano M, Watanabe R (2021) Amplification-free RNA detection with CRISPR–Cas13. Commun Biology 4(1):476
doi: 10.1038/s42003-021-02001-8
Gayet RV, de Puig H, English MA, Soenksen LR, Nguyen PQ, Mao AS, Collins JJ (2020) Creating CRISPR-responsive smart materials for diagnostics and programmable cargo release. Nat Protoc 15(9):3030–3063
pubmed: 32807909
doi: 10.1038/s41596-020-0367-8
Silva FS, Erdogmus E, Shokr A, Kandula H, Thirumalaraju P, Kanakasabapathy MK, Shafiee H (2021) SARS-CoV‐2 RNA detection by a cellphone‐based amplification‐free system with CRISPR/CAS‐dependent enzymatic (CASCADE) assay. Adv Mater Technol 6(12):2100602
pubmed: 34514084
pmcid: 8420437
doi: 10.1002/admt.202100602
Huang D, Ni D, Fang M, Shi Z, Xu Z (2021) Microfluidic ruler-readout and CRISPR Cas12a-responded hydrogel-integrated paper-based analytical devices (µReaCH-PAD) for visible quantitative point-of-care testing of invasive fungi. Anal Chem 93(50):16965–16973
pubmed: 34889094
doi: 10.1021/acs.analchem.1c04649
Shao N, Han X, Song Y, Zhang P, Qin L (2019) CRISPR-Cas12a coupled with platinum nanoreporter for visual quantification of SNVs on a volumetric bar-chart chip. Anal Chem 91(19):12384–12391
pubmed: 31461619
doi: 10.1021/acs.analchem.9b02925
Zhuang J, Zhao Z, Lian K, Yin L, Wang J, Man S, Ma L (2022) SERS-based CRISPR/Cas assay on microfluidic paper analytical devices for supersensitive detection of pathogenic bacteria in foods. Biosens Bioelectron 207:114167
pubmed: 35325722
doi: 10.1016/j.bios.2022.114167
Chen Y, Mei Y, Jiang X (2021) Universal and high-fidelity DNA single nucleotide polymorphism detection based on a CRISPR/Cas12a biochip. Chem Sci 12(12):4455–4462
pubmed: 34163711
pmcid: 8179484
doi: 10.1039/D0SC05717G
Chen Y, Shi Y, Chen Y, Yang Z, Wu H, Zhou Z, Chen H (2020) Contamination-free visual detection of SARS-CoV-2 with CRISPR/Cas12a: a promising method in the point-of-care detection. Biosens Bioelectron 169:112642
pubmed: 32979593
pmcid: 7502227
doi: 10.1016/j.bios.2020.112642
Xiang X, Li F, Ye Q, Shang Y, Chen M, Zhang J, Wu Q (2022) High-throughput microfluidic strategy based on RAA-CRISPR/Cas13a dual signal amplification for accurate identification of pathogenic Listeria. Sens Actuators B 358:131517
doi: 10.1016/j.snb.2022.131517
Li P, Zeng X, Xue H, Ye X, Yang B, Kong J, Fang X (2022) CRISPR-microfluidic array for single-copy DNA mini barcoding and rapid field species identification. Sens Actuators B 359:131567
doi: 10.1016/j.snb.2022.131567
Chen Y, Xu X, Wang J, Zhang Y, Zeng W, Liu Y, Zhang X (2022) Photoactivatable CRISPR/Cas12a strategy for one-pot DETECTR molecular diagnosis. Anal Chem 94(27):9724–9731
pubmed: 35762828
doi: 10.1021/acs.analchem.2c01193
Zong N, Gao Y, Chen Y, Luo X, Jiang X (2022) Automated centrifugal microfluidic chip integrating pretreatment and molecular diagnosis for hepatitis B virus genotyping from whole blood. Anal Chem 94(12):5196–5203
pubmed: 35289612
doi: 10.1021/acs.analchem.2c00337
Wu H, Qian S, Peng C, Wang X, Wang T, Zhong X, Wu J (2021) Rotary valve-assisted fluidic system coupling with CRISPR/Cas12a for fully integrated nucleic acid detection. ACS Sens 6(11):4048–4056
pubmed: 34665590
doi: 10.1021/acssensors.1c01468
Wu H, Chen Y, Yang Q, Peng C, Wang X, Zhang M, Wu J (2021) A reversible valve-assisted chip coupling with integrated sample treatment and CRISPR/Cas12a for visual detection of Vibrio parahaemolyticus. Biosens Bioelectron 188:113352
