Hole wave functions and transport with deazaadenines replacing adenines in DNA.

Transport of a hole along the base stack of DNA is relatively facile for a series of adenines (As) paired with thymines (Ts) or for a series of guanines (Gs) paired with cytosines (Cs). However, the speed at which a hole was found to travel was much too small to make useful semiconductor-type devices. Quite recently it was found that replacing one of the electronegative nitrogens (N3 or N7) with a carbon and a hydrogen, thus turning A into deazaadenine, increased the hole speed in what was A/T by a factor 30. To study the effect of the substitution we have carried out simulations for the wave function of a hole on an A/T oligomer with As modified by replacing N3 or N7, or both, with C-H's. The simulations were carried out using QM/MM and the code CP2K. We find, for either N, or both, replaced, the wave function of the hole behaves similarly to that of a hole on A/T in being delocalized immediately after hole insertion for up to ∼20 fs, and then becoming localized on one of the modified As. The time for localization could be decreased by placing additional water within ∼1.8 Šof N3 or N7, encouraging the formation of hydrogen bonds with these nitrogens. Because of their positive charge the hydrogen bonds tend to repel holes. However, these bonds were found to decay on a femtosecond time scale, thus unlikely to affect the hole hopping, which occurs on approximately a nanosecond scale in A/T. Replacement with a C-H of one or both of the electronegative Ns, along with the structural changes that result, is expected to decrease the activation energy and thus account for the larger hole hopping rate in the deaza-modified DNA.

Effect of negative differential conductance in carbon nanotubes.

Measurements of transport at high electric fields in metallic single-walled carbon nanotubes (CNTs) have shown either saturation of the current or a region of negative differential conductance (NDC) characterized by the current, after reaching a maximum, decreasing with further increase in voltage. We point out that both types of behavior are characteristic of NDC, but the NDC is masked in samples showing current saturation due to generation of space charge, leading to a nonuniform electric field. We derive the relation between the carrier concentration, the electric field at which the drift velocity peaks, and the length of the sample that is required for the NDC to be manifest as saturation.

Duplex polarons in DNA.

In earlier work we calculated the wavefunction and energy of the solvated polaron in DNA with a simple model in which the charge was taken to be on a single chain of bases at the center of the double helix. To better approximate the actual situation, we have now extended the calculations to the case in which the charge is distributed on two chains of bases, complementary to each other, one on each side of the center. The binding energy of the resulting polaron is somewhat larger than that obtained for the single-chain polaron, the result of each chain of the polaron being closer to some of the polarization charge it induces. Carrying out the calculations for a number of different sequences, we find that the polaron wavefunction is predominantly on one of the two chains, this usually being the one on which the charge was originally placed, despite the availability of lower energy sites on the other chain. This finding is in agreement with recent experiments of Schuster's group(Joy, A.; Ghosh, A. K.; Schuster, G. B. J. Am. Chem. Soc. 2006, 128, 5346-5347). Thus, in contradiction to the ideas of many researchers, there is no transport in which a hole zigzags from one chain to the other, as has been suggested for a sequence of guanines and cytosines (GCGCGC....), for example.

Base sequence effects on transport in DNA.

Given the success of the polaron model based on solvation in accounting for the width of a hole polaron on an all-adenine (A) sequence on DNA, we extend the calculations to other sequences. We find excellent agreement with the free energy differences measured by Lewis et al. (J. Am. Chem. Soc. 2000, 122, 12037-12038) between a guanine (G) cation and a pair of bases, GG, or a triple of bases, GGG, in all cases surrounded by As, by treating AGGA and AGGGA as solvated polarons. There is additional support for hole polaron formation in DNA from experiments in which oxidative damage due to injected holes is investigated in sequences involving Gs and As. Theory and comparison with transport measurements on repeated sequences involving multiple thymines (Ts) or combinations such as ATs or GCs, where C is cytosine, led to the suggestion that the basic sequences in these cases must be polarons whose wave functions have substantial amplitudes on both chains in a duplex. The size of an electron polaron in DNA is predicted to be similar to that of a hole polaron, approximately 4 or 5 bases. Although experiments have shown that polaron hopping is the dominant mode of charge transport in DNA with repeated sequences such as AGGA, further investigations, particularly of temperature dependence of site energies and transfer integrals, are needed to determine to what extent hole transport takes place by polaron hopping for arbitrary DNA sequences.

Charge transport in DNA in solution: the role of polarons.

Since the discovery a decade ago of rapid photoinduced electron transfer in DNA over a distance >4 nm, a large number of experiments and theories have been advanced in the attempt to characterize the transfer, mainly of a radical cation or hole. Particularly influential experiments were carried out by Giese [Giese, B. (2000) Acc. Chem. Res. 33, 631-636] on the sequence G(A)(n)GGG, where G is guanine and A is adenine. These experiments were interpreted as showing that for n > 3, after the holes tunnel through the first three As, they hop onto the bridge of As, where they are localized on a single A and travel further by hopping between neighboring As. Recent experiments of Barton and coworkers [Shao, F., O'Neill, M. A. & Barton, J. K. (2004) Proc. Natl. Acad. Sci. USA 101, 17914-17919] have, however, established that the hole wavefunctions are delocalized. One of the mechanisms based on delocalized hole wavefunctions that had been investigated, both experimentally and theoretically, is transport by polarons. For one type of polaron, the properties are determined by polarization of the surrounding medium (water and ions, in this case). Theory predicts that this type of polaron is delocalized over approximately four bases in DNA. Transport by these polarons could explain the results of Giese et al. [Giese, B., Amaudrut, J., Köhler, A.-K., Spormann, M. & Wessely, S. (2001) Nature 412, 318-320], recent experimental results of O'Neill and Barton [O'Neill, M. A. & Barton, J. K. (2004) J. Am. Chem. Soc. 126, 11471-11483] concerning the size of the region over which the hole is delocalized, and other experimental observations.