Electronic and structural dynamics in DNA single strands

The absorption, conversion and transport of electronic energy in molecular aggregates is at the heart of many important natural and artificial photochemical systems, including organic solar cell materials, photosynthetic light-harvesting complexes and DNA oligomers. The photochemical function of these systems is built on the interactions between their aggregated chromophores, which determine the dynamic evolution of their photoexcited states. In this thesis, DNA oligomers are investigated as multi-chromophoric model systems, where the coupling of individual nucleobases is key to their photoprotection mechanism against high-energy ultraviolet (UV) radiation. In this respect, the pairing and stacking interactions of the nucleobases enable the formation of exciton states with charge transfer character, which govern the photochemical dynamics in DNA. In this thesis, the electronic and structural dynamics of adenine single strands are studied with broadband, polarization-controlled transient absorption spectroscopy in the deep-UV. This spectral region gives direct access to the excited state dynamics encoded in the UV-transitions of the nucleobases and by comparing different base-sequences, strand-lengths, solvent environments, and photoexcitation conditions, the role of the base-stacking interaction in energy and charge transfer processes in DNA systems is investigated.

By comparing adenosine homopolymers of different strand lengths, it is found that the initially formed charge-transfer (CT) exciton spans two stacked bases, whereas the maximum charge separation sensitively depends on the structural arrangement and solvation shell of the stack. Importantly, these aspects also determine the lifetime of the excitons: in dimers with large inter-base distances, charge recombination dynamics are a factor of two slower than in closely packed oligomers with 20 bases. Through transient absorption anisotropy experiments in deuterated buffer solutions, an intra-strand proton transfer is identified as the main quenching process governing the CT exciton lifetime and its structural relaxation to a minimum-energy configuration on the 10 ps scale is observed.

2-aminopurine (2AP) is used as a sensitive local structural probe as its strong fluorescence is quenched via stacking. By integrating 2AP in adenine strands charge and energy transfer processes are studied. Varying the base sequence reveals that two coupled 2AP bases play an important role in the excited state dynamics. By comparing the dynamics after direct excitation of 2AP and indirect excitation via adenine bases, the fast energy transfer from adenine to 2AP is observed. A charge transfer state, responsible for the quenching of 2AP’s strong emission, is detected.