Live-cell imaging reveals the trade-off between target search flexibility and efficiency for Cas9 and Cas12a

Abstract

AbstractCRISPR-Cas systems have widely been adopted as genome editing tools, with two frequently employed Cas nucleases beingSpyCas9 andLbCas12a. Although both nucleases use RNA guides to find and cleave target DNA sites, the two enzymes differ in terms of protospacer-adjacent motif (PAM) requirements, guide architecture and cleavage mechanism. In the last years, rational engineering led to the creation of PAM-relaxed variantsSpRYCas9 and impLbCas12a to broaden the targetable DNA space. By employing their catalytically inactive variants (dCas9/dCas12a), we quantified how the protein-specific characteristics impact the target search process. To allow quantification, we fused these nucleases to the photoactivatable fluorescent protein PAmCherry2.1 and performed single-particle tracking in cells ofEscherichia coli. From our tracking analysis, we derived kinetic parameters for each nuclease with a non-targeting RNA guide, strongly suggesting that interrogation of DNA byLbdCas12a variants proceeds faster than that ofSpydCas9. In the presence of a targeting RNA guide, both simulations and imaging of cells confirmed thatLbdCas12a variants are faster and more efficient in finding a specific target site. Our work demonstrates the trade-off of relaxing PAM requirements inSpydCas9 andLbdCas12a using a powerful framework, which can be applied to other nucleases to quantify their DNA target search.