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Mechanistic Insight into Catalytic Activity of BBA-Metallonucleases (This model system, Vibrio vulnificus, is thought to have the same cleavage mechanism as the HNH domain.)

Catalytic Mechanisms of Restriction and Homing Endonucleases (A general overview of both one- and two-metal reactions, not specifically theory-oriented.)

The Nucleophile in Ribozyme Catalysis (Not directly related, but an analogous cleavage reaction. The SI also has lots of detailed information on their QM/MM simulations.)

RNA coarse grain models:

http://pubs.acs.org/doi/abs/10.1021/jp104926t

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