Recent advances in CRISPR/Cas12a-based biosensors for food safety detection

YU Liya; XIE Gang; ZHANG Yan; WU Qiankun

doi:10.13995/j.cnki.11-1802/ts.041628

Food and Fermentation Industries >

2025 , Vol. 51 >Issue 18: 378 - 388

DOI: https://doi.org/10.13995/j.cnki.11-1802/ts.041628

Recent advances in CRISPR/Cas12a-based biosensors for food safety detection

YU Liya ,
XIE Gang ,
ZHANG Yan ,
WU Qiankun

Expand

1(School of Healthy Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China)
2(Academy of National Food and Strategic Reserves Administration, Beijing 100037, China)

Received date: 2024-11-19

Revised date: 2024-12-31

Online published: 2025-10-16

Fold

Abstract

Food safety is a critical global public health concern.Foods are susceptible to physical, chemical, and biological contamination at various stages of the food supply chain, including production, processing, distribution, and consumption.To address food safety challenges and safeguard consumer health, the development of effective and precise detection technologies is essential.The CRISPR/Cas12a system, characterized by its unique trans-cleavage activity upon target recognition, has emerged as a powerful tool in biosensing due to its high accuracy and efficiency.This system holds significant promise for enhancing food safety detection.This paper first reviews the mechanisms and classification of CRISPR/Cas systems, then describes the methods and types of signal amplification and output in CRISPR/Cas12a-based biosensors, next summarizes recent advances in applying CRISPR/Cas12a-based biosensors to detect foodborne pathogens, genetically modified organisms (GMOs), mycotoxins, heavy metal ions, and pesticide residues, and finally discusses current challenges and future prospects of CRISPR/Cas12a-based biosensors for food safety detection.

Key words： CRISPR/Cas12a; biosensor; signal amplification; signal output; food safety

Cite this article

YU Liya , XIE Gang , ZHANG Yan , WU Qiankun . Recent advances in CRISPR/Cas12a-based biosensors for food safety detection[J]. Food and Fermentation Industries, 2025 , 51(18) : 378 -388 . DOI: 10.13995/j.cnki.11-1802/ts.041628

