CRISPR-Cas Systems: Mechanisms, Variants, and Biomedical Applications: A Comprehensive Review
Abstract
Objectives: This review aims to provide a comprehensive synthesis of the mechanisms, classification, emerging variants, and biomedical applications of CRISPR-Cas systems, while critically evaluating current limitations and future directions in genome editing.
Data Sources: Peer-reviewed literature was sourced from PubMed, Google Scholar, and institutional databases. Sources included primary research articles, systematic reviews, clinical trial reports, and authoritative commentary up till 2025.
Study Selection: Studies were selected based on relevance to CRISPR-Cas mechanism, classification, therapeutic application, and emerging technologies. Priority was given to high-impact journals in molecular biology, genetics, and clinical medicine.
Summary: CRISPR-Cas systems, originally characterized as adaptive immune mechanisms in prokaryotes, have been repurposed as highly precise genome engineering platforms. The two major system classes, defined by multi-protein versus single-effector complexes, encompass diverse types with distinct nuclease activities and target specificities. Key variants, including base editors, prime editors, and diagnostic platforms such as SHERLOCK and DETECTR, have substantially expanded functional capabilities. Biomedical applications span therapeutic gene correction in monogenic disorders, cancer immunotherapy, antiviral strategies, functional genomics, and disease modelling. Persistent challenges include off-target effects, delivery limitations, immune responses, and ethical concerns surrounding germline editing.
Conclusion: CRISPR-Cas technology represents a paradigm shift in molecular biology. Continued refinement of editing fidelity, delivery systems, and ethical frameworks will be essential for its safe and equitable clinical translation.
Keywords: CRISPR-Cas systems, genome editing, Cas9 nuclease, gene knockout, gene therapy, base editing, prime editing
Keywords:
CRISPR-Cas systems, Genome editing, Cas9 nuclease, Gene knockout, Gene therapy, Base editing, Prime editingDOI
https://doi.org/10.22270/jddt.v16i4.7692References
1. Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science. 2007;315(5819):1709-12. https://doi.org/10.1126/science.1138140 PMid:17379808
2. Marraffini LA. CRISPR-Cas immunity in prokaryotes. Nature. 2015;526(7571):55-61. https://doi.org/10.1038/nature15386 PMid:26432244
3. Grainy J, Garrett S, Graveley BR, Terns MP. CRISPR repeat sequences and relative spacing specify DNA integration by Pyrococcus furiosus Cas1 and Cas2. Nucleic Acids Res. 2019;47(14):7518-31. https://doi.org/10.1093/nar/gkz548 PMid:31219587 PMCid:PMC6698737
4. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2012;337(6096):816-21. https://doi.org/10.1126/science.1225829 PMid:22745249 PMCid:PMC6286148
5. Doudna JA, Charpentier E. The new frontier of genome engineering with CRISPR-Cas9. Science. 2014;346(6213):1258096. https://doi.org/10.1126/science.1258096 PMid:25430774
6. Liu SC, Feng YL, Sun XN, Chen RD, Liu Q, Xiao JJ, et al. Target residence of Cas9-sgRNA influences DNA double-strand break repair pathway choices in CRISPR/Cas9 genome editing. Genome Biol. 2022;23: 165. https://doi.org/10.1186/s13059-022-02736-5 PMid:35915475 PMCid:PMC9341079
7. Hsu PD, Lander ES, Zhang F. Development and applications of CRISPR-Cas9 for genome engineering. Cell. 2014;157(6):1262-78. https://doi.org/10.1016/j.cell.2014.05.010 PMid:24906146 PMCid:PMC4343198
8. Komor AC, Kim YB, Packer MS, Zuris JA, Liu DR. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature. 2016;533(7603):420-4. https://doi.org/10.1038/nature17946 PMid:27096365 PMCid:PMC4873371
9. Gupta RM, Musunuru K. Expanding the genetic editing toolkit: Zinc finger nucleases and TALENs. J Clin Invest. 2014;124(10):4154-61. https://doi.org/10.1172/JCI72992 PMid:25271723 PMCid:PMC4191047
10. Ghorui A, Baksi S. CRISPR/Cas9 technology: Challenges and drawbacks. J Adv Zool. 2023;44(S6):1965-71. https://doi.org/10.17762/jaz.v44iS6.2680
11. Vasiliou SK, Diamandis EP. CRISPR-Cas9 system: Opportunities and concerns. Clin Chem. 2016;62(10):1304-5. https://doi.org/10.1373/clinchem.2016.263186 PMid:27551006 PMCid:PMC12014773
