Poster Presentation 39th Annual Lorne Genome Conference 2018

Efficient homology-directed repair using single-stranded DNA templates (#120)

Michel Cannieux 1
  1. Integrated DNA Technologies (IDT), Baulkham Hills, NSW, Australia

Homology-directed repair (HDR) is a valuable tool for genome editing when combined with the CRISPR/Cas9 system. HDR with a targeted repair template after a double-stranded DNA (dsDNA) break enables the generation of knock-in strains or animal models, including insertion of reporter genes or the introduction of specific mutations. Double-stranded DNA can be used as a repair template, however knock-in efficiency can be low. Further, linear double-stranded templates can insert at any break present in the genome, including off-target sites. Several recent studies have demonstrated that single-stranded DNAs (ssDNAs) are superior HDR templates. ssDNAs can be obtained as synthetic oligonucleotides or made from longer dsDNA templates. Here, we report optimal conditions to make point mutations and epitope tag insertions using IDT Ultramer® Oligonucleotide ssDNA HDR templates delivered with a Cas9 ribonucleoprotein complex. Investigations of strand choice (targeting vs. non-targeting strand), homology arm length, strand symmetry, Cas9 variants (wildtype, nickase, HiFi), chemical modification, and Ultramer purification conditions are shown and a rule set for HDR using oligonucleotide-based templates of 200 bases or less is presented. IDT Megamer™ ssDNA fragments are used for insertions of 200-2000 bases. Initial experiments suggest that these long ssDNA HDR templates show similar advantages and behavior as their shorter oligonucleotide counterparts. Furthermore, Megamer ssDNA fragments injected with Cas9 ribonucleoprotein complexes into mouse zygotes successfully produce correctly targeted alleles in live offspring.