References

[1] WORLD HEALTH ORGANIZATION.Food safety[EB/OL].(2024-10-04)[2024-10-31].https://www.who.int/news-room/fact-sheets/detail/food-safety.
[2] TANG J, GAO Z Y, XU L F, et al.Smartphone-assisted colorimetric biosensor for the rapid visual detection of natural antioxidants in food samples[J].Food Chemistry, 2025, 462:141026.
[3] SUN Y N, WEN T J, ZHANG P, et al.Recent advances in the CRISPR/Cas-based nucleic acid biosensor for food analysis:A review[J].Foods, 2024, 13(20):3222.
[4] WU H, CHEN X Y, ZHANG M Y, et al.Versatile detection with CRISPR/Cas system from applications to challenges[J].TrAC Trends in Analytical Chemistry, 2021, 135:116150.
[5] CHEN J S, MA E B, HARRINGTON L B, et al.CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity[J].Science, 2018, 360(6387):436-439.
[6] ZAVVAR T S, KHOSHBIN Z, RAMEZANI M, et al.CRISPR/Cas-engineered technology:Innovative approach for biosensor development[J].Biosensors and Bioelectronics, 2022, 214:114501.
[7] CHARPENTIER E, RICHTER H, VAN DER OOST J, et al.Biogenesis pathways of RNA guides in archaeal and bacterial CRISPR-Cas adaptive immunity[J].FEMS Microbiology Reviews, 2015, 39(3):428-441.
[8] GASIUNAS G, SINKUNAS T, SIKSNYS V.Molecular mechanisms of CRISPR-mediated microbial immunity[J].Cellular and Molecular Life Sciences, 2014, 71(3):449-465.
[9] SHMAKOV S, SMARGON A, SCOTT D, et al.Diversity and evolution of class 2 CRISPR-Cas systems[J].Nature Reviews Microbiology, 2017, 15(3):169-182.
[10] HILLARY V E, CEASAR S A.A review on the mechanism and applications of CRISPR/Cas9/Cas12/Cas13/Cas14 proteins utilized for genome engineering[J].Molecular Biotechnology, 2023, 65(3):311-325.
[11] NATH S.Advancements in food quality monitoring:Integrating biosensors for precision detection[J].Sustainable Food Technology, 2024, 2(4):976-992.
[12] LI S Y, CHENG Q X, WANG J M, et al.CRISPR-Cas12a-assisted nucleic acid detection[J].Cell Discovery, 2018, 4:20.
[13] MUÑOZ H E, RICHE C T, KONG J E, et al.Fractal LAMP:Label-free analysis of fractal precipitate for digital loop-mediated isothermal nucleic acid amplification[J].ACS Sensors, 2020, 5(2):385-394.
[14] LIU S T, XU L, HUANG Z H, et al.Recent advances of nanoparticles-assisted CRISPR/Cas biosensors[J].Microchemical Journal, 2024, 199:109930.
[15] 苏邵, 李晶, 汪联辉.基于纳米材料比色传感器的构建及其应用[J].南京邮电大学学报(自然科学版), 2018, 38(3):98-110.
SU S, LI J, WANG L H.Construction and application of nanomaterials-based colorimetric sensors[J].Journal of Nanjing University of Posts and Telecommunications(Natural Science Edition), 2018, 38(3):98-110.
[16] YIN L J, DUAN N H, CHEN S, et al.Ultrasensitive pathogenic bacteria detection by a smartphone-read G-quadruplex-based CRISPR-Cas12a bioassay[J].Sensors and Actuators B:Chemical, 2021, 347:130586.
[17] DAI Y F, SOMOZA R A, WANG L, et al.Exploring the trans-cleavage activity of CRISPR-Cas12a (cpf1) for the development of a universal electrochemical biosensor[J].Angewandte Chemie, 2019, 131(48):17560-17566.
[18] XU J R, ZHANG T X, LV X R, et al.An RPA-based CRISPR/Cas12a assay in combination with a lateral flow assay for the rapid detection of Shigella flexneri in food samples[J].Foods, 2024, 13(19):3200.
[19] XING G W, SHANG Y T, WANG X R, et al.Multiplexed detection of foodborne pathogens using one-pot CRISPR/Cas12a combined with recombinase aided amplification on a finger-actuated microfluidic biosensor[J].Biosensors and Bioelectronics, 2023, 220:114885.
[20] LEE S Y, KIM U, KIM Y, et al.Enhanced detection of Listeria monocytogenes using tetraethylenepentamine-functionalized magnetic nanoparticles and LAMP-CRISPR/Cas12a-based biosensor[J].Analytica Chimica Acta, 2023, 1281:341905.
[21] DUAN M L, LI B Y, HE Y W, et al.A CG@MXene nanocomposite-driven E-CRISPR biosensor for the rapid and sensitive detection of Salmonella Typhimurium in food[J].Talanta, 2024, 266:125011.
