Conformational dependence of the electronic coupling for singlet excitation energy transfer in DNA. An INDO/S study

Using the INDO/S method, we study the effects of structural fluctuations on the interaction of singlet excited states in homogeneous poly(dA)-poly(dT) and alternating poly(dAdT)(2) stacks. The coupling for excitation energy transfer (EET) between intra- and inter-strand nucleobases is derived with the fragment excitation difference scheme (Hsu, et al. J. Phys. Chem. C 2008, 112, 1204). In this approach, both Coulomb and short-range contributions to the EET coupling are properly accounted for. 15 000 conformations for each nucleobase dimer were considered. Conformational fluctuations of DNA are shown to result in a large variation of the transfer integral. The root mean square coupling values are used to characterize the interaction of pi-pi* states in DNA. The intra-strand and inter-strand couplings between adenines are found to be significantly smaller than those for thymines. Our findings suggest that (1) EET couplings in DNA are significantly more sensitive to conformational changes of the pi stack than is estimated within the dipole-dipole scheme; (2) singlet excitation energy transfer in poly(dA)-poly(dT) should dominantly occur through thymine bases; (3) pi-pi* excited states in homogeneous stacks are more delocalized than in alternating sequences; (4) structural fluctuations can strongly affect the exciton distribution.