Operating CRISPR/Cas12a in a complex nucleic acid sequence background

Since their discovery, CRISPR-Cas systems have been widely applied in areas ranging from genome editing to biosensing, owing to their specific, RNA-guided target recognition. Their performance in complex biological environments has been extensively studied, particularly to optimize guide RNA (gRNA) design and minimize off-target cleavage. Here, we focus on the kinetic inhibition of the interaction between Cas12a-a Class 2, Type V effector-and its target, caused by interference from non-cognate background nucleic acids. This effect is particularly relevant for sensing applications in complex mixtures or cellular contexts, where genome- and transcriptome-derived sequences may impede CRISPR-Cas activity. Using in vitro assays under defined conditions, we systematically examine the influence of background single-stranded RNA and double-stranded DNA (dsDNA) on reaction kinetics. We find that both the purine-to-pyrimidine ratio and the GC content of the gRNA seed region significantly affect kinetic inhibition by background polynucleotides. gRNAs with low GC content and a high purine fraction in the seed region were least affected by background sequences. A gRNA with high uracil content in the seed region exhibited particularly strong inhibition in the presence of a dsDNA background. Experiments with dCas12a-based gene activation in living cells indicate that our in vitro findings may also be relevant for in vivo applications.