π stack structure and hole transfer couplings in DNA hairpins and DNA.: A combined QM/MD study

Many key characteristics of hole transfer (HT) in DNA have been derived from spectroscopic studies of DNA hairpins. Because the capping groups in the hairpins can remarkably influence the structure and flexibility of the pi stack, and therefore, the charge transfer rate, the question arises of whether the HT parameters obtained for hairpins may be transferred to DNA oligomers. On the basis of large-time scale QM/MD simulations, we compare structural and electronic parameters of AT stacks in hairpins and DNA oligomers. We find that even in short hairpins, Sa-AA-Sd and Sa-AAA-Sd, the effects of the capping chromophores on the structure of the pi stack and the HT couplings properly averaged over MD trajectories are relatively small, and therefore, the hairpins are good models to study hole transfer through DNA. By contrast, the calculations of the electronic couplings based on the average structures of the systems lead to essential errors in the HT rate and the misleading statement that the charge transfer properties of DNA domains within hairpins are quite different from those of normal sequences.