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Resonance Enhanced Multi-photon Spectroscopy of DNA

  • Author(s): Ligare, Marshall Robert
  • Advisor(s): deVries, Mattanjah
  • et al.
Abstract

ABSTRACT

Resonance Enhanced Multi-photon Spectroscopy of DNA

by

Marshall Robert Ligare

For over 50 years DNA has been studied to better understand its connection to life and evolution. These past experiments have led to our understanding of its structure and function in the biological environment but the interaction of DNA with UV radiation at the molecular level is still not very well understood. Unique mechanisms in nucleobase chromaphores protect us from adverse chemical reactions after UV absorption. Studying these processes can help develop theories for prebiotic chemistry and the possibility of alternative forms of DNA. Using resonance enhanced multi-photon spectroscopic techniques in the gas phase allow for the structure and dynamics of individual nucleobases to be studied in detail. Experiments studying different levels of structure/complexity with relation to their biological function are presented.

Resonant IR multiphoton dissociation spectroscopy in conjunction with molecular mechanics and DFT calculations are used to determine gas phase structures of anionic nucleotide clusters. A comparison of the identified structures with known biological function shows how the hydrogen bonding of the nucleotides and their clusters free of solvent create favorable structures for quick incorporation into enzymes such as DNA polymerase.

Resonance enhanced multi-photon ionization (REMPI) spectroscopy techniques such as resonant two photon ionization (R2PI) and IR-UV double resonance are used to further elucidate the structure and excited state dynamics of the bare nucleobases thymine and uracil. Both exhibit long lived excited electronic states that have been implicated in DNA photolesions which can ultimately lead to melanoma and carcinoma. Our experimental data in comparison with many quantum chemical calculations suggest a new picture for the dynamics of thymine and uracil in the gas phase. A high probability of UV absorption from a vibrationally hot ground state to the excited electronic state shows that the stability of thymine and uracil comes from its intrinsic molecular properties and possibly a hydrogen bonding solvent capable of dissipating excess vibrational energy.

Due to the high specificity and sensitivity of resonant two photon ionization coupled with molecular beam mass spectrometry a new analytical technique for identifying molecular markers in archaeological vessels is presented. The xanthine alkaloids theobromine, theophylline and caffeine are identified in Central American and North American pottery sherds by direct desorption/resonant laser ionization mass spectrometry.

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