This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. There have been many experiments to determine how fast a missing electron (hole) moves on the base stack in DNA in solution. Its motion in some sequences, such as duplex A/T, has been found to be much faster than in others. The experiments have shown that the hole traverses one or two bases by tunneling. For distances greater than 3 or 4 bases one school of thought has it that the hole is localized on a single base and hops from base to base, while another school has it that the hole, polarizing the water around the DNA, travels by hopping or drift as a polaron spread over 3 or 4 bases. In either case fluctuations due to the thermal movement of the bases are expected to have an important effect on the hole wavefunction and its motion. Recent calculations treating the effect of the fluctuations on the hole wavefunction by Molecular Dynamics have favored the polaron idea, finding the hole on the average spread over 3 to 4 bases. It is important then to study the effect of fluctuations on the motion of the hole polaron. We plan to do this by first using AMBER to obtain the potential energy landscape of DNA undergoing fluctuations, then finding the wave function of a hole polaron in this landscape and following its motion to obtain its diffusion constant D. Having D we can obtain the mobility of the hole from the Einstein relation. This will be the first use of Molecular Dynamics to obtain information about the motion of a hole in an electric field in a fluctuating DNA.
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