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

Abstract

The structure and electronic properties of the 6-carboxypurine (PurC) self pair with Cu2+, PurC–Cu–PurC, 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 PurC–Cu–PurC, comparisons with the A–Cu–PurC, PurC–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.