Charge transfer and transport in DNA

Abstract

We explore charge migration in DNA, advancing two distinct mechanisms of charge separation in a donor ( In 1962, Eley and Spivey proposed (1) that -interactions between stacked base pairs in double-strand DNA could provide a pathway for rapid, one-dimensional charge separation. In spite of subsequent theoretical and experimental effort in this intriguing field (2-7), experimental evidence for such ''molecular wire'' type conduction in DNA remained elusive. The studies of Warman et al. (8) in 1996 of radiation-induced conductivity in hydrated DNA argued against one-dimensional conduction confined to the base pair core. Interest in this fascinating subject (9-31) was triggered recently by the studies of Barton and her colleagues (9-19), which seemed to indicate the occurrence of long-range, almost distance-independent charge separation in DNA, manifesting ''chemistry at a distance'' (17). The problem of charge separation in DNA (9-31) is pertinent for the realization of a particular DNA repair mechanism as an alternative to the DNA-photolyase (20-23), which rests on long-range charge transfer to the defect site, i.e., a thymine dimer followed by concurrent or sequential bond breaking. Moreover, a deeper understanding of charge migration processes and of the effects of electronic excess charges localized at specific nucleic bases has wide range implications for (i) protein binding to DNA. Because electrostatic interactions are primarily responsible for the association of proteins to nucleic bases, changes in the charge density at the DNA core induced by charge separation may affect the specificity of protein binding; (ii) DNA sequencing. The control of duplex formation via charge migration may be important for specific DNA sequencing; and (iii) DNA-based biosensors. The development of biosensors, which depend on specific long-range charge separation along duplex structures in solution and preferentially at electrodes, is of considerable potential.The interpretation of the early experiments of Barton, Turro, and their colleagues (9-13) on charge separation between donor and acceptor complexes attached to DNA was fraught with some difficulties because of the possibility of aggregation effects (24). The recent data of Dandliker, Holmlin, and Barton (17-19) on hole migration between the electronically excited metal intercalator Rh(phi) 2 DMB ϩ3 and the thymine dimer, both of which are specifically incorporated in a 16-bp DNA duplex, provide evidence for long-range hole separation (over a distance scale of r ϭ 19-26 Å) with the yield being independent of donor-acceptor distance (R). These results (17)(18)(19) are in dramatic conflict with other experiments on charge separation in DNA (25-27), as well as with the standard electron transfer theory (32-40). For a donor (d)-bridge-acceptor (a) system, the theory (33-40) predicts an exponential (donor-acceptor) distance R dependence of the hole (or electron) transfer rate, k ϭ (2͞)V 2 F of the MarcusLevich-Jortner equation (33-40):Here, F is the thermally averaged n...

Electron Transfer Rates in Bridged Molecular Systems 2. A Steady-State Analysis of Coherent Tunneling and Thermal Transitions

“…In that case, the mean time for a diffusing particle starting at one end of a 1-dimensional path to reach, for the first time, the other end scales like N 2 . 49,68 The mean first passage time is, therefore, not a good measure for the steady-state rate and the associated conduction, but it may represent the intermediate-time behavior in transient experiments.…”

“…It should be noted that the above analysis cannot be applied to the model 49 in which incoherent hopping is associated with irregular vibronic coupling between bridge sites in a system with E D > E bridge . In this model, the effect of lowering the electronic origin of one bridge site on the overall transfer rate depends on details of the energydependent density of states and the Franck-Condon factors that control coupling between bridge sites.…”

“…Furthermore, when the donor level is substantially higher than the ground bridge energy, incoherent sequential hopping may result from the irregular nature of the coupling between states belonging to vibronic manifolds on neighboring bridge sites, even without thermal dephasing. 49 An interesting way to distinguish between the coherent tunneling and sequential hopping modes of electron transfer has been suggested by Grozema et al 70 in their analysis of electron transfer in donor-DNA-acceptor systems. These authors have pointed out that, for a bridge of adenine-thymine (AT) base pairs, the exchange of an AT base pair by a guanine-cytosine (GC) base pair, which corresponds to a lower energy of this "impurity" bridge site, increases the electron-transfer rate.…”

“…Phase loss leading to sequential migration may take place in this case because of the irregular character of the coupling between different vibronic levels in the D, B, and A entities. 49 The transition between the superexchange (tunneling) and the sequential hopping regimes has attracted some attention recently. 50,51 In particular, Felts, Pollard, and Friesner 52 have investigated this issue in the framework of the Redfield density matrix theory, 53 and Mukamel and collaborators have advanced a more elaborate density matrix formalism using higher-order correlation functions for the system-thermal bath coupling.…”

Self-assembled guanine ribbons as wide-bandgap semiconductors

“…Band conduction and hopping mechanism have been also invoked to describe charge migration in other guanine-rich systems (e.g. G-quartets) or poly(dG)-poly(dC) DNA [2,6,7,8,9]; however, no conclusive agreement was reached so far in this respect.…”