Methods and compositions for improving the specificity of genome-editing nucleases (e.g., RNA-guided CRISPR-Cas nucleases or engineered zinc finger nucleases) and customizable DNA-binding domain fusion proteins (e.g., RNA-guided dead-Cas9, RNA-guided dead-Cpf1, or engineered zinc finger arrays fused to transcriptional regulatory domains) for use as research reagents, in gene drives, or as therapeutic agents.