[22] GU X J, TANG Q, KANG X X, et al.A portable CRISPR-Cas12a triggered photothermal biosensor for sensitive and visual detection of Staphylococcus aureus and Listeria monocytogenes[J].Talanta, 2024, 271:125678.
[23] SUN X D, SHAN Y J, JIAN M H, et al.A multichannel fluorescence isothermal amplification device with integrated internet of medical things for rapid sensing of pathogens through deep learning[J].Analytical Chemistry, 2023, 95(41):15146-15152.
[24] ZHOU Y, ZHAO J P, CHEN R, et al.A portable deep-learning-assisted digital single-particle counting biosensing platform for amplification-free nucleic acid detection using a lens-free holography microscope[J].Nano Today, 2024, 56:102238.
[25] FU X R, SUN J D, YU B Q, et al.Investigating enzyme kinetics and fluorescence sensing strategy of CRISPR/Cas12a for foodborne pathogenic bacteria[J].Analytica Chimica Acta, 2024, 1290:342203.
[26] SONG Y, XU Y W, WANG R R, et al.CRISPR-Cas12a-based nanoparticle biosensor for detection of pathogenic bacteria in food[J].Microchemical Journal, 2024, 207:111813.
[27] LIANG Q Q, WANG X H, XIE Q Q, et al.Development of highly sensitive one-pot ERA-CRISPR assays for on-site detection of CaMV35S promoter and NOS terminator in genetically modified crops[J].Food Control, 2025, 170:111049.
[28] WANG J B, LUO J W, LIU H, et al.“Blue-red-purple” multicolored lateral flow immunoassay for simultaneous detection of GM crops utilizing RPA and CRISPR/Cas12a[J].Talanta, 2025, 282:127010.
[29] LI X H, LIU M L, XIA X H, et al.Deep learning assisted, smartphone based universal Multi-RPA-CRISPR/Cas12a-G4 portable chip for simultaneous detection of CaMV35S and NOS[J].Food Control, 2025, 168:110947.
[30] LIU M L, LI X H, XU J B, et al.Sensitive detection of CaMV35S based on exponential rolling circle amplification reaction and CRISPR/Cas12a using a portable 3D-printed visualizer[J].Microchemical Journal, 2024, 205:111313.
[31] PENG C, WANG Y L, CHEN X Y, et al.A localized CRISPR assay that detects short nucleic acid fragments in unamplified genetically modified samples[J].ACS Sensors, 2023, 8(3):1054-1063.
[32] WANG J B, WANG Y, LIU H, et al.An ultra-sensitive test strip combining with RPA and CRISPR/Cas12a system for the rapid detection of GM crops[J].Food Control, 2023, 144:109383.
[33] ZHU L L, HE G W, YANG G Q, et al.A rapid on-site visualization platform based on RPA coupled with CRISPR-Cas12a for the detection of genetically modified papaya ‘Huanong No.1’[J].Talanta, 2024, 277:126437.
[34] WU C Y, WANG X J, GUO L, et al.An electrochemical aptasensor based on exonuclease III-assisted signal amplification coupled with CRISPR-Cas12a for ochratoxin A detection[J].Food Control, 2023, 148:109631.
[35] ESMAELPOURFARKHANI M, RAMEZANI M, ALIBOLANDI M, et al.CRISPR-Cas12a-based colorimetric aptasensor for aflatoxin M₁ detection based on oxidase-mimicking activity of flower-like MnO₂ nanozymes[J].Talanta, 2024, 271:125729.
[36] WU C Y, YUE Y Y, HUANG B C, et al.CRISPR-powered microfluidic biosensor for preamplification-free detection of ochratoxin A[J].Talanta, 2024, 269:125414.
[37] XIANG X R, SONG M H, XU X W, et al.Microfluidic biosensor integrated with signal transduction and enhancement mechanism for ultrasensitive noncompetitive assay of multiple mycotoxins[J].Analytical Chemistry, 2023, 95(20):7993-8001.
[38] ZHAO X X, WANG Z X, ZHANG H, et al.Highly sensitive one-pot isothermal assay combining rolling circle amplification and CRISPR/Cas12a for aflatoxin B₁ detection[J].Analytical Chemistry, 2024, 96(45):18070-18078.
[39] WANG Z L, WEI L Y, RUAN S L, et al.CRISPR/Cas12a-assisted chemiluminescence sensor for aflatoxin B₁ detection in cereal based on functional nucleic acid and in-pipet rolling circle amplification[J].Journal of Agricultural and Food Chemistry, 2023, 71(10):4417-4425.
[40] YAN H, HE B S, ZHAO R Y, et al.Electrochemical aptasensor based on CRISPR/Cas12a-mediated and DNAzyme-assisted cascade dual-enzyme transformation strategy for zearalenone detection[J].Chemical Engineering Journal, 2024, 493:152431.
