Metal ions play a critical role in various chemical, biological, and environmental processes. This review reports on emerging chemical mechanisms in the catalysis of DNA and RNA. We provide an overview of the metal-dependent mechanisms of DNA cleavage in CRISPR (clustered regularly interspaced short palindromic repeats)-Cas systems that are transforming life sciences through genome editing technologies, and showcase intriguing metal-dependent mechanisms of RNA cleavages. We show that newly discovered CRISPR-Cas complexes operate as protein-assisted ribozymes, highlighting RNA's versatility and the enhancement of CRISPR-Cas functions through strategic metal ion use. We demonstrate the power of computer simulations in observing chemical processes as they unfold and in advancing structural biology through innovative approaches for refining cryo-electron microscopy maps. Understanding metal ion involvement in nucleic acid catalysis is crucial for advancing genome editing, aiding therapeutic interventions for genetic disorders, and improving the editing tools' specificity and efficiency.