Metal Interactions with Nucleobases, Base Pairs, and Oligomer Sequences; Computational Approach

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Abstract

This chapter concerns some of the computational studies devoted to interactions of metal cations with nucleobases, nucleotides, and short oligonucleotides considered as DNA/RNA models. Our topic is fairly complex, therefore the results obtained using mainly ab initio and DFT methods are discussed. The first part focuses on the interactions of isolated bases with metal cations either in bare, hydrated, or ligated forms. We begin with interactions of naked cations with nucleobases in gas phase. Subsequently, solvation effects using polarizable continuum models are analyzed together with a comparison to explicitly hydrated ions. In the second part, adducts of various metals with base pairs and oligomeric models of DNA/RNA are discussed. Separate sections are devoted to complexes of promising anticancer drugs. Stacked bases and larger systems (quadruplexes) studied by semiempirical and QM/MM methods are mentioned in the last part.

Keywords

Metal Cation Activation Barrier Hepatitis Delta Virus Purine Base Aqua Ligand 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
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Notes

Acknowledgments

The study was supported by projects Grant Agency of the Czech Republic (GAČR) No. P208/12/0622. The authors thank the Meta-Centers in Prague (Charles University and Czech Technical University), Brno (Masaryk University), Pilsen (University of West Bohemia) for the generous support of the computational resources.

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Authors and Affiliations

  1. 1.Faculty of Mathematics and PhysicsCharles University in PraguePrague 2Czech Republic

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