12. Ishino Y, Shinagawa H, Makino K, Amemura M, Nakata A. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. J Bacteriol. 1987;169(12):5429-33. https://doi.org/10.1128/jb.169.12.5429-5433.1987 PMid:3316184 PMCid:PMC213968
13. Mojica FJ, Díez-Villaseñor C, García-Martínez J, Soria E. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J Mol Evol. 2005;60(2):174-82. https://doi.org/10.1007/s00239-004-0046-3 PMid:15791728
14. Shmakova AA, Shmakova OP, Karpukhina AA, Vassetzky YS. CRISPR/Cas: History and perspectives. Russ J Dev Biol. 2022; 53:272-82. https://doi.org/10.1134/S1062360422040075
15. Ishino Y, Krupovic M, Forterre P. History of CRISPR-Cas from encounter with a mysterious repeated sequence to genome editing technology. J Bacteriol. 2018;200(7):e00580-17. https://doi.org/10.1128/JB.00580-17 PMid:29358495 PMCid:PMC5847661
16. Yuan Z. From origin to the present: Establishment, mechanism, evolutions and biomedical applications of the CRISPR/Cas-based macromolecular system in brief. Molecules. 2025;30(4):947. https://doi.org/10.3390/molecules30040947 PMid:40005257 PMCid:PMC11858448
17. Rath D, Amlinger L, Rath A, Lundgren M. The CRISPR-Cas immune system: Biology, mechanisms and applications. Biochimie. 2015; 117:119-28. https://doi.org/10.1016/j.biochi.2015.03.025 PMid:25868999
18. Abudayyeh OO, Gootenberg JS, Konermann S, Joung J, Slaymaker IM, Cox DBT, et al. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science. 2016;353(6299): aaf5573. https://doi.org/10.1126/science.aaf5573 PMid:27256883 PMCid:PMC5127784
19. Makarova KS, Wolf YI, Alkhnbashi OS, Costa F, Shah SA, Saunders SJ, et al. Evolutionary classification of CRISPR-Cas systems: A burst of class 2 and derived variants. Nat Rev Microbiol. 2020;18(2):67-83. https://doi.org/10.1038/s41579-019-0299-x PMid:31857715 PMCid:PMC8905525
20. Nimkar S, Anand B. Cas3/I-C mediated target DNA recognition and cleavage during CRISPR interference are independent of the composition and architecture of Cascade surveillance complex. Nucleic Acids Res. 2020;48(5):2486-501. https://doi.org/10.1093/nar/gkaa021 PMid:31919507 PMCid:PMC7026661
21. Zheng Y, Li J, Wang B, Han J, Hao Y, Wang S, et al. Endogenous Type I CRISPR-Cas: From foreign DNA defense to prokaryotic engineering. Front Bioeng Biotechnol. 2020; 8:62. https://doi.org/10.3389/fbioe.2020.00062 PMid:32195227 PMCid:PMC7064716
22. Niewoehner O, Garcia-Doval C, Rostøl JT, Berk C, Schwede F, Bigler L, et al. Type III CRISPR-Cas systems produce cyclic oligoadenylate second messengers. Nature. 2017;548(7669):543-8. https://doi.org/10.1038/nature23267 PMid:28682306 PMCid:PMC5576860
23. Grüschow S, Adamson CS, White MF. Specificity and sensitivity of an RNA targeting type III CRISPR complex coupled with a NucC endonuclease effector. Nucleic Acids Res. 2021;49(22):13122-34. https://doi.org/10.1093/nar/gkab1098 PMid:34850140 PMCid:PMC8643669
24. Burmistrz M, Krakowski K, Krawczyk-Balska A. RNA-targeting CRISPR-Cas systems and their applications. Int J Mol Sci. 2020;21(3):1122. https://doi.org/10.3390/ijms21031122 PMid:32046217 PMCid:PMC7036953
25. Pinilla-Redondo R, Mayo-Muñoz D, Russel J, Garrett RA, Randau L, Sørensen SJ, et al. Type IV CRISPR-Cas systems are highly diverse and involved in competition between plasmids. Nucleic Acids Res. 2020;48(4):2000-12. https://doi.org/10.1093/nar/gkz1140 PMid:31828325 PMCid:PMC7038934
26. Newire E, Aydin A, Juma S, Enne VI, Roberts AP. Identification of a Type IV-A CRISPR-Cas system located exclusively on IncHI1B/IncFIB plasmids in Enterobacteriaceae. Front Microbiol. 2020; 11:1937. https://doi.org/10.3389/fmicb.2020.01937 PMid:32903441 PMCid:PMC7434947
27. Chen JS, Ma E, Harrington LB, Da Costa M, Tian X, Palefsky JM, et al. CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity. Science. 2018;360(6387):436-9. https://doi.org/10.1126/science.aar6245 PMid:29449511 PMCid:PMC6628903
28. Anders C, Niewoehner O, Duerst A, Jinek M. Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease. Nature. 2014;513(7519):569-73. https://doi.org/10.1038/nature13579 PMid:25079318 PMCid:PMC4176945
