# Simplified Protocol for the Purification of Native Cas Nucleases for DNA-Free Genome Editing

**Authors:** Margherita D’Amico, Flavia Angela Maria Maggiolini, Lucia Rosaria Forleo, Maria Francesca Cardone, Riccardo Velasco, Teodora Basile, Carlo Bergamini

PMC · DOI: 10.3390/mps8010016 · Methods and Protocols · 2025-02-07

## TL;DR

This paper introduces a simpler way to purify CRISPR nucleases for DNA-free genome editing, making the technology more accessible to labs without specialized equipment.

## Contribution

A simplified and accessible purification protocol for native Cas nucleases optimized for DNA-free genome editing.

## Key findings

- The simplified protocol uses streamlined affinity and ion exchange chromatography with minimal downstream processing.
- Purified ribonucleoprotein complexes showed efficient DNA target cleavage in vitro.
- The protocol enables broader access to DNA-free genome editing for under-equipped labs.

## Abstract

DNA-free genome editing by the direct delivery of CRISPR-associated nucleases has emerged as a promising technology due to its precision and reduced risk of off-target effects. However, existing purification protocols for native Cas proteins require the use of complex instrumentation, which limits their application. Here, we present a simplified protocol for the purification of native Cas9, Cas12RR and dCas9-VP64 nucleases optimized for DNA-free genome editing. Our approach leverages a streamlined affinity and ion exchange chromatography coupled with minimal downstream processing, ensuring a good yield and activity of the purified proteins. The in vitro analysis of the purified ribonucleoprotein complex demonstrated a good efficiency of DNA target cleavage. This simplified protocol increases the opportunity to adopt CRISPR technology, and enables broader access to DNA-free genome editing tools also for laboratories that are not specifically equipped for protein purification.

## Linked entities

- **Proteins:** cas9 (type II CRISPR RNA-guided endonuclease Cas9)

## Full-text entities

- **Diseases:** injury to people or property (MESH:C000719191)
- **Chemicals:** Kanamycin sulfate (MESH:D007612), Zinc (MESH:D015032), DTT (MESH:D004229), Silver (MESH:D012834), Glycerol (MESH:D005990), Ni-NTA (-), HEPES (MESH:D006531), NaCl (MESH:D012965), resin (MESH:D012116), Bis-Tris (MESH:C026272), nitrogen (MESH:D009584), SDS (MESH:D012967), acrylamide (MESH:D020106), Coomassie blue (MESH:C048139), Agarose (MESH:D012685), water (MESH:D014867), KCl (MESH:D011189), ice (MESH:D007053), EDTA (MESH:D004492), Imidazole (MESH:C029899), crystal violet (MESH:D005840), Ni (MESH:D009532), ethanol (MESH:D000431), Magnesium chloride hexahydrate (MESH:D015636), TCEP (MESH:C080938), SP (MESH:C000604007), ammonium acetate (MESH:C018824), methanol (MESH:D000432), His (MESH:D006639), Heparin (MESH:D006493), LDS (MESH:C028913), agar (MESH:D000362), salt (MESH:D012492)
- **Species:** Escherichia coli BL21 (strain) [taxon 511693], Escherichia coli BL21(DE3) (strain) [taxon 469008], Escherichia coli (E. coli, species) [taxon 562], Francisella tularensis subsp. novicida (subspecies) [taxon 264]
- **Mutations:** F565S, G548R, K611R, arginine-197-to-leucine
- **Cell lines:** pET-dCas9 — Homo sapiens (Human), Embryonic stem cell (CVCL_C6TU)

## Full text

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## Figures

6 figures with captions in the complete paper: https://tomesphere.com/paper/PMC11857876/full.md

## References

18 references — full list in the complete paper: https://tomesphere.com/paper/PMC11857876/full.md

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Source: https://tomesphere.com/paper/PMC11857876