A team from Tufts University and Washington State University presents findings from an analysis focused on sequences that are particularly prone to alternative end joining — a potentially inaccurate form of double-strand DNA break repair — after being clipped by the Cas9 enzyme used in CRISPR-Cas9-based gene editing. Using deep sequencing and computational analyses, the researchers profiled some 1,100 semi-randomized DNA plasmid constructs that had been injected alongside single-guide RNA into Drosophila fruit fly embryos that expressed the Cas9 enzyme, focusing on synthesis-dependent microhomology-mediated end joining (SD-MMEJ) repair. "We find evidence at single nucleotide resolution for sequence characteristics that drive successful SD-MMEJ repair," the authors write. "These include optimal primer repeat length, distance of repeats from the break, flexibility of DNA sequence between primer repeats, and positioning of microhomology templates relative to preferred primer repeats."