Photoinitiated-processes in adenine oligonucleotides: Examining the nature of pi-stacking interactions in multi-chromophore systems

DNA provides the genetic code which is almost universal in all living organisms. When DNA is exposed to ultra-violet light it can cause cell degradation and mutation which are two of the major causes which lead to cancer. The nature of decay in DNA oligomers is a widely studied topic. Fluorescence and Transient Absorption (TA) experiments on polynucleotides which compare the behavior of the decay to the monomer bases have revealed the presence of longer-lived components in the multimeric systems. There has been heated debate over the character of the excited states responsible for the long-lived signals. Theoretical methods are well suited to compliment experiment by providing a description of processes and physical properties on the molecular level. We have studied pi-stacked adenines in the gas-phase with Quantum Mechanical (QM) methods, but also in the helical environment using high-level ab initio methods, classical simulations and the combination of the two (QM/MM). Inclusion of the environmental interactions dramatically alters the shape of the potential energy surfaces due to steric interactions from the backbone and interactions with the surrounding bases and environment. This work examines the complete picture of photophysical processes occuring in adenine oligonucleotides within the helical environment after the absorption of a photon: the nature of initial absorption and the subsequent radiative and non-radiative decay pathways. It contributes key discoveries inherent to the mechanisms which govern photo-initiated processes in DNA, and also contributes to our fundamental knowledge of the photophysical behavior of pi-stacked chromophores. The work reveals the effects of ?-stacking interactions and the environment on photo-initiated processes in oligonucleotides. It reveals that excitonic coupling is responsible for the key differences in features in the absorption spectrum of adenine oligomers compared to the isolated bases, illustrates the role of charge transfer (CT) mixing in both absorption and decay processes, and the importance of bonded excimers in deactivation. The work also illustrates that CT excimers are responsible for the long-lived signals evidenced in Transient Absorption and Fluorescence experiments and that neutral excimers can exist within the DNA helical environment. It also adds to the discussion in the field on the nature of photodecay mechanisms occurring within the DNA helix.