Research Progress on Nucleic Acid Detection and Genome Editing of CRISPR/Cas12 System

Overview

Journal Mol Biol Rep

Specialty Molecular Biology

Date 2023 Jan 17

PMID 36648696

Authors

Yanhua Yang

Dandan Wang

Peng Lu

Shangshang Ma

Keping Chen

Affiliations

Soon will be listed here.

Abstract

Purpose: This work characterizes the applications of CRISPR/Cas12 system, including nucleic acid detection, animal, plant and microbial genome editing.

Methods: The literature on CRISPR/Cas12 system was collected and reviewed.

Results: CRISPR/Cas system is an acquired immune system derived from bacteria and archaea, which has become the most popular technology around the world because of its outstanding contribution in genome editing. Type V CRISPR/Cas systems are distinguished by a single RNA-guided RuvC nuclease domain with single effector molecule. Cas12a, the first reported type V CRISPR/Cas system, targets double-stranded DNA (dsDNA) adjacent to PAM sequences and trans-cleaves single-stranded DNA (ssDNA). We present the applications of CRISPR/Cas12 system for nucleic acid detection and genome editing in animals, plants and microorganisms. Furthermore, this review also summarizes the applications of other Cas12 proteins, such as Cas12b, Cas12c, Cas12d, and so on, which further widen the application prospects of CRISPR/Cas12 system.

Conclusions: Knowledge of the applications of CRISPR/Cas12 system is necessary for improving the understanding of the functional diversity of CRISPR/Cas12 system and also provides significant references for further research and utilization of CRISPR/Cas12 in other new fields.

Citing Articles

Important applications of DNA nanotechnology combined with CRISPR/Cas systems in biotechnology.

Huang Y, Chen Z, Huang H, Ding S, Zhang M RSC Adv. 2025; 15(8):6208-6230.

PMID: 40008014 PMC: 11851101. DOI: 10.1039/d4ra08325c.

Advancements in genome editing tools for genetic studies and crop improvement.

Ahmadikhah A, Zarabizadeh H, Nayeri S, Abbasi M Front Plant Sci. 2025; 15:1370675.

PMID: 39963359 PMC: 11830681. DOI: 10.3389/fpls.2024.1370675.

Research Status of Clustered Regulary Interspaced Short Palindromic Repeats Technology in the Treatment of Human Papillomavirus (HPV) Infection Related Diseases.

Tang M Cancer Control. 2025; 32():10732748241300654.

PMID: 39834176 PMC: 11748153. DOI: 10.1177/10732748241300654.

An MSRE-Assisted Glycerol-Enhanced RPA-CRISPR/Cas12a Method for Methylation Detection.

Lu Z, Ye Z, Li P, Jiang Y, Han S, Ma L Biosensors (Basel). 2024; 14(12).

PMID: 39727873 PMC: 11674872. DOI: 10.3390/bios14120608.

CRISPR/Cas system and its application in the diagnosis of animal infectious diseases.

Rasool H, Chen Q, Gong X, Zhou J FASEB J. 2024; 38(24):e70252.

PMID: 39726403 PMC: 11671863. DOI: 10.1096/fj.202401569R.

References

Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S . CRISPR provides acquired resistance against viruses in prokaryotes. Science. 2007; 315(5819):1709-12. DOI: 10.1126/science.1138140. View

Makarova K, Wolf Y, Iranzo J, Shmakov S, Alkhnbashi O, Brouns S . Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants. Nat Rev Microbiol. 2019; 18(2):67-83. PMC: 8905525. DOI: 10.1038/s41579-019-0299-x. View

Leung R, Cheng Q, Wu Z, Khan G, Liu Y, Xia H . CRISPR-Cas12-based nucleic acids detection systems. Methods. 2021; 203:276-281. DOI: 10.1016/j.ymeth.2021.02.018. View

Zetsche B, Gootenberg J, Abudayyeh O, Slaymaker I, Makarova K, Essletzbichler P . Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell. 2015; 163(3):759-71. PMC: 4638220. DOI: 10.1016/j.cell.2015.09.038. View

Fonfara I, Richter H, Bratovic M, Le Rhun A, Charpentier E . The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA. Nature. 2016; 532(7600):517-21. DOI: 10.1038/nature17945. View

Li S, Cheng Q, Liu J, Nie X, Zhao G, Wang J . CRISPR-Cas12a has both cis- and trans-cleavage activities on single-stranded DNA. Cell Res. 2018; 28(4):491-493. PMC: 5939048. DOI: 10.1038/s41422-018-0022-x. View

