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.