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A QM/MM refinement of an experimental DNA structure with metal-mediated base pairs

Type of publication Peer-reviewed
Publikationsform Original article (peer-reviewed)
Publication date 2013
Author Kumbhar Sadhana, Johannsen Silke, Sigel Roland K. O., Waller Mark P., Müller Jens,
Project Metal Ion-Guided Assembly and Structures of the Catalytic Core of Ribozymes
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Original article (peer-reviewed)

Journal Journal of Inorganic Biochemistry
Volume (Issue) 127
Page(s) 203 - 210
Title of proceedings Journal of Inorganic Biochemistry
DOI 10.1016/j.jinorgbio.2013.03.009


A series of hybrid quantum mechanical/molecular mechanical (QM/MM) calculations was performed on models of a DNA duplex with artificial silver(I)-mediated imidazole base pairs. The optimized structures were compared to the original experimental NMR structure (Nat. Chem. 2 (2010) 229-234). The metal⋯metal distances are significantly shorter (~0.5Å) in the QM/MM model than in the original NMR structure. As a result, argentophilic interactions are feasible between the silver(I) ions of neighboring metal-mediated base pairs. Using the computationally determined metal⋯metal distances, a re-refined NMR solution structure of the DNA duplex was obtained. In this new NMR structure, all experimental constraints remain fulfilled. The new NMR structure shows less deviation from the regular B-type conformation than the original one. This investigation shows that the application of QM/MM models to generate additional constraints to be used during NMR structural refinements represents an elegant approach to obtaining high-resolution NMR structures.