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CRISPR/Cas Systems and Genome Editing—3rd Edition
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CRISPR/Cas Systems and Genome Editing—3rd Edition

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: 20 February 2026 | Viewed by 3255

Special Issue Editor

Dr. Dmitry Karpov

E-Mail Website
Guest Editor
Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
Interests: CRISPR/Cas; genome editing; yeast; intracellular proteolysis; transcription regulation; bacillii; stress responses
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The harnessing of CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated genes) systems for the detection, chemical modification, and sequence editing of nucleic acids has dramatically changed many fields of fundamental science, biotechnology, and biomedicine. It is thus no wonder that the inventors of the technology, Emmanuelle Charpentier and Jennifer Doudna, were awarded the Nobel Prize in 2020. Natural CRISPR/Cas systems are well suited to disrupting coding and non-coding sequences in the genome, are much less effective at distinguishing and editing sequences with single-nucleotide differences, and are prone to recognizing similar sequences in the genome. Therefore, further exploration of the CRISPR/Cas field continues both to find new genome and epigenome editors, and to engineer known editors to overcome their shortcomings to make their applications more efficient, predictable, and safe. Notably, in late 2023, the FDA approved a cellular product obtained by CRISPR/Cas9-based genome editing—CasgevyTM—for the treatment of sickle cell disease. Thus, ten years after the first application of the CRISPR/Cas9 system for genome editing in mammalian cells, the first CRISPR/Cas9-based cellular product for curing human disease marked the beginning of the era of CRISPR/Cas therapies for humans.

The aim of this Special Issue is to gather knowledge on the current state of the rapidly growing field of CRIPSR/Cas systems and other genome editing tools in fundamental science, biotechnology, and biomedicine.

Dr. Dmitry Karpov
Guest Editor

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Keywords

  • CRISPR/Cas
  • bacterial argonauts
  • transcription regulation
  • genome editing
  • genome editing tools

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Published Papers (3 papers)

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Research

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19 pages, 1877 KB  
Article
PAM-Independent Cas12a Detection of Specific LAMP Products by Targeting Amplicon Loops
by Konstantin G. Ptitsyn, Leonid K. Kurbatov, Svetlana A. Khmeleva, Daria D. Morozova, Olga S. Timoshenko, Elena V. Suprun, Sergey P. Radko and Andrey V. Lisitsa
Int. J. Mol. Sci. 2025, 26(16), 8014; https://doi.org/10.3390/ijms26168014 - 19 Aug 2025
Viewed by 951
Abstract
A straightforward approach is suggested to selectively recognize specific products of loop-mediated isothermal amplification (LAMP) with the Cas12a nuclease without a need for a protospacer adjacent motif (PAM) in the sequence of LAMP amplicons (LAMPlicons). This strategy is based on the presence of [...] Read more.
A straightforward approach is suggested to selectively recognize specific products of loop-mediated isothermal amplification (LAMP) with the Cas12a nuclease without a need for a protospacer adjacent motif (PAM) in the sequence of LAMP amplicons (LAMPlicons). This strategy is based on the presence of single-stranded DNA loops in LAMPlicons and the ability of Cas12a to be trans-activated via the binding of guide RNA (gRNA) to single-stranded DNA in the absence of PAM. The approach feasibility is demonstrated on Clavibacter species—multiple bacterial plant pathogens that cause harmful diseases in agriculturally important plants. For Clavibacter species, the detection sensitivity of the developed PAM-independent LAMP/Cas12a system was determined by that of LAMP. The overall detection selectivity was enhanced by the Cas12a analysis of LAMPlicons. It was shown that the LAMP/Cas12a detection system can be fine-tuned by carefully designing gRNA to selectively distinguish C. sepedonicus from other Clavibacter species based on single nucleotide substitutions in the targeted LAMPlicon loop. The suggested loop-based Cas12a analysis of LAMPlicons was compatible with the format of a single test tube assay with the option of naked-eye detection. The findings broaden the palette of approaches to designing PAM-independent LAMP/Cas12a detection systems with potential for on-site testing. Full article
(This article belongs to the Special Issue CRISPR/Cas Systems and Genome Editing—3rd Edition)
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18 pages, 2970 KB  
Article
Prime Editing Modification with FEN1 Improves F508del Variant Editing in the CFTR Gene in Airway Basal Cells
by Olga V. Volodina, Anna G. Demchenko, Arina A. Anuchina, Oxana P. Ryzhkova, Valeriia A. Kovalskaya, Ekaterina V. Kondrateva, Ekaterina V. Artemova, Vyacheslav Y. Tabakov, Maxim A. Ignatov, Natalia Y. Vorobyeva, Andreyan N. Osipov, Alexander V. Lavrov and Svetlana A. Smirnikhina
Int. J. Mol. Sci. 2025, 26(16), 7943; https://doi.org/10.3390/ijms26167943 - 18 Aug 2025
Viewed by 1839
Abstract
Prime editing is a promising approach for correcting pathogenic variants, but its efficiency remains variable across genomic contexts. Here, we systematically evaluated 12 modifications of the PEmax system for correcting the CFTR F508del pathogenic variant that caused cystic fibrosis in patient-derived airway basal [...] Read more.
Prime editing is a promising approach for correcting pathogenic variants, but its efficiency remains variable across genomic contexts. Here, we systematically evaluated 12 modifications of the PEmax system for correcting the CFTR F508del pathogenic variant that caused cystic fibrosis in patient-derived airway basal cells. We chose EXO1 and FEN1 nucleases to improve the original system. While all tested variants showed comparatively low efficiency in this AT-rich genomic region, 4-FEN modification demonstrated significantly improved editing rates (up to 2.13 fold) compared to standard PEmax. Our results highlight two key findings: first, the persistent challenge of AT-rich target sequence correction even with optimized editors, and second, the performance of 4-FEN suggests its potential value for other genomic targets. Full article
(This article belongs to the Special Issue CRISPR/Cas Systems and Genome Editing—3rd Edition)
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Review

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32 pages, 768 KB  
Review
Pig Genome Editing for Agriculture: Achievements and Challenges
by Elena Mikhaylova, Emil Khusnutdinov, Mikhail Terekhov, Daniil Pozdeev and Oleg Gusev
Int. J. Mol. Sci. 2025, 26(24), 12140; https://doi.org/10.3390/ijms262412140 - 17 Dec 2025
Abstract
The remaining problems in pig farming may no longer be solved with traditional methods. The search for genetic variants associated with desired characteristics and involvement of animals with superior genetics in breeding programs is rarely effective for polygenic traits and pleiotropic genes. The [...] Read more.
The remaining problems in pig farming may no longer be solved with traditional methods. The search for genetic variants associated with desired characteristics and involvement of animals with superior genetics in breeding programs is rarely effective for polygenic traits and pleiotropic genes. The lack of diversity in the germplasm also limits the use of breeding, but some beneficial mutations that did not occur naturally can be introduced manually via genome editing methods. Mutations discovered in other species, such as cattle, can be reproduced in pigs. Traits that were previously pursued for centuries might be achieved by genome editing in a few years. Enormous progress has been made in producing pigs resistant to viruses and in increasing meat productivity and quality. But there are still pressing problems such as lameness and damaging behaviors that probably cannot be solved without genome editing techniques. Their wider application is complicated by the requirement for large amounts of biomaterial, surgical manipulations and cell culture, as well as by the shift towards biomedical research. This review concentrates on the main achievements and challenges in pig agricultural genetics that can be addressed by genome editing. Full article
(This article belongs to the Special Issue CRISPR/Cas Systems and Genome Editing—3rd Edition)
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