CRISPR-based gene editing in mammalian cells is a powerful research tool which has demonstrated efficient site-specific gene modifications and is showing promise as a therapeutic for patients with genetic diseases. Multiple different CRISPR systems have been identified, each with its own target DNA recognition sequence, expanding the editable mammalian genome. It is also now appreciated that chemically modified nucleic acids can substitute for unmodified nucleotides in guide RNAs, providing protection from exonuclease degradation and improving gene editing efficiency. CRISPR-Cpf1 unlike CRISPR-Cas9, has a substantially lower propensity for off-target genomic cleavage, making it a preferred gene editing system for many applications. Here we provide a detailed protocol for use of CRISPR-Cpf1 and chemically modified guide RNAs in cell lines, outlining the steps from designing guide RNAs to a target gene of interest, delivery and expression in cells, and analysis of gene editing events.
Keywords: CRISPR-Cpf1; Cas12a; Chemically modified nucleic acid; Gene editing; Guide RNA; Surveyor nuclease assay; Synthetic CRISPR RNA.