Mg 2+ and Mn 2+ ions are critical to the functioning of phosphoryl transfer enzymes, such as restriction endonucleases. Although these ions play similar roles in the chemical steps, they govern substrate specificity via modulating sequence discrimination by up to a factor of 10 5 with Mg 2+ and only up to a factor of 10 with Mn 2+ . To explain whether such diversity originates in fundamental differences in the electronic structures of the nucleobase-hydrated-metal ion complexes, structures and interaction energies were determined at the density functional (DFT) and second-order Møller-Plesset (MP2) levels of theory. Although both metal ions favor identical binding sites, Mn 2+ complexes exhibit greater distortions from the ideal octahedral geometry and larger variability than the corresponding Mg 2+ systems. In inner-shell complexes, with direct contact between the metal and the nucleobase, Mg 2+ is preferred over Mn 2+ in the gas phase, due primarily to nonelectrostatic effects. The interaction energies of the two metal ions are more similar in the outer-shell complexes, likely due to reduced charge transfer between the hydrated metal ion and the base moieties. Inclusion of solvation effects can amplify the relative nucleobase preferences of Mg 2+ and Mn
2+, indicating that bulk hydration modulates the balance between electrostatic and nonelectrostatic terms. In most cases, the base substitutions in solution are facilitated more by Mn 2+ than by Mg
2+. Electrostatic properties of the environment were demonstrated to have a major influence on the nucleobase preferences of the two metal ions. Overall, quantum chemical calculations suggest that the contrasting selectivity of Mg 2+ and Mn 2+ cofactors toward nucleobases derives from the larger flexibility of the Mn 2+ complexes accompanied by the excessive polarization and charge-transfer effects as well as less favorable solvation.
IntroductionDivalent metal ions are critical to the proper functioning of various biomolecules. These ions can assemble and stabilize protein structures 1,2 and can induce complex formation with their substrates. 3,4 Many enzymes utilize them as cofactors to facilitate chemical conversions. [5][6][7] Divalent metal ions play a distinguished role in nucleic acid biochemistry. 8 In the catalytic machinery of enzymatic phosphoryl transfer, they act as Lewis acids to reduce the accumulation of negative charge in the transition state. 9-11 Divalent metal ions are crucial for folding of RNA as well as for the catalytic machinery of ribozymes. 12 Magnesium and calcium ions were reported to interfere with the structure of DNA in a sequence specific manner that is dependent on the ion type as well. 13 Mg 2+ ions primarily bind to phosphate groups of the DNA backbone via a solvent molecule in a so-called outer-shell mode. 14,15 Divalent metal ions were also observed to penetrate into the grooves, 16,17 where by crosslinking the base atoms of the opposite strands, they can modify the groove width and promote kinking of the DNA. Such sequence-spec...