Yang H, Gao P, Rajashankar K, Patel D . PAM-Dependent Target DNA Recognition and Cleavage by C2c1 CRISPR-Cas Endonuclease. Cell. 2016; 167(7):1814-1828.e12. PMC: 5278635. DOI: 10.1016/j.cell.2016.11.053. View

Shmakov S, Abudayyeh O, Makarova K, Wolf Y, Gootenberg J, Semenova E . Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems. Mol Cell. 2015; 60(3):385-97. PMC: 4660269. DOI: 10.1016/j.molcel.2015.10.008. View

Harrington L, Burstein D, Chen J, Paez-Espino D, Ma E, Witte I . Programmed DNA destruction by miniature CRISPR-Cas14 enzymes. Science. 2018; 362(6416):839-842. PMC: 6659742. DOI: 10.1126/science.aav4294. View

10.

Chen J, Ma E, Harrington L, Da Costa M, Tian X, Palefsky J . CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity. Science. 2018; 360(6387):436-439. PMC: 6628903. DOI: 10.1126/science.aar6245. View

11.

Li S, Cheng Q, Wang J, Li X, Zhang Z, Gao S . CRISPR-Cas12a-assisted nucleic acid detection. Cell Discov. 2018; 4:20. PMC: 5913299. DOI: 10.1038/s41421-018-0028-z. View

12.

Li L, Li S, Wu N, Wu J, Wang G, Zhao G . HOLMESv2: A CRISPR-Cas12b-Assisted Platform for Nucleic Acid Detection and DNA Methylation Quantitation. ACS Synth Biol. 2019; 8(10):2228-2237. DOI: 10.1021/acssynbio.9b00209. View

13.

Teng F, Guo L, Cui T, Wang X, Xu K, Gao Q . CDetection: CRISPR-Cas12b-based DNA detection with sub-attomolar sensitivity and single-base specificity. Genome Biol. 2019; 20(1):132. PMC: 6604390. DOI: 10.1186/s13059-019-1742-z. View

14.

Wang B, Wang R, Wang D, Wu J, Li J, Wang J . Cas12aVDet: A CRISPR/Cas12a-Based Platform for Rapid and Visual Nucleic Acid Detection. Anal Chem. 2019; 91(19):12156-12161. DOI: 10.1021/acs.analchem.9b01526. View

15.

Xia X, Ma B, Zhang T, Lu Y, Khan M, Hu Y . G-Quadruplex-Probing CRISPR-Cas12 Assay for Label-Free Analysis of Foodborne Pathogens and Their Colonization . ACS Sens. 2021; 6(9):3295-3302. DOI: 10.1021/acssensors.1c01061. View

16.

Wang Y, Li J, Li S, Zhu X, Wang X, Huang J . LAMP-CRISPR-Cas12-based diagnostic platform for detection of Mycobacterium tuberculosis complex using real-time fluorescence or lateral flow test. Mikrochim Acta. 2021; 188(10):347. DOI: 10.1007/s00604-021-04985-w. View

17.

Zhang Y, Chen M, Liu C, Chen J, Luo X, Xue Y . Sensitive and rapid on-site detection of SARS-CoV-2 using a gold nanoparticle-based high-throughput platform coupled with CRISPR/Cas12-assisted RT-LAMP. Sens Actuators B Chem. 2021; 345:130411. PMC: 8257267. DOI: 10.1016/j.snb.2021.130411. View

18.

Bai L, Wang L, Huang S, Bai R, Lv X, Sun L . Rapid, Visual, and Sequence-Specific Detection of in Egg Liquid with vis-NEAA, a CRISPR/Cas12 Empowered New Strategy. J Agric Food Chem. 2022; 70(7):2401-2409. DOI: 10.1021/acs.jafc.1c06715. View

19.

Ding R, Long J, Yuan M, Zheng X, Shen Y, Jin Y . CRISPR/Cas12-Based Ultra-Sensitive and Specific Point-of-Care Detection of HBV. Int J Mol Sci. 2021; 22(9). PMC: 8125043. DOI: 10.3390/ijms22094842. View

20.

Ali Z, Aman R, Mahas A, Rao G, Tehseen M, Marsic T . iSCAN: An RT-LAMP-coupled CRISPR-Cas12 module for rapid, sensitive detection of SARS-CoV-2. Virus Res. 2020; 288:198129. PMC: 7434412. DOI: 10.1016/j.virusres.2020.198129. View