pubmed: 34038837
doi: 10.1016/j.bios.2021.113352
Liu FX, Cui JQ, Park H, Chan KW, Leung T, Tang BZ, Yao S (2022) Isothermal background-free nucleic acid quantification by a one-pot Cas13a assay using droplet microfluidics. Anal Chem 94(15):5883–5892
pubmed: 35387453
doi: 10.1021/acs.analchem.2c00067
Wu H, Cao X, Meng Y, Richards D, Wu J, Ye Z, deMello AJ (2022) DropCRISPR: a LAMP-Cas12a based digital method for ultrasensitive detection of nucleic acid. Biosens Bioelectron 211:114377
pubmed: 35609453
doi: 10.1016/j.bios.2022.114377
Yue H, Shu B, Tian T, Xiong E, Huang M, Zhu D, Zhou X (2021) Droplet Cas12a assay enables DNA quantification from unamplified samples at the single-molecule level. Nano Lett 21(11):4643–4653
pubmed: 34038136
doi: 10.1021/acs.nanolett.1c00715
Park JS, Hsieh K, Chen L, Kaushik A, Trick AY, Wang TH (2021) Digital CRISPR/Cas-Assisted assay for rapid and sensitive detection of SARS‐CoV‐2. Adv Sci 8(5):2003564
doi: 10.1002/advs.202003564
Wu X, Tay JK, Goh CK, Chan C, Lee YH, Springs SL, Yu H (2021) Digital CRISPR-based method for the rapid detection and absolute quantification of nucleic acids. Biomaterials 274:120876
pubmed: 34034027
doi: 10.1016/j.biomaterials.2021.120876
Ding X, Yin K, Li Z, Sfeir MM, Liu C (2021) Sensitive quantitative detection of SARS-CoV-2 in clinical samples using digital warm-start CRISPR assay. Biosens Bioelectron 184:113218
pubmed: 33878591
pmcid: 8052607
doi: 10.1016/j.bios.2021.113218
Bruch R, Johnston M, Kling A, Mattmüller T, Baaske J, Partel S, Dincer C (2021) CRISPR-powered electrochemical microfluidic multiplexed biosensor for target amplification-free miRNA diagnostics. Biosens Bioelectron 177:112887
pubmed: 33493854
doi: 10.1016/j.bios.2020.112887
Bruch R, Baaske J, Chatelle C, Meirich M, Madlener S, Weber W, Urban GA (2019) CRISPR/Cas13a-powered electrochemical microfluidic biosensor for nucleic acid amplification‐free miRNA diagnostics. Advanced materials 31(51): 1905311
Najjar D, Rainbow J, Sharma Timilsina S, Jolly P, De Puig H, Yafia M, Ingber DE (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. Nature biomedical engineering 6(8): 968–978
Zhou T, Huang R, Huang M, Shen J, Shan Y, Xing D (2020) CRISPR/Cas13a powered portable electrochemiluminescence chip for ultrasensitive and specific MiRNA detection. Adv Sci 7(13):1903661
doi: 10.1002/advs.201903661
Ramachandran A, Huyke DA, Sharma E, Sahoo MK, Huang C, Banaei N, Santiago JG (2020) Electric field-driven microfluidics for rapid CRISPR-based diagnostics and its application to detection of SARS-CoV-2. Proceedings of the National Academy of Sciences 117(47): 29518–29525
Lee H, Choi J, Jeong E, Baek S, Kim HC, Chae JH, Kim SJ (2018) dCas9-mediated nanoelectrokinetic direct detection of target gene for liquid biopsy. Nano Lett 18(12):7642–7650
pubmed: 30421614
doi: 10.1021/acs.nanolett.8b03224
Nguyen PQ, Soenksen LR, Donghia NM, Angenent-Mari NM, de Puig H, Huang A, Collins JJ (2021) Wearable materials with embedded synthetic biology sensors for biomolecule detection. Nat Biotechnol 39(11):1366–1374
pubmed: 34183860
doi: 10.1038/s41587-021-00950-3
Yang B, Kong J, Fang X (2022) Programmable CRISPR-Cas9 microneedle patch for long-term capture and real-time monitoring of universal cell-free DNA. Nat Commun 13(1):3999
pubmed: 35810160
pmcid: 9271037
doi: 10.1038/s41467-022-31740-3
