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How are the homology arms for HDR donor oligos selected by the HDR Design Tool?
For wild-type Cas9, one of the homology arms is positioned relative to the CRISPR cut site, and the other one is positioned relative to the specific mutation site. The default homology arm length for standard HDR donor oligo designs is 40 bases. The default homology arm length for longer Megamer donors is 200 bases. In contrast, for nickase designs, there are 2 CRISPR nick sites instead of a single cut site. The mutation is typically located between the 2 guides, and the homology arms are positioned relative to these 2 CRISPR nick sites.