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Open Access Publications from the University of California

Excited State Dynamics of Isolated Nucleobases and Base Pairs

  • Author(s): Siouri, Faady Mohammad
  • Advisor(s): de Vries, Mattanjah S
  • et al.
Abstract

Environmental conditions such as solar irradiation can induce biochemical reactions and pose a threat to organic molecules necessary in life. How DNA responds to radiation is relevant to human health because radiation damage can affect genetic propagation and lead to cancer. A detailed photochemistry is unraveled by studying the intrinsic properties of individual DNA/RNA building blocks, followed by extrapolation to larger systems such as base pairs via gas phase laser spectroscopy. Moreover, the photodynamics of nucleobases may further our understanding of prebiotic chemistry and its role in developing life as we know it. Electronic structure and excited state dynamics of nucleobases and base pairs have been studied in the past; however, detailed spectroscopy has not been reported for all of them. Moreover, some nucleobase analogues were never studied in the gas phase. As a result, we attempt to build on what was previously established on nucleobases and base pairs and then take a step further to explore a nucleobase analogue.

This work reports studies of electronic structure and excited state dynamics of biological molecules via resonance-enhanced multiphoton ionization in the gas phase. First, we measured well-resolved vibronic spectra of all the molecules we studied by resonant two-photon ionization. Then, we performed double-resonance spectroscopy to further elucidate the structure and excited state dynamics of the target molecules. Because biomolecules typically exist in several tautomeric forms which are isolated under gas phase jet-cooled conditions, we used UV-UV double resonance spectroscopy to determine the number of tautomers present and their origins. We used IR-UV double resonance spectroscopy to obtain tautomer-specific IR spectra. We measured excited state lifetimes of tautomer-selected nucleobases by nanosecond and picosecond pump-probe spectroscopy. Using these methods, we were able to draw a new picture for the dynamics of bare nucloebases thymine and uracil in the gas phase. In the gas phase jet expansion, both molecules were present in the keto form and exhibited long lived excited states. These long lived states have been implicated in the formation of DNA photolesions by causing the formation of a cyclobutane pyrimidine dimer, which can lead to cancers such as melanoma and carcinoma. We also determined that replacing the oxygen in guanine with sulfur results in drastically different dynamics due to the heavy atom effect.

With the use of a free-electron laser, we were able to collect IR spectra for multiple base pairs in the far-IR region (<880 cm-1). Although the far IR region has been difficult to access both experimentally and computationally, we were able to structurally characterize the molecules with the help of Born–Oppenheimer Molecular Dynamics (BOMD). This far-IR region yields new information because it is characterized by large-scale delocalized vibrations that cannot be observed in the mid-IR region.

Finally, we used R2PI in combination with supersonic jet cooling and mass spectrometry to examine archaeological samples. We studies organic residues within pottery sherds from Maya vessels (600−900 CE) and Mississippian vessels (1100−1200 CE), successfully detecting three molecular markers, caffeine, theobromine, and theophylline, associated with the use of cacao.

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