Moon J, Kwon HJ, Yong D, Lee IC, Kim H, Kang H, Kang T (2020) Colorimetric detection of SARS-CoV-2 and drug-resistant pH1N1 using CRISPR/dCas9. ACS Sens 5(12):4017–4026
pubmed: 33270431
doi: 10.1021/acssensors.0c01929
Qin P, Park M, Alfson KJ, Tamhankar M, Carrion R, Patterson JL, Du K (2019) Rapid and fully microfluidic Ebola virus detection with CRISPR-Cas13a. ACS Sens 4(4):1048–1054
pubmed: 30860365
doi: 10.1021/acssensors.9b00239
Hass KN, Bao M, He Q, Liu L, He J, Park M, Du K (2020) Integrated micropillar polydimethylsiloxane accurate CRISPR detection system for viral DNA sensing. ACS Omega 5(42):27433–27441
pubmed: 33134706
pmcid: 7594154
doi: 10.1021/acsomega.0c03917
He Q, Yu D, Bao M, Korensky G, Chen J, Shin M, Du K (2020) High-throughput and all-solution phase African swine fever virus (ASFV) detection using CRISPR-Cas12a and fluorescence based point-of-care system. Biosens Bioelectron 154:112068
pubmed: 32056963
doi: 10.1016/j.bios.2020.112068
Zeng R, Wang W, Chen M, Wan Q, Wang C, Knopp D, Tang D (2021) CRISPR-Cas12a-driven MXene-PEDOT: PSS piezoresistive wireless biosensor. Nano Energy 82:105711
doi: 10.1016/j.nanoen.2020.105711
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(21):14846–14852
pubmed: 33064442
doi: 10.1021/acs.analchem.0c03883
English MA, Soenksen LR, Gayet RV, de Puig H, Angenent-Mari NM, Mao AS, Collins JJ (2019) Programmable CRISPR-responsive smart materials. Science 365(6455):780–785
pubmed: 31439791
doi: 10.1126/science.aaw5122
Barnes KG, Lachenauer AE, Nitido A, Siddiqui S, Gross R, Beitzel B, Sabeti PC (2020) Deployable CRISPR-Cas13a diagnostic tools to detect and report Ebola and Lassa virus cases in real-time. Nat Commun 11(1):4131
pubmed: 32807807
pmcid: 7431545
doi: 10.1038/s41467-020-17994-9
Broughton JP, Deng X, Yu G, Fasching CL, Servellita V, Singh J, Chiu CY (2020) CRISPR–Cas12-based detection of SARS-CoV-2. Nat Biotechnol 38(7):870–874
pubmed: 32300245
pmcid: 9107629
doi: 10.1038/s41587-020-0513-4
Joung J, Ladha A, Saito M, Segel M, Bruneau R, Mee-li WH, Zhang F (2020) Point-of-care testing for COVID-19 using SHERLOCK diagnostics. MedRxiv
Ooi KH, Tay JWD, Teo SY, Liu MM, Kaewsapsak P, Jin S, Tan MH (2020) A CRISPR-based SARS-CoV-2 diagnostic assay that is robust against viral evolution and RNA editing. BioRxiv 2020-07
Yin K, Ding X, Li Z, Sfeir MM, Ballesteros E, Liu C (2021) Autonomous lab-on-paper for multiplexed, CRISPR-based diagnostics of SARS-CoV-2. Lab Chip 21(14):2730–2737
pubmed: 34100058
pmcid: 8277744
doi: 10.1039/D1LC00293G
Xiong E, Jiang L, Tian T, Hu M, Yue H, Huang M, Zhou X (2021) Simultaneous dual-gene diagnosis of SARS‐CoV‐2 based on CRISPR/Cas9‐mediated lateral flow assay. Angew Chem Int Ed 60(10):5307–5315
doi: 10.1002/anie.202014506
Huang D, Shi Z, Qian J, Bi K, Fang M, Xu Z (2021) A CRISPR-Cas12a‐derived biosensor enabling portable personal glucose meter readout for quantitative detection of SARS‐CoV‐2. Biotechnol Bioeng 118(4):1568–1577
doi: 10.1002/bit.27673
Zhou B, Ye Q, Li F, Xiang X, Shang Y, Wang C, Wu Q (2022) CRISPR/Cas12a based fluorescence-enhanced lateral flow biosensor for detection of Staphylococcus aureus. Sens Actuators B 351:130906
doi: 10.1016/j.snb.2021.130906
Li Z, Ding X, Yin K, Avery L, Ballesteros E, Liu C (2022) Instrument-free, CRISPR-based diagnostics of SARS-CoV-2 using self-contained microfluidic system. Biosens Bioelectron 199:113865
pubmed: 34906838
doi: 10.1016/j.bios.2021.113865