29. Stinson BM, Moreno AT, Walter JC, Loparo JJ. A mechanism to minimize errors during non-homologous end joining. Mol Cell. 2020;77(5):1-12. https://doi.org/10.1016/j.molcel.2019.11.018 PMid:31862156 PMCid:PMC7060804
30. Anzalone AV, Randolph PB, Davis JR, Sousa AA, Koblan LW, Levy JM, et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature. 2019;576(7785):149-57. https://doi.org/10.1038/s41586-019-1711-4 PMid:31634902 PMCid:PMC6907074
31. Kellner MJ, Koob JG, Gootenberg JS, Abudayyeh OO, Zhang F. SHERLOCK: Nucleic acid detection with CRISPR nucleases. Nat Protoc. 2019; 14:2986-3012. https://doi.org/10.1038/s41596-019-0210-2 PMid:31548639 PMCid:PMC6956564
32. Gootenberg JS, Abudayyeh OO, Kellner MJ, Joung J, Collins JJ, Zhang F. Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6. Science. 2017;356(6336):438-42. https://doi.org/10.1126/science.aaq0179 PMid:29449508 PMCid:PMC5961727
33. Sander JD, Joung JK. CRISPR-Cas systems for genome editing, regulation and targeting. Nat Biotechnol. 2014;32(4):347-55. https://doi.org/10.1038/nbt.2842 PMid:24584096 PMCid:PMC4022601
34. Frangoul H, Altshuler D, Cappellini MD, Chen YS, Domm J, Eustace BK, et al. CRISPR-Cas9 gene editing for sickle cell disease and β-thalassemia. N Engl J Med. 2021;384(3):252-60. https://doi.org/10.1056/NEJMoa2031054 PMid:33283989
35. Sanjana NE. Genome-scale CRISPR pooled screens. Anal Biochem. 2017; 532:95-9. https://doi.org/10.1016/j.ab.2015.06.021 PMid:26095399 PMCid:PMC4591182
36. Abbott TR, Dhamdhere G, Liu Y, Lin X, Goudy L, Zeng L, et al. Development of CRISPR as an antiviral strategy to combat SARS-CoV-2 and influenza. Cell. 2020;181(4):865-76. https://doi.org/10.1016/j.cell.2020.04.020 PMid:32353252 PMCid:PMC7189862
37. Fu Y, Foden JA, Khayter C, Maeder ML, Reyon D, Joung JK, et al. High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat Biotechnol. 2013;31(9):822-6. https://doi.org/10.1038/nbt.2623 PMid:23792628 PMCid:PMC3773023
38. Lino CA, Harper JC, Carney JP, Timlin JA. Delivering CRISPR: A review of the challenges and approaches. Drug Deliv. 2018;25(1):1234-57. https://doi.org/10.1080/10717544.2018.1474964 PMid:29801422 PMCid:PMC6058482
39. Baltimore D, Berg P, Botchan M, Carroll D, Charo RA, Church G, et al. A prudent path forward for genomic engineering and germline gene modification. Science. 2015;348(6230):36-8. https://doi.org/10.1126/science.aab1028 PMid:25791083 PMCid:PMC4394183
40. Gonzalez-Avila LU, Vega-López JM, Pelcastre-Rodríguez LI, Cabrero-Martínez OA, Hernández-Cortez C, Castro-Escarpulli G. The challenge of CRISPR-Cas toward bioethics. Front Microbiol. 2021; 12:657981. https://doi.org/10.3389/fmicb.2021.657981 PMid:34122373 PMCid:PMC8195329
41. Lorenzo D, Esquerda M, Palau F, Cambra FJ, Grup Investigació en Bioètica. Ethics and genomic editing using the CRISPR-Cas9 technique: Challenges and conflicts. NanoEthics. 2022; 16:313-21. https://doi.org/10.1007/s11569-022-00425-y
42. Biswas I. Ethical dimensions and societal implications: Ensuring the social responsibility of CRISPR technology. Front Genome Ed. 2025; 7:1593172. https://doi.org/10.3389/fgeed.2025.1593172 PMid:40909132 PMCid:PMC12405698
43. Dominguez AA, Lim WA, Qi LS. Beyond editing: Repurposing CRISPR-Cas9 for precision genome regulation and interrogation. Nat Rev Mol Cell Biol. 2016;17(1):5-15. https://doi.org/10.1038/nrm.2015.2 PMid:26670017 PMCid:PMC4922510
44. Jeong SH, Lee HJ, Lee SJ. Recent advances in CRISPR-Cas technologies for synthetic biology. J Microbiol. 2023; 61:13-36. https://doi.org/10.1007/s12275-022-00005-5 PMid:36723794 PMCid:PMC9890466
Published
Abstract Display: 28
PDF Downloads: 15
PDF Downloads: 2 How to Cite
Issue
Section
Copyright (c) 2026 Augustine Chinedu Ihim, Kelechi Caroline Obi, Patrick Chinedu Obi, Ini Edeh, Donatus F.N. Ozuruoke , Tochukwu Anthony Ikwelle

This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
Authors who publish with this journal agree to the following terms:
- Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0). that allows others to share the work with an acknowledgment of the work's authorship and initial publication in this journal.
- Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgment of its initial publication in this journal.
- Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).

.