Repair mechanisms for damaged DNA are essential for the proliferation of nearly all forms of life. Although DNA is quite robust, the vital information-storing molecule can often be damaged from environmental exposures such as ultra-violet (UV) light. Exposure to UV light can result in various types of mutagens creating structural damages. One specific type of UV-induced damage is the creation of a cyclobutylpyrimidine dimer (CPD). This specific type of lesion can be efficiently repaired by the flavoenzyme DNA photolyase (PL). DNA photolyase is an ancient protein found across kingdoms and plays a crucial role in preventing mutagenesis and cell death. DNA photolyase is a monomeric flavoprotein that utilizes blue light to repair UV-induced CPD lesions in DNA via an electron transfer mechanism. All photolyases contain at least one flavin adenine dinucleotide (FAD) molecule as the catalytic cofactor responsible for initiating the electron transfer induced repair process. Flavin cofactors are intriguing because of their unique ability to donate one or two electrons. The conservation of FAD and the unique U-shaped configuration of FAD in PL led researchers to question if the adenine moiety of the FAD molecule was essential in the DNA repair mechanism and generated a spectral signature indicative of a radical adenine species. The importance of the adenine moiety could be linked to structural changes associated with environmental temperature. The rate of electron transfer is exponentially dependent on temperature and DNA photolyase is found in organisms which thrive in harsh environments that vary in temperature, pH, ionic strength etc. Photolyase presents a unique opportunity to study the adaptations that are required for proteins to function in extreme environments where temperature dependent processes should show dramatic differences. We have used ultrafast transient absorption spectroscopy to compare the similarities and differences in excited state dynamics of the FAD cofactor. Photolyase isolated from the hyperthermophilic archaea Sulfolobus solfataricus (SsPL) is compared to PL isolated from the mesophilic E. coli (EcPL). These results indicate differences in the dynamics of fully reduced flavin between enzymes as a function of temperature. We present evidence for charge separation in the FAD cofactor in the thermophilic enzyme previously seen in computation studies of photolyase. To investigate the excited state charge redistribution of flavin which is critical to its role in nature, the charge redistribution of the precursors to flavin biosynthesis were examined. Lumazine is a precursor in the biosynthetic pathway of flavins. As such, lumazine could have served as an enzymatic cofactor prior to flavins. Lumazine has been identified in biological processes, however it is not as prevalent as flavins. We utilize Stark spectroscopy to examine the charge redistribution in excited state lumazine to understand / Chemistry

An overexposure to ultraviolet radiation can cause sunburn and some forms of skin cancer. UV light causes many different photoproducts. The cys-syn cyclobutylpyrimidine dimer (CPD) is the major photoproduct upon UV irradiation. DNA photolyase (PL) is a light-driven flavoprotein that repairs CPD in UV-damaged DNA. This repair process occurs in the presence of blue light through ultrafast photo-induced electron transfer from reduced anionic flavin adenine dinucleotide (FADH¯) to the CPD by an unknown mechanism. Since the excited state flavin transfers an electron to repair the damaged DNA, it is of utmost importance that we understand better the excited state properties of the flavins. In this work the excited state electronic properties of all three-oxidation states of flavin: oxidized form (FAD), semiquinone radical form (FADH•) and reduced anionic form (FADH¯) were studied using Stark spectroscopy and complimented by time dependent density functional theory (TD-DFT) calculations. These results are presented and discussed in Chapter 3 and 4. The difference dipole moments (Δμ) and the difference polarizabilities (Tr(Δα01)) were experimentally determined for first two lowest optically accessible states. The results are discussed in the context of photoreduction of flavins in wider class of flavoprotein blue light photoreceptors and catalytic electron transfer process in DNA repair. In the later part of this thesis (Chapters 5 and 6) the excited state electronic properties of monomeric 2-Aminopurine (2AP), 8-Vinyladenine 8VA were presented. These 8VA, 2AP are examples of fluorescent nucleotide analogues of adenine that can be incorporated into DNA with little perturbation of the normal double-helical structure. The fluorescence of these analogues is quenched when incorporated in double-stranded DNA (dsDNA). The basic mechanism underlying the fluorescence quenching by base stacking of 2AP and 8VA are is not well understood, and thus exploring the excited state electronic structures of these bases is an important first step. We have explored the excited state properties of 2AP and 8VA in frozen LiCl and ethanol solutions using Stark spectroscopy. High-level ab initio and TD-DFT calculations were performed to compliment the experimental results. / Chemistry

