Welcome to CRISPR fly design

Check out our new preprint describing efficient Cas12a gene editing in Drosophila:

Multiplexed conditional gene editing with Cas12a in Drosophila

CRISPR genome engineering allows the introduction of targeted genome alterations with unprecedented ease and precision. We have been among the first groups to adopt the CRISPR/Cas system for genome engineering in the model organism Drosophila melanogaster. Our approach has focused on the use of transgenic CRISPR components, which mediate targeted mutagenesis with remarkably high efficiency. At the heart of our system are transgenic cas9 fly lines expressing the RNA-guided endonuclease Cas9 under ubiquitous or germline specific promoters or linked to the Gal4/UAS system for expression in any tissue. These are complemented with optimised sgRNA expression vectors containing different U6 or UAS promoters or tRNA-sgRNA arrays. Plasmids encoding target specific gRNAs can be injected into cas9 embryos or integrated into the genome and crossed to cas9 strains. By choosing appropriate tools it is possible to generate loss-of-function mutations in essential or non-essential genes in a germline restricted, ubiquitous or tissue-specific fashion. It is also possible to introduce designer mutations by homology directed repair, ranging from single nucleotide changes to GFP knock-ins. Publications describing our CRISPR/Cas tools are available here, here and here.

The idea behind the creation of this website was to establish a platform to facilitate collaboration, sharing and open access. We launched CRISPRflydesign in August 2013, shortly after starting to send our transgenic cas9 lines to interested labs. The website allowed us to describe unpublished materials and share experiences with their use. Many of our key results have been available here many months before formal publication. For the same reason we have also posted preprints of all our primary papers on the Biorxiv preprint server. You can find a list of our publications along with an open access link below.


Port F, Strein C, Stricker M, Rauscher B, Heigwer F, Zhou J, Beyersdörffer C, Frei J, Hess A, Kern K, Lange L, Langner N, Malamud R, Pavlović B, Rädecke K, Schmitt L, Voos L, Valentini E, Boutros M. A large-scale resource for tissue-specific CRISPR mutagenesis in Drosophila.
eLife. 2020 Feb 13;9. link

Port F, Bullock SL. Augmenting CRISPR applications in Drosophila with tRNA-flanked sgRNAs. Nature Methods, AOP link

Port F, Chen HM, Lee T, Bullock SL. Optimized CRISPR/Cas tools for efficient germline and somatic genome engineering in Drosophila. PNAS, 2014 Jul 22. link

Port F, Muschalik N, Bullock SL. Systematic Evaluation of Drosophila CRISPR Tools Reveals Safe and Robust Alternatives to Autonomous Gene Drives in Basic Research. G3, 2015 May 20. link

Akbari OS, Bellen HJ, Bier E, Bullock SL, Burt A, Church GM, Cook KR, Duchek P, Edwards OR, Esvelt KM, Gantz VM, Golic KG, Gratz SJ, Harrison MM, Hayes KR, James AA, Kaufman TC, Knoblich J, Malik HS, Matthews KA, O’Connor-Giles KM, Parks AL, Perrimon N, Port F, Russell S, Ueda R, Wildonger J. Biosafety. Safeguarding gene drive experiments in the laboratory. Science, 2015 Aug 28. link