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Dicer initiates RNAi by generating cleaved RNA products that bind to a target mRNA to promote gene silencing. Mutations to the Dicer catalytic domain cause DICER1 syndrome, which increases the risk of cancers, including early childhood variants. However, the catalytic mechanism remains poorly defined due to the lack of structural data for Dicer bound to a substrate (or substrate mimic) in the presence of divalent ions known to be critical for nuclease activity. This study uses molecular dynamics (MD) simulations to uncover the first atomic level structure of the wild\u2010type Dicer\u2013RNA complex, including the binding pattern of two catalytically essential Mg\n                    <jats:sup>2+<\/jats:sup>\n                    ions. Subsequently, quantum mechanics\/molecular mechanics (QM\/MM) techniques are used to elucidate the Dicer catalytic mechanism for phosphodiester bond cleavage. Among three fully characterized pathways, our data suggest catalysis is only feasible when both active site Mg\n                    <jats:sup>2+<\/jats:sup>\n                    ions are directly coordinated to the RNA substrate and a hydroxide ion nucleophile is bound to an active site Mg\n                    <jats:sup>2+<\/jats:sup>\n                    ion. Phosphodiester bond hydrolysis proceeds through a two\u2010step mechanism involving a phosphorane intermediate that is stabilized by direct Mg\n                    <jats:sup>2+<\/jats:sup>\n                    \u2013substrate coordination and a hydrogen bond with K1806. This newly identified mechanism is consistent with experimental kinetic data, the impact of mutating the corresponding lysine in mouse Dicer, and the active site architectures and proposed mechanisms for other related nucleases. Directed by the enhanced understanding of wild\u2010type Dicer function, MD simulations subsequently show that six known DICER1 syndrome\u2010causing mutants likely impede catalysis by inducing unique active site disruptions that inhibit Mg\n                    <jats:sup>2+<\/jats:sup>\n                    \u2010ion coordination to the substrate. By furthering our knowledge of the structure and catalytic mechanism of wild\u2010type and mutant Dicer, this work unveils the molecular underpinnings of DICER1 syndrome and opens the door for the development of enhanced RNAi\u2010based therapeutics and biotechnologies.\n                  <\/jats:p>","DOI":"10.1002\/jcc.70446","type":"journal-article","created":{"date-parts":[[2026,7,4]],"date-time":"2026-07-04T06:04:51Z","timestamp":1783145091000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["How Do\n                    <scp>DICER1<\/scp>\n                    Syndrome Mutations Disrupt Catalysis? 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