Department of Physics
Condensed Matter Seminar

The transfer of electric charge through DNA is a biologically important process that has a potential for nanotechnology applications. Hole-type conductivity has been observed in many experiments; the rate of hole transfer through DNA is affected by such factors as the DNA sequence, structure, temperature, and environment. We will review the experimental findings and existing models of the charge transfer in DNA, and present our study of the effect of thermal fluctuations on the charge transfer mechanism in DNA and its biomimetic cousin, peptide nucleic acid (PNA). Experiments show that the holes in DNA reside predominantly on guanine bases (G), whereas the adenine bases (A) play the role of bridge states. The mechanism of hole transfer from G to G famously changes with distance: superexchange tunneling is thought to be dominant on short distances when the Gs are separated by 1 to 3 As, whereas thermally-induced hopping prevails on longer distances. We address the effect of room-temperature structural fluctuations on the hole transfer mechanism. Ensembles of conformations are generated for DNA and PNA with a "donor-bridge-acceptor" sequence G(A/T)n(G)m. Molecular orbitals of each conformation are then computed by the semiempirical INDO/s method. The results show a significant hitherto unappreciated hole delocalization between the Gs and the A bridge. Such a fluctuation-driven delocalization suggests a significant contribution of thermally-induced hopping to the charge transfer within DNA and PNA even on short distances. The degree of charge delocalization is found to be dramatically affected by the DNA/PNA sequence: moving the As from one helical strand to the other can change the probability of hole delocalization from 10% to 90%. Thus, a complete physical model of the nucleic acid charge transfer should take into account both the 3-dimensional structure and the thermal fluctuations of the nucleic acid molecule. Between the two nucleic acids, the PNA conductivity is found to be higher; either due to the differences in the nucleic base organization or due to an increased flexibility with a more frequent access to "conducting" conformations. Thus, PNA may become a better-conducting molecular wire than DNA.