Biomedical subjects

E M Conwell

Publications and source records attributed to E M Conwell.

7 recordsLinked to original sources

PubMed2006

Effect of water drag on diffusion of drifting polarons in DNA.

It has been shown, theoretically and experimentally, that a hole or an excess electron on a DNA molecule in solution forms a delocalized wave function, a polaron. For an all-adenine (A) sequence or a mixed sequence of guanines (G's) and A's, calculations taking into account the polarization of the solution give the wave function spread over approximately four bases, which appears to be in agreement with experiment. The polaron may move by hopping or by drift. Drift can take place in a region with all the same bases, for example, A's, by the polaron dropping an A on the trailing edge and picking up an A on the leading edge. For drift that is not too rapid, the necessity of the polarization changing as the polaron moves exerts a drag on the polaron. We calculate the drag by using a model introduced earlier to describe the polaron. We find the drag to be proportional to the velocity of the polaron and to the orientational relaxation time of the water molecules. The drag is also a function of the Coulomb interactions of the fractional charges on the bases constituting the polaron, as modified by the polarization charge induced in the solution. The diffusion rate and mobility for all A polarons, calculated taking into account the drag, are 8 x 10(-5) cm(2)/s and 3 x 10(-3) cm(2)/(V s), respectively. We believe that in the experimental studies that have been carried out on hole propagation in a series of A's it was drift being observed rather than the hopping of a localized hole between adjacent A's, as was assumed to be the case.

Adenine↗

PubMed2005

Polarons in DNA: transition from guanine to adenine transport.

Experiments on hole transport in DNA have been interpreted as showing that a hole introduced onto a guanine (G) followed by a series of adenines (As) in a DNA duplex travels through the first three As by tunneling and then, with thermal energy, makes the transition onto the bridge of As. It has been widely believed that, once on the bridge, the hole is localized on a single A and proceeds by hopping between As. In the experiments, the holes on the A bridge diffuse, with little attenuation, until trapped by a GGG sequence. Recently, it has been discovered by Bixon and Jortner that the model of tunneling followed by hopping between As cannot account for the very weak dependence on bridge size of the relative chemical yields and the ratios of the rates for the two processes. In earlier calculations, we have shown that interaction with water results in the hole becoming a polaron spread over approximately four As. According to these calculations, the energy of the hole on the polaron is decreased so much that it is lower than that of the hole on G and even that of GGG. Estimates of energy fluctuations, due to fluctuations in the environment and conformational changes of the DNA, find them to be large enough so that GGG, and even G, can still act as hole traps, but trapping on the former is still very much more likely because of its lower energy.

Adenine↗

PubMed2002

Self-trapping versus trapping: application to hole transport in DNA.

We address the problem of interplay between self-trapping effects and effects of an external potential, which may be relevant for many physical systems, such as polarons in solids or a Bose-Einstein condensate with attraction. If the potential consists of two different wells, the system initially localized in the shallower well may relax into the deeper well, or may not if stabilized by the self-trapping effect. We show how this picture can be applied to interpret results of recent experiments on electron transfer in the DNA molecule [Giese et al., Nature 412, 318 (2001)]. The results of our calculations agree well with the experimental findings, giving evidence that hole transport in DNA involves polaronic effects.

Chemical Phenomena↗

PubMed2002

Effect of solvation on hole motion in DNA.

An excess charge on a DNA chain in solution interacts with polar solvent molecules and mobile counterions. We give the first theoretical estimate of the resulting hole self-localization energy and calculate the corresponding contribution to hole mobility on a DNA stack consisting of a single base pair repeated.

DNA↗

PubMed2002

Stationary polaron motion in a polymer chain at high electric fields.

We study the stationary motion of a polaron in a conducting polymer in the presence of a high electric field. Using the Su-Schrieffer-Heeger model plus an electric field, we find that at polaron velocities not exceeding the sound velocity, the dissipation of the electronic energy into the lattice occurs via emission of phonons with single selected wave vector. For this case the corresponding contribution to the polaron mobility can be calculated analytically. We discuss the issue of the polaron stability with respect to dissociation in a very high field at supersonic velocities.

Journal Article↗

PubMed2001

Hole traps in DNA.

Sequences of guanines, GG and GGG, are known to be readily oxidized, forming radical cations, i.e., hole traps, on DNA. The trapping probability of GG is less than that of GGG. Lewis et al. (J. Am. Chem. Soc. 2000, 122, 12037) have used measurements on synthetic hairpins to determine the free energy liberated when a hole goes from the radical cation G(+) to GG or to GGG. They find these free energies to be of the order of thermal energy at room temperature, in contradiction to the expectation by many of much greater trap depths. We have calculated the wave function of a hole on G, on GG, and on GGG surrounded by adenines, as in the Lewis et al. experiments, using a simple tight-binding model. We find that to account for the shallow traps found by them it is necessary that the difference in ionization potentials of contiguous guanine and adenine be smaller by about 0.2 eV than the 0.4 eV found for isolated bases. Using this value and taking into account polaron formation, we find the wave functions of holes trapped on G, GG, or GGG to extend over approximately 6 sites (bases) and with energy level differences in good agreement with the values found by Lewis et al.

Cations↗

PubMed2000

Polarons in DNA.

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 beta under the assumption that it describes an exponential decay with distance. The reported values range from beta < 0.2/A to beta > 1. 4/A. For the larger values of beta, 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 [Henderson, P. T. , Jones, D., Hampikian, G., Kan, Y. & Schuster, G. B. (1999) Proc. Natl. Acad. Sci. USA 96, 8353-8358 and Ly, D., Sanii, L. & Schuster, G. B. (1999) J. Am. Chem. Soc. 121, 9400-9410] proposed that transport occurs by polaron hopping between sites having approximately equal energies as a result of overlap. A recent experimental determination by Wan et al. [Wan, C., Fiebig, T., Kelley, S. O., Treadway, C. R., Barton, J. K. & Zewail, A. H. (1999) Proc. Natl. Acad. Sci. USA 96, 6014-6019] of the time required for an injected hole on DNA to travel a known distance leads to a large value of the diffusion constant. From this constant, a mobility of 0. 2 cm(2)/V small middle dots was deduced, orders of magnitude larger than typical hopping mobilities. We suggest that this ultrafast transport is due to polaron drift, which has been shown to lead to similar mobilities in chains of conjugated polymers. Using a simple model for the polaron, similar to that used for conjugated polymers such as polyacetylene, we show that, for reasonable values of the parameters, an injected electron or hole can form a polaron on a DNA stack.

Base Pairing↗