Dai Y, Somoza RA, Wang L, Welter JF, Li Y, Caplan AI, Liu CC (2019) Exploring the trans-cleavage activity of CRISPR‐Cas12a (cpf1) for the development of a universal electrochemical biosensor. Angew Chem 131(48):17560–17566
doi: 10.1002/ange.201910772
Xu W, Jin T, Dai Y, Liu CC (2020) Surpassing the detection limit and accuracy of the electrochemical DNA sensor through the application of CRISPR Cas systems. Biosens Bioelectron 155:112100
pubmed: 32090878
doi: 10.1016/j.bios.2020.112100
Zhao KR, Wang L, Liu PF, Hang XM, Wang HY, Ye SY, Liang GX (2021) A signal-switchable electrochemiluminescence biosensor based on the integration of spherical nucleic acid and CRISPR/Cas12a for multiplex detection of HIV/HPV DNAs. Sens Actuators B 346:130485
doi: 10.1016/j.snb.2021.130485
Tian T, Shu B, Jiang Y, Ye M, Liu L, Guo Z, Zhou X (2020) An ultralocalized Cas13a assay enables universal and nucleic acid amplification-free single-molecule RNA diagnostics. ACS Nano 15(1):1167–1178
pubmed: 33498106
doi: 10.1021/acsnano.0c08165
Yu F, Zhang K, Wang Y, Li D, Cui Z, Huang J, Zhang L (2021) CRISPR/Cas12a-based on-site diagnostics of Cryptosporidium parvum IId-subtype-family from human and cattle fecal samples. Parasites Vectors 14:1–10
doi: 10.1186/s13071-021-04709-2
Yang Y, Liu J, Zhou X (2021) A CRISPR-based and post-amplification coupled SARS-CoV-2 detection with a portable evanescent wave biosensor. Biosens Bioelectron 190:113418
pubmed: 34119838
pmcid: 8182983
doi: 10.1016/j.bios.2021.113418
Xia Y, Rao R, Xiong M, He B, Zheng B, Jia Y, Yang Y (2024) CRISPR-powered strategies for amplification-free diagnostics of infectious diseases. Analytical Chemistry
Nouri R, Tang Z, Dong M, Liu T, Kshirsagar A, Guan W (2021) CRISPR-based detection of SARS-CoV-2: a review from sample to result. Biosens Bioelectron 178:113012
pubmed: 33497879
pmcid: 7826142
doi: 10.1016/j.bios.2021.113012
Patchsung M, Jantarug K, Pattama A, Aphicho K, Suraritdechachai S, Meesawat P, Uttamapinant C (2020) Clinical validation of a Cas13-based assay for the detection of SARS-CoV-2 RNA. Nat Biomedical Eng 4(12):1140–1149
doi: 10.1038/s41551-020-00603-x
Zhang WS, Pan J, Li F, Zhu M, Xu M, Zhu H, Su G (2021) Reverse transcription recombinase polymerase amplification coupled with CRISPR-Cas12a for facile and highly sensitive colorimetric SARS-CoV-2 detection. Analytical chemistry 93(8): 4126–4133
Jiang Y, Hu M, Liu AA, Lin Y, Liu L, Yu B, Pang DW (2021) Detection of SARS-CoV-2 by CRISPR/Cas12a-enhanced colorimetry. ACS Sens 6(3):1086–1093
pubmed: 33683104
doi: 10.1021/acssensors.0c02365
Zhu X, Wang X, Li S, Luo W, Zhang X, Wang C, Wang Y (2021) Rapid, ultrasensitive, and highly specific diagnosis of COVID-19 by CRISPR-based detection. ACS Sens 6(3):881–888
pubmed: 33645226
doi: 10.1021/acssensors.0c01984
Basiri A, Heidari A, Nadi MF, Fallahy MTP, Nezamabadi SS, Sedighi M, Rezaei N (2021) Microfluidic devices for detection of RNA viruses. Rev Med Virol 31(1):1–11
pubmed: 32844526
doi: 10.1002/rmv.2154
Weng Z, You Z, Yang J, Mohammad N, Lin M, Wei Q, Zhang Y (2023) CRISPR-Cas biochemistry and CRISPR‐based molecular diagnostics. Angew Chem Int Ed 62(17):e202214987
doi: 10.1002/anie.202214987
Nouri R, Jiang Y, Lian XL, Guan W (2020) Sequence-specific recognition of HIV-1 DNA with solid-state CRISPR-Cas12a-assisted nanopores (SCAN). ACS Sens 5(5):1273–1280
pubmed: 32370494
doi: 10.1021/acssensors.0c00497
