Efficient CRISPR/Cas9 mediated large insertions using long single-stranded oligonucleotide donors in C. elegans

Highly efficient generation of deletions, substitutions, and small insertions (up to similar to 150 bp) into the Caenorhabditis elegans genome by CRISPR/Cas9 has been facilitated by the use of single-stranded oligonucleotide donors as repair templates. However, insertion of larger sequences such as fluorescent markers and other functional domains remains challenging due to uncertainty of optimal performance between single-stranded or double-stranded repair templates and labor-intensive as well as inefficient protocols for their preparations. Here, we simplify the generation of long ssDNA as donors in CRISPR/Cas9. High yields of ssDNA can be rapidly generated using a standard PCR followed by a single enzymatic digest with lambda exonuclease. Comparison of long ssDNA donors obtained using this method to dsDNA demonstrates orders of magnitude increased insertion frequency for ssDNA donors. This can be leveraged to simultaneously generate multiple large insertions as well as successful edits without the use of selection or co-conversion (co-CRISPR) markers when necessary. Our approach complements the CRISPR/Cas9 toolkit for C. elegans to enable highly efficient insertion of longer sequences with a simple, standardized, and labor-minimal protocol.

Automated summary

Highly efficient insertion of deletions, substitutions, and small insertions (up to 150 bp) into the Caenorhabditis elegans genome using CRISPR/Cas9 has been made easier with the use of single-stranded oligonucleotide donors. However, inserting larger sequences such as fluorescent markers and functional domains remains challenging due to uncertainty and labor-intensive protocols. In this study, a simplified method for generating long single-stranded DNA (ssDNA) donors in CRISPR/Cas9 is presented, which shows significantly increased insertion frequency compared to double-stranded DNA (dsDNA) donors. This approach complements the existing CRISPR/Cas9 toolkit for C. elegans and enables efficient insertion of longer sequences with a simple and standardized protocol.