Proton Transfer in Adenine−Thymine Radical Cation Embedded in B-Form DNA

Abstract

On the basis of pK a measurements, it has been predicted that proton transfer will not occur in the radical cation of the A/T base pair (A: adenine, T: thymine). Testing this prediction, we have performed simulations as a function of time on an A/T oligomer missing one electron, in solution, using the code CP2K. We find that proton transfer occurs rapidly at temperatures below room temperature. We suggest that the difference in behavior of (A/T)·+ from that predicted on the basis of pK a measurements is the effect of hydration. Hydration also appears to have effects not previously considered on hole motion in solution.

The Role of Hole Traps in DNA

“…It was found that immediately upon introduction of the hole its wavefunction is spread over 5 adenines, the length of the QM region in this simulation [8,9]. Within 20 fs, however, the hole is localized on a single one of these adenines [8,10]. It was shown that the contraction of the hole, that we have called self-trapping, is due to the polarization set up by the hole in the surrounding water [10,11].…”

“…Perhaps the shortest time for reorganization is that involved in the response of the water to introduction of a hole. This time has been deduced by simulations using cp2k for a DNA consisting of a series of ATs in water [8,9]. It was found that immediately upon introduction of the hole its wavefunction is spread over 5 adenines, the length of the QM region in this simulation [8,9].…”

“…This time has been deduced by simulations using cp2k for a DNA consisting of a series of ATs in water [8,9]. It was found that immediately upon introduction of the hole its wavefunction is spread over 5 adenines, the length of the QM region in this simulation [8,9]. Within 20 fs, however, the hole is localized on a single one of these adenines [8,10].…”

Temperature and Electric Field Effect on Proton Transfer in Adenine-thymine

“…23,24 Conwell et al demonstrated that the water hydration induces hole localization on one base, instead of several bases. 16 In our calculations, if the waters are dealt with quantum mechanics, which the distance with the helix less than 8 angstroms, the hole would localize on waters.…”

“…[12][13][14][15] Related studies pointed out that DNA is sensitive to environmental factors, such as solute, temperature et al Recently Conwell group pointed out that proton transfer appears on radical cation of AT base pair at low temperature in water. 16 At higher temperature, what would happen? In this paper, we investigate whether proton transfer could be found at higher temperature in water, then the proton behaviors under the external electric field are discussed.…”