Kong H, Yi K, Mintz RL, Wang B, Xu Y, Lao YH, Li M (2024) CRISPR/Cas detection with nanodevices: moving deeper into liquid biopsy. Chemical Communications
Ding R, Long J, Yuan M, Zheng X, Shen Y, Jin Y, Duan G (2021) CRISPR/Cas12-based ultra-sensitive and specific point-of-care detection of HBV. Int J Mol Sci 22(9):4842
pubmed: 34063629
pmcid: 8125043
doi: 10.3390/ijms22094842
Yuan T, Mukama O, Li Z, Chen W, Zhang Y, de Dieu Habimana J, Zeng L (2020) A rapid and sensitive CRISPR/Cas12a based lateral flow biosensor for the detection of Epstein–Barr virus. Analyst 145(19):6388–6394
pubmed: 32985619
doi: 10.1039/D0AN00663G
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(12):8561–8568
pubmed: 32390420
pmcid: 7588651
doi: 10.1021/acs.analchem.0c01459
Liu JM, Yan XP (2012) Competitive aptamer bioassay for selective detection of adenosine triphosphate based on metal-paired molecular conformational switch and fluorescent gold nanoclusters. Biosens Bioelectron 36(1):135–141
pubmed: 22560440
doi: 10.1016/j.bios.2012.04.015
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(12):e17365
doi: 10.1002/aic.17365
Qiu E, Jin S, Xiao Z, Chen Q, Wang Q, Liu H, Han S (2021) CRISPR-based Detection of Helicobacter pylori in Stool Samples. Helicobacter 26(4): e12828
Ma L, Peng L, Yin L, Liu G, Man S (2021) CRISPR-Cas12a-powered dual-mode biosensor for ultrasensitive and cross-validating detection of pathogenic bacteria. Acs Sens 6(8):2920–2927
pubmed: 34281340
doi: 10.1021/acssensors.1c00686
Wu Q, Suo C, Brown T, Wang T, Teichmann SA, Bassett AR (2021) INSIGHT: a population-scale COVID-19 testing strategy combining point-of-care diagnosis with centralized high-throughput sequencing. Sci Adv 7(7):eabe5054
pubmed: 33579697
pmcid: 7880595
doi: 10.1126/sciadv.abe5054
Song F, Wei Y, Wang P, Ge X, Li C, Wang A, Li J (2021) Combining tag-specific primer extension and magneto-DNA system for Cas14a-based universal bacterial diagnostic platform. Biosens Bioelectron 185:113262
pubmed: 33930753
doi: 10.1016/j.bios.2021.113262
Ge X, Meng T, Tan X, Wei Y, Tao Z, Yang Z, Wan Y (2021) Cas14a1-mediated nucleic acid detectifon platform for pathogens. Biosens Bioelectron 189:113350
pubmed: 34049081
doi: 10.1016/j.bios.2021.113350
Chen Y, Qian S, Yu X, Wu J, Xu J (2023) Microfluidics: the propellant of CRISPR-based nucleic acid detection. Trends Biotechnol 41(4):557–574
pubmed: 35989112
doi: 10.1016/j.tibtech.2022.07.015
Gupta S, Kaur R, Bhardwaj A, Parashar D (2024) Multifunctional nanomaterials: recent advancements in Cancer therapeutics and vaccines. Indian J Microbiol 1–18
Hao L, Zhao RT, Welch NL, Tan EKW, Zhong Q, Harzallah NS, Bhatia SN (2023) CRISPR-Cas-amplified urinary biomarkers for multiplexed and portable cancer diagnostics. Nat Nanotechnol 18(7):798–807
pubmed: 37095220
pmcid: 10359190
doi: 10.1038/s41565-023-01372-9
Shi C, Andino-Pavlovsky V, Lee SA, Costa T, Elloian J, Konofagou EE, Shepard KL (2021) Application of a sub–0.1-mm3 implantable mote for in vivo real-time wireless temperature sensing. Sci Adv 7(19):eabf6312
pubmed: 33962948
pmcid: 8104878
doi: 10.1126/sciadv.abf6312
Li B, Shao Z, Chen Y (2021) An exonuclease protection and CRISPR/Cas12a integrated biosensor for the turn-on detection of transcription factors in cancer cells. Anal Chim Acta 1165:338478
pubmed: 33975701
doi: 10.1016/j.aca.2021.338478
Wang M, Han D, Zhang J, Zhang R, Li J (2021) High-fidelity detection of DNA combining the CRISPR/Cas9 system and hairpin probe. Biosens Bioelectron 184:113212
