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An experimental investigation and theoretical study of the duplex DNA sequences d(5′-GAGG-3′)‚ d(3′-CTCC-5′) and d(5′-GTGG-3′)‚d(3′-CACC-5′) was carried out. The experiments show that the efficiency of radical cation transport, revealed by strand cleavage after treatment with piperidine, is the same in both sequences. Density functional theory (DFT) calculations reveal essentially identical ionization potentials and hole distributions for these sequences when they are properly hydrated. The effect of hydration on the electronic properties of these sequences was examined theoretically. Calculations on dry DNA (i.e., having no water molecules) gives “phantom” electronic transitions to orbitals associated with the sodium counterions. However, these transitions vanish even with a minimal level of hydration. Meaningful theoretical results for DNA are obtained only when the counterions and hydrating water molecules are properly considered.

Effect of Base Sequence and Hydration on the Electronic and Hole Transport Properties of Duplex DNA: Theory and Experiment