The excited state electronic structures of several biologically important chromophores were studied by Stark spectroscopy. The extent of charge redistribution upon excitation to the lowest excited states of the oxidized and semiquinone forms of flavin adenine dinucleotide (FAD) bound to the light activated DNA repair enzyme DNA photolyase have been studied previously by this technique. This work focuses on the catalytically active form, the two-electron reduced anion. To facilitate analysis of this experiment, the Stark spectra of a simple flavin derivative that is soluble in organic solvents was measured. The results of the analysis of these data are in agreement with previously a published linear dichroism experiment that found the absorption spectrum of flavins in this redox state arises from two distinct electonic transitions in the visible/near-ultraviolet spectral range, a fact that has not been incorporated into the analysis of many ultrafast spectroscopic experiments of reduced anionic flavins/flavoproteins. The difference dipole moment of the second, more intense, transition was found to be about twice as large as that of the lowest energy transition. With the aid of ab initio calculations, the directions of these dipole moments in the molecular frame were assigned. For both transitions, it was found that negative charge density is shifted toward the xylene ring of the flavin upon excitation. Another important consideration for the correct analysis of the photolyase spectra is the possibility of contamination by small amounts of the antenna chromophore, which also has absorption intensity in the near-ultraviolet region. We chose to study the cofactor for E. coli photolyase, 5,10-methenyltetrahydrofolate, and its photodecomposition product, 5,10-methylenetetrahydrofolate. The difference dipole moments for the lowest energy transitions of both of these chromophores were found to be quite large, ranging from 9-12 D fc and lying primarily along the transition dipole moment. Additionally, the difference polarizability of both chromophores was large, on the order of 200-300 Å3 fc2 . The Stark spectra of reduced anionic FAD in photolyase agrees well with the findings of the experiments on flavin in organic solvent; the magnitude of the difference dipole moments in both cases match within experimental error. While the direction of the difference dipole moment for the lowest transition is also the same in both cases, that of the second transition is changed in the protein matrix. The assignment of these vectors in the molecular frame shows that the two dipole moments are coincident for the cofactor bound to photolyase. This finding, where electron density is shifted toward the point of the flavin ring closes to the DNA lesion bound to the enzyme, is strong evidence that direct electron transfer takes place from the isoalloxazine ring of FAD to the DNA substrate in the catalytic cycle. The usefulness of Stark spectroscopy in investigating photoinduced charge redistribution was also shown for the donor-π-acceptor flavin dyad, azobenzylflavin (ABFL). The difference dipole moment was found to be 22 D, an approximately three-fold increase from the largest difference dipole moment found in naturally occurring flavins. This extensive charge redistribution corresponds to a large hyperpolarizability of the chromophore that suggests that ABFL may be useful in nonlinear optical applications. Transient absorption was used to supplement these experiments by monitoring the decay kinetics of ABFL after excitation. It was found that ABFL undergoes ultrafast charge recombination within 6 ps after excitation, leading to depopulation of the charge separated state before useful work can be performed for applications requiring electron transfer. These studies provide the ground work for rational design of other ABFL-like derivatives for use in a variety of applications. / Chemistry

Elektronische, optische und kollektive Vielteilcheneigenschaften molekularer Systeme in polaren Umgebungen werden durch elektrische Wechselwirkungen, die bei Terahertz-Frequenzen (THz) fluktuieren, beeinflusst. Diese Arbeit nutzt die Fortschritte bei Hochfeld-THz-Quellen, um Einblicke in die lokalen Wechselwirkungen und die Dynamik elektrischer Felder auf relevanten Zeitskalen bei Umgebungstemperaturen zu gewinnen. Die Forschung wird von drei miteinander verbundenen Zielen geleitet: (1) Die optische Gleichrichtung mit gekippten Pulsfronten in LiNbO3 erzeugt starke Pikosekunden-THz-Pulse, die bei 0,6 THz zentriert sind und durch eine metallische Antennenstruktur verstärkt werden, um elektrische Spitzenfelder bis zu 3 MV/cm zu erreichen. (2) Wir stellen eine neue Methode der THz-Stark-Spektroskopie vor. Die Experimente basieren auf einem Pump-Probe-Schema, bei dem starke elektrische Felder von THz-Pulsen nicht-resonant mit einem Chromophor wechselwirken und Änderungen der molekularen elektronischen Absorptionsbanden hervorrufen. Die Änderungen werden dann frequenz- und zeitaufgelöst mit optischen Femtosekunden-Pulsen abgebildet. Die Zeitskala der THz-Pulse ist viel kürzer als die molekularen Umorientierungsprozesse, so dass die Experimente die quasi-instante Reaktion molekularer Systeme in einer eingefrorenen Strukturanordnung abbilden. Aus den vollständig reversiblen elektronischen Absorptionsänderungen kann man eine Dipoldifferenz zwischen dem Grund- und dem angeregten Zustand und Einblicke in die lokale elektrische Umgebung gewinnen. (3) Nach Photoanregung freier Elektronen in polaren Flüssigkeiten führt die ultraschnelle Relaxation der Elektronen zu stark unterdämpften kohärenten Ladungsschwingungen mit Frequenzen zwischen 0,1-2 THz. Solche Anregungen stellen longitudinale Polaronen dar, bei denen ein überschüssiges Elektron an Zehntausende von Lösungsmittelmolekülen gekoppelt ist und ein Polaron von Nanometergröße bildet. / The behavior of molecular systems in polar environments is influenced by electric interactions fluctuating at terahertz (THz) frequencies, shaping their electronic, optical, and collective many-body properties. This thesis leverages the advancements in high-field THz sources to gain insights into the local electric-field interactions and dynamics at relevant timescales under ambient temperatures. The research is guided by three interconnected objectives: (1) Tilted-pulse-front optical rectification in LiNbO3 generates strong picosecond THz pulses centered at 0.6 THz which are enhanced by a metallic antenna structure to reach peak electric fields up to 3 MV/cm. (2) We introduce a novel method of THz Stark spectroscopy. The experiments are based on a pump-probe scheme, where strong electric fields of THz pulses interact non-resonantly with a chromophore and induce changes of molecular electronic absorption bands. The changes are then mapped in a frequency- and time-resolved manner using femtosecond optical probe pulses. The time-scale of the THz pulses is much shorter than the molecular reorientation processes, thus, the experiments map the quasi-instantaneous response of molecular systems in a frozen structural arrangement. From the fully reversible electronic absorption changes, one can obtain a dipole difference between the ground and the excited state, and insights into the local electric environment. (3) Following photoexcitation of free electron in polar liquids, the ultrafast relaxation of electrons leads to highly underdamped coherent charge oscillations at frequencies between 0.1-2 THz. Such excitations represent longitudinal polarons, where an excess electron is coupled to tens of thousands of solvent molecules forming a polaron of nanometer dimensions.