pubmed: 33862567
doi: 10.1016/j.bios.2021.113212
Zhou T, Huang M, Lin J, Huang R, Xing D (2021) High-fidelity CRISPR/Cas13a trans-cleavage-triggered rolling circle amplified DNAzyme for visual profiling of microRNA. Anal Chem 93(4):2038–2044
pubmed: 33411517
doi: 10.1021/acs.analchem.0c03708
Hattakam S, Elong Ngono A, McCauley M, Shresta S, Yamabhai M (2021) Repeated exposure to dengue virus elicits robust cross neutralizing antibodies against Zika virus in residents of Northeastern Thailand. Sci Rep 11(1):9634
pubmed: 33953258
pmcid: 8100282
doi: 10.1038/s41598-021-88933-x
Avaro AS, Santiago JG (2023) A critical review of microfluidic systems for CRISPR assays. Lab Chip 23(5):938–963
pubmed: 36601854
doi: 10.1039/D2LC00852A
Labib M, Philpott DN, Wang Z, Nemr C, Chen JB, Sargent EH, Kelley SO (2020) Magnetic ranking cytometry: profiling rare cells at the single-cell level. Acc Chem Res 53(8):1445–1457
pubmed: 32662263
doi: 10.1021/acs.accounts.0c00179
Mair B, Aldridge PM, Atwal RS, Philpott D, Zhang M, Masud SN, Kelley SO (2019) High-throughput genome-wide phenotypic screening via immunomagnetic cell sorting. Nat Biomedical Eng 3(10):796–805
doi: 10.1038/s41551-019-0454-8
Balbino TA, Azzoni AR, de La Torre LG (2013) Microfluidic devices for continuous production of pDNA/cationic liposome complexes for gene delivery and vaccine therapy. Colloids Surf B 111:203–210
doi: 10.1016/j.colsurfb.2013.04.003
Laohakunakorn N, Lavickova B, Swank Z, Laurent J, Maerkl SJ (2021) Steady-state cell-free gene expression with microfluidic chemostats. Synth Gene Circuits: Methods Protocols 189–203
Ahmadi S, Rabiee N, Bagherzadeh M, Karimi M (2021) Microfluidic devices for gene delivery systems. Biomedical Applications of Microfluidic devices. Academic, pp 187–208
Niculescu AG, Chircov C, Bîrcă AC, Grumezescu AM (2021) Fabrication and applications of microfluidic devices: A review. International Journal of Molecular Sciences 22(4): 2011
Del Giovane S, Bagheri N, Di Pede AC, Chamorro A, Ranallo S, Migliorelli D, Porchetta A (2024) Challenges and perspectives of CRISPR-based technology for diagnostic applications. TRAC Trends Anal Chem 117594
Wang J, Maier SA, Tittl A (2022) Trends in Nanophotonics-enabled optofluidic biosensors. Adv Opt Mater 10(7):2102366
doi: 10.1002/adom.202102366
Murphy RR, Adams J, Gandudi VBM (2020) Robots are playing many roles in the coronavirus crisis–and offering lessons for future disasters. The Conversation 22
Karlikow M, da Silva SJR, Guo Y, Cicek S, Krokovsky L, Homme P, Pardee K (2022) Field validation of the performance of paper-based tests for the detection of the Zika and Chikungunya viruses in serum samples. Nat Biomedical Eng 6(3):246–256
doi: 10.1038/s41551-022-00850-0
Karthik K, Babu RPA, Dhama K, Chitra MA, Kalaiselvi G, Senthilkumar TMA, Raj GD (2020) Biosafety concerns during the collection, transportation, and processing of COVID-19 samples for diagnosis. Arch Med Res 51(7):623–630
pubmed: 32948378
pmcid: 7486853
doi: 10.1016/j.arcmed.2020.08.007
Verma D, Singh KR, Yadav AK, Nayak V, Singh J, Solanki PR, Singh RP (2022) Internet of things (IoT) in nano-integrated wearable biosensor devices for healthcare applications. Biosens Bioelectronics: X 11:100153
Kaur R, Bhardwaj A, Gupta S (2023) Cancer treatment therapies: traditional to modern approaches to combat cancers. Mol Biol Rep 50(11):9663–9676
pubmed: 37828275
doi: 10.1007/s11033-023-08809-3