[41] ZHU F X, ZHAO Q.Competitive aptamer assay for aflatoxin B₁ detection using CRISPR/Cas12a as a signal amplifier[J].Microchemical Journal, 2024, 207:112054.
[42] LIU M L, LI X H, ZHOU S Y, et al.Ultrasensitive detection of mycotoxins using a novel single-Atom, CRISPR/Cas12a-Based nanozymatic colorimetric biosensor[J].Chemical Engineering Journal, 2024, 497:154418.
[43] YUE Y Y, WANG S T, JIN Q, et al.A triple amplification strategy using GR-5 DNAzyme as a signal medium for ultrasensitive detection of trace Pb²⁺ based on CRISPR/Cas12a empowered electrochemical biosensor[J].Analytica Chimica Acta, 2023, 1263:341241.
[44] ONO A, TOGASHI H.Highly selective oligonucleotide-based sensor for mercury(II) in aqueous solutions[J].Angewandte Chemie International Edition, 2004, 43(33):4300-4302.
[45] KONG F G, WANG C X, PENG S C, et al.CRISPR-Hg:Rapid and visual detection of Hg²⁺ based on PCR coupled with CRISPR/Cas12a[J].Talanta, 2024, 277:126379.
[46] SHI K, CHEN J X, LI Y H, et al.Hg²⁺-triggered cascade strand displacement assisted CRISPR-Cas12a for Hg²⁺ quantitative detection using a portable glucose meter[J].Analytica Chimica Acta, 2023, 1278:341756.
[47] XU S Q, WANG S T, GUO L, et al.Nanozyme-catalysed CRISPR-Cas12a system for the preamplification-free colorimetric detection of lead ion[J].Analytica Chimica Acta, 2023, 1243:340827.
[48] YU Y, ZHANG Y, LI W H, et al.DNA nanocage confined DNAzyme for detection of lead ions coupled with CRISPR-Cas12a system[J].Chemical Engineering Journal, 2024, 480:148177.
[49] PAN J F, DENG F, LIU Z, et al.Construction of molecular logic gates using heavy metal ions as inputs based on catalytic hairpin assembly and CRISPR-Cas12a[J].Talanta, 2023, 255:124210.
[50] WEN J L, DENG H J, HE D G, et al.Dual-functional DNAzyme powered CRISPR-Cas12a sensor for ultrasensitive and high-throughput detection of Pb²⁺ in freshwater[J].Science of the Total Environment, 2024, 911:168708.
[51] YANG C Y, DU C Y, YUAN F Y, et al.CRISPR/Cas12a-derived ratiometric fluorescence sensor for high-sensitive Pb²⁺ detection based on CDs@ZIF-8 and DNAzyme[J].Biosensors and Bioelectronics, 2024, 251:116089.
[52] YU H M, LIANG G X, WANG H Y, et al.A MnO₂ nanosheet-mediated CRISPR/Cas12a system for the detection of organophosphorus pesticides in environmental water[J].Analyst, 2024, 149(3):729-734.
[53] TIAN F Y, JIANG L, WANG Z Y, et al.Mn²⁺-activated CRISPR-Cas12a strategy for fluorescence detection of the insecticide carbaryl[J].Sensors and Actuators B:Chemical, 2024, 398:134695.
[54] LI W, LI Y, ZHAO L D, et al.Triple-helix as a target converter for trace pesticide detection based on CRISPR/Cas12a-based ECL biosensor[J].Sensors and Actuators B:Chemical, 2024, 409:135599.
[55] ZHU L, ZHANG X M, YANG L, et al.Primer exchange reaction activation of CRISPR/Cas12a system to construct a versatile and label-free electrochemical sensing platform[J].Sensors and Actuators B:Chemical, 2025, 423:136791.
[56] YAN C, SHI G, CHEN J H.Fluorescent detection of two pesticides based on CRISPR-Cas12a and its application for the construction of four molecular logic gates[J].Journal of Agricultural and Food Chemistry, 2022, 70(39):12700-12707.
[57] WANG Y S, DU P F, WANG X H, et al.A novel HCR-CRISPR/Cas12a immunosensor for the sensitive detection of pesticide residues in animal-derived foods[J].Food Bioscience, 2024, 62:105131.
[58] PENG X G, HE Y, ZHAO J W, et al.CRISPR/Cas12a-mediated aptasensor based on tris-(8-hydroxyquinoline) aluminum microcrystals with crystallization-induced enhanced electrochemiluminescence for acetamiprid analysis[J].Analytical Chemistry, 2023, 95(26):10068-10076.
[59] COLLIAS D, BEISEL C L.CRISPR technologies and the search for the PAM-free nuclease[J].Nature Communications, 2021, 12(1):555.

Options

Outlines

模态框（Modal）标题

Abstract

Cite this article

References