A One-Step Method for Efficient Purification of Functional Cas9 Protein

The CRISPR/Cas9 system is a cornerstone technology in genome editing. Delivery of pre-assembled Cas9 ribonucleoprotein (RNP) complexes exhibits distinct advantages, including reduced off-target effects and lower immunogenicity. Conventional methods for purifying Cas9 protein typically involve multi-step chromatography and the cleavage of fusion tag, which are time-consuming and result in diminished yields. In this study, we present a simplified, one-step purification strategy for functional Streptococcus pyogenes Cas9 (SpCas9) using the ubiquitin (Ub) fusion system in Escherichia coli. The N-terminal Ub fusion not only improves protein solubility but also facilitates high-yield production of the His-Ub-Cas9 fusion protein. Importantly, the Ub tag does not require proteolytic removal during purification, allowing direct one-step purification of the fusion protein via nickel-affinity chromatography. The purified His-Ub-Cas9 retains robust DNA cleavage activity in vivo, as validated in zebrafish embryos. This protocol greatly simplifies the production of functional Cas9 protein, facilitating its broad application in genome editing. Key features • The Ub fusion system enables single-step purification of Cas9 in E. coli using Ni-NTA chromatography, eliminating the protease cleavage step. • This method yields over 8 mg/L of high purity (>95%), functional Cas9 protein, suitable for direct use in RNP complex assembly. • The purified His-Ub-Cas9 maintains high genome editing activity in vivo, as demonstrated in zebrafish embryos.