Farboud B, Meyer BJ. Dramatic Enhancement of Genome Editing by CRISPR/Cas9 Through Improved Guide RNA Design. Genetics. 2015 Feb 18. PMID: 25695951.
From the abstract: "... Here we describe and validate a strategy for Caenorhabditis elegans ... The key innovation was to design guide RNAs with a GG motif at the 3' end of their target-specific sequences. All guides designed using this simple principle induced a high frequency of targeted mutagenesis via nonhomologous end joining (NHEJ) and a high frequency of precise DNA integration from exogenous DNA templates via homology-directed repair (HDR). Related guide RNAs having the GG motif shifted by only three nucleotides showed severely reduced or no genome editing. ..."
Will this prove true in Drosophila as well? There are certainly guide designs reported to be effective in flies that break the GG rule. And it is hard to believe that the design algorithms developed by various groups would not have picked this up. Nevertheless, it's tempting to give it a try.