From Hack and Tip to AI Precision: the Evolution of CRISPR gRNA Design Invited
DOI:
https://doi.org/10.70099/BJ/2025.02.03.15Keywords:
CRISPR, gRNA Design, Genome Editing, Artificial Intelligence, Deep Learning, Machine Learning, Computational Biology, Bioinformatics, CRISPR-Cas9Abstract
The CRISPR/Cas9 technology is a game-changer in the field of molecular genetics, enabling the first rapid and efficient genomic editing in virtually any organism. The gRNA is a crucial factor in the technology that determines editing efficiency and specificity. The field has progressively moved away from empirical recipes towards computer-aided precision-engineering methodologies based on artificial intelligence (AI) and deep learning over the last decade. This review discusses important breakthroughs in gRNA design, remaining limitations, and prospects, with an emphasis on translational and biotechnological applications.
References
1. Chuai G, Ma H, Yan J, et al. DeepCRISPR: optimized CRISPR guide RNA design by deep learning. Genome Biol. 2018;19(1). https://doi.org/10.1186/s13059-018-1459-4
2. Mohr SE, Hu Y, Ewen-Campen B, et al. CRISPR guide RNA design for research applications. FEBS J. 2016;283(17):3232–3238. https://doi.org/10.1111/febs.13777
3. Hoberecht L, Perampalam P, Lun A, Fortin J. A comprehensive Bioconductor ecosystem for the design of CRISPR guide RNAs. Nat Commun. 2022;13(1). https://doi.org/10.1038/s41467-022-34320-7
4. Motoche-Monar C, Ordoñez JE, Chang O, & Gonzales-Zubiate FA (2023). gRNA Design: How Its Evolution Impacted on CRISPR/Cas9 Systems Refinement. Biomolecules, 13(12), 1698. https://doi.org/10.3390/biom13121698
5. Pausch P, Al-Shayeb B, Banfield JF, Doudna JA. CRISPR–CasΦ from huge phages is a hypercompact genome editor. Science. 2022;369(6511):333–337. https://doi.org/10.1126/science.abf0858
6. Nuñez JK, Chen J, Pommier GC, et al. Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing. Cell. 2021;184(9):2503–2519.e17. https://doi.org/10.1016/j.cell.2021.03.025
7. Nijkamp JF, Woldringh G, Mahfouz A. Foundation models for DNA and protein engineering. Nat Biotechnol. 2024;42(5):567–572. https://doi.org/10.1038/s41587-024-01945-3
8. Manguy J, Glover N, Calo E, Jaganathan V. Kingdom-Wide CRISPR Guide Design with ALLEGRO. bioRxiv. 2025. https://doi.org/10.1101/2025.02.13.638206
Published
How to Cite
License

This work is licensed under a Creative Commons Attribution 4.0 International License.
Authors who publish with BioNatura Journal agree to the following terms: Authors retain copyright and grant the BioNatura Institutional Publishing Consortium (BIPC) right of first publication with the work simultaneously licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0). This allows others to share the work with an acknowledgment of the work's authorship and initial publication in this journal.This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.