An efficient CRISPR-based strategy to insert small and large fragments of DNA using short homology arms

Elife. 2019 Nov 1:8:e51539. doi: 10.7554/eLife.51539.


We previously reported a CRISPR-mediated knock-in strategy into introns of Drosophila genes, generating an attP-FRT-SA-T2A-GAL4-polyA-3XP3-EGFP-FRT-attP transgenic library for multiple uses (Lee et al., 2018a). The method relied on double stranded DNA (dsDNA) homology donors with ~1 kb homology arms. Here, we describe three new simpler ways to edit genes in flies. We create single stranded DNA (ssDNA) donors using PCR and add 100 nt of homology on each side of an integration cassette, followed by enzymatic removal of one strand. Using this method, we generated GFP-tagged proteins that mark organelles in S2 cells. We then describe two dsDNA methods using cheap synthesized donors flanked by 100 nt homology arms and gRNA target sites cloned into a plasmid. Upon injection, donor DNA (1 to 5 kb) is released from the plasmid by Cas9. The cassette integrates efficiently and precisely in vivo. The approach is fast, cheap, and scalable.

Keywords: CRIMIC; CRISPR; D. melanogaster; drop-in; drosophila; genetics; genomics; homologous recombination.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Clustered Regularly Interspaced Short Palindromic Repeats*
  • DNA / genetics
  • DNA, Single-Stranded / genetics
  • Drosophila
  • Gene Knock-In Techniques / methods*
  • Homologous Recombination*
  • Mutagenesis, Insertional / methods*


  • DNA, Single-Stranded
  • DNA