Structure and properties of a copper-mediated nucleobase pair from density functional theory investigation

The structure and electronic properties of the 6-carboxypurine (Pur(C)) self pair with Cu2+, Pur(C)-Cu-Pur(C), a new copper-mediated base pair having a core purine and close to Watson-Crick natural adenine-thymine base pair in a DNA double helix, were determined by using density functional theory and employing the M06-L exchange-correlation functional. With the aim to better evaluate the influence of the ligand nature on binding energy of Pur(C)-Cu-Pur(C), comparisons with the A-Cu-Pur(C), Pur(C)-Cu-T systems have been performed. The computations on the corresponding zinc-mediated DNA dimer allow to explore also the role of the metal. The two employed models have different molecular size due to the presence of the sugar-phosphate group in the larger one. Results evidence as the copper ion complexes prefer to assume a square-planar complex that hence preserves the geometrical features of hydrogen-bonded natural base pairs. The computed binding energies well agree with the experimental melting point temperatures. (C) 2016 Elsevier B.V. All rights reserved.