Enhancement of CRISPR/Cas12a <i>trans</i>-cleavage activity using hairpin DNA reporters
Marianna Rossetti, Rosa Merlo, Neda Bagheri, Danila Moscone, Anna Valenti, Aakash Saha, Pablo Arantes, Rudy Ippodrino, Francesco Ricci, Ida Treglia, Elisabetta Delibato, John van der Oost, Giulia Palermo, Giuseppe Perugino, Alessandro Porchetta
Abstract
The RNA programmed non-specific (trans) nuclease activity of CRISPR-Cas Type V and VI systems has opened a new era in the field of nucleic acid-based detection. Here, we report on the enhancement of trans-cleavage activity of Cas12a enzymes using hairpin DNA sequences as FRET-based reporters. We discover faster rate of trans-cleavage activity of Cas12a due to its improved affinity (Km) for hairpin DNA structures, and provide mechanistic insights of our findings through Molecular Dynamics simulations. Using hairpin DNA probes we significantly enhance FRET-based signal transduction compared to the widely used linear single stranded DNA reporters. Our signal transduction enables faster detection of clinically relevant double stranded DNA targets with improved sensitivity and specificity either in the presence or in the absence of an upstream pre-amplification step.