Polarons in DNA

Abstract

Many experiments have been done to determine how far and how freely holes can move along the stack of base pairs in DNA. The results of these experiments are usually described in terms of a parameter ␤ under the assumption that it describes an exponential decay with distance. The reported values range from ␤ < 0.2͞Å to ␤ > 1.4͞Å. For the larger values of ␤, the transport can be accounted for as single step superexchange-mediated hole transfer. To account for the smaller values, hopping models have been proposed, the simplest being nearest-neighbor hopping. This model assumes that, between hops, the hole is localized on a single base with no overlap to neighbors. Noting that an electron or hole added to a DNA stack, as to other essentially one-dimensional entities, should distort its structure to form a polaron, Schuster and coworkers It is generally, although perhaps not universally, believed that DNA has no free carriers in its thermal equilibrium state because of the gap of many eV (1 eV ϭ 1.602 ϫ 10 Ϫ19 J) between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO). Electrons (radical anions) or holes (radical cations) may be introduced by ionizing radiation, injection from contacts, photoinduced electron transfer involving an impurity, etc. Of particular interest has been the transport of electrons and holes along the stack of base pairs. The process is important, because radical migration through DNA may play a crucial role in mutagenesis and carcinogenesis. The suggestion that the -interaction between the base pairs could support extended transport was made almost 40 years ago (1). It has long been known that electrons and holes created by ionizing radiation can have a range of many base pairs (2). Recent results suggest that these carriers migrate over distances greater than 30 bases at room temperature (3). However, these results were apparently not considered evidence that electrons and holes introduced by other means could migrate relatively freely over the base-pair stack.Particularly in the last decade, many different experiments have been carried out to determine the range of a hole on the base-pair stack. In a frequently used technique, photoexcitation of an acceptor associated with the stack in some fashion, sometimes intercalated, allows transfer of an electron, usually from a guanine (G) base, leaving a hole on the stack. In some experiments, the migrating hole is trapped at a GG step on the stack, and its range is determined by observing strand cleavage at the trap site (4, 5). In other experiments, the range is determined by observation of fluorescence quenching of a donor intercalated in the stack (6-8).On the expectation of the electron or hole transfer decreasing exponentially with distance R according to exp(Ϫ␤R), as predicted by Marcus theory, the observed penetration distance for the hole was described in terms of a parameter ␤. ␤ values ranging from greater than 1.4 Å Ϫ1 to less than 0.1 Å Ϫ1 have been reported. Values from 1.2 Å Ϫ1 to 1.6 Å Ϫ1

Electrical conductance in duplex DNA: Helical effects and low-frequency vibrational coupling

“…where n is the electronic wave function at site n. This expression generalizes the equation of motion usually considered within the framework of the Su-Schrieffer-Heeger Hamiltonian, 34 including the quadratic dependence n,n±1 2 in the off-diagonal terms ͑instead of a linear one͒. Thus, nonlinearity emerges in Eq.…”

“…͑4͔͒ so that the charge gets localized by its interaction with the lattice ͑polaronic effect͒. [34][35][36] In the + case, however, the transfer integral becomes negative ͑ + = −1.3t 0 Ӎ −0.2 eV͒ and charge becomes delocalized instead. The normal modes corresponding to the DNA codon shown in Fig.…”

Electrical Conductance in Biological Molecules

“…DNA dynamics is known to dramatically affect the relevant charge transfer/transport processes, as demonstrated by the pertinent systematic experiments (see, for example, [100,101] and the references therein). Meanwhile, theoretical description of these effects is usually carried out at the level of polaronic theories.…”

Backbone-induced semiconducting behavior in shortDNAwires

“…14 To our knowledge, at the present time, only few densityfunctional-theory ͑DFT͒ calculations for DNA molecules are available. 7,15 In a parallel development particular aspects of the DNA transport phenomenology have been explained as mediated by polarons, 16 solitons, 17 electrons or holes. 1,18 Such lack of a unifying theoretical scheme calls for reproducible and unambiguous experimental results that are still a great technological challenge.…”