Photophysics and Photochemistry of a DNA–Protein Cross-Linking Model: A Synergistic Approach Combining Experiments and Theory

Abstract

The photophysical and photochemical properties of 5-benzyluracil and 5,6-benzyluracil, the latter produced by photocyclization of the former through irradiation with femtosecond UV laser pulses, are investigated both experimentally and theoretically. The absorption spectra of the two molecules are compared, and the principal electronic transitions involved are discussed, with particular emphasis on the perturbation induced on the two chromophore species (uracil and benzene) by their proximity. The photoproduct formation for different irradiation times was verified with high-performance liquid chromatography and nuclear magnetic resonance measurements. The steady-state fluorescence demonstrates that the fluorescence is a distinctive physical observable for detection and selective identification of 5- and 5,6-benzyluracil. The principal electronic decay paths of the two molecules, obtained through TDDFT calculations, explain the features observed in the emission spectra and the photoreactivity of 5-benzyluracil. The order of magnitude of the lifetime of the excited states is derived with steady-state fluorescence anisotropy measurements and rationalized with the help of the computational findings. Finally, the spectroscopic data collected are used to derive the photocyclization and fluorescence quantum yields. In obtaining a global picture of the photophysical and photochemical properties of the two molecules, our findings demonstrates that the use of 5-benzyluracil as a model system to study the proximity relations of a DNA base with a close-lying aromatic amino acid is valid at a local level since the main characteristics of the decay processes from the excited states of the uracil/thymine molecules remain almost unchanged in 5-benzyluracil, the main perturbation arising from the presence of the close-lying aromatic group.

A multi-scale time-resolved study of photoactivated dynamics in 5-benzyl uracil, a model for DNA/protein interactions

“…Indeed, a statistical survey of the X-ray protein structure shows that the majority of the pyrimidine bases interacting with a protein exhibit close contact (often involving pp stacking) with the side chain of a phenylalanine (a benzene ring) or of a tyrosine (a phenol ring). 30 Recent theoretical studies, using the multireference selfconsistent field (state-averaged CASSCF) method, of the photophysics and photochemistry of a single base 31 and the steadystate optical response of 5BU 32,33 confirm the extreme interest of this system in many respects. In fact, the first and second singlet excited-states of 5BU identified possible relaxation pathways on the Potential Energy Surfaces (PESs) of the molecule, different from the pathways found for the individual moieties of uracil and benzene.…”

Ultrafast Hydrogen Migration in Photoionized Glycine

“…25 With the same experimental approach the non-adiabatic relaxation as well as the nuclear rearrangement following the ionization by an XUV attosecond pulse train have been demonstrated for 5-Fluoro-and 5-Bromo-Uracil radiosensitizers 26,27 and DNA building blocks such as thymine and thymidine 28 , and it could be used in the future to investigate the ultrafast dynamics in model systems for the DNA-protein interaction such as 5-Benzil-Uracil. 29,30,31 Here we present a time-resolved study of intramolecular hydrogen migration in glycine triggered by the sudden ionization induced by an XUV attosecond pulse train and probed by few-femtosecond near-infrared (NIR) pulses.…”

Understanding the modulation mechanism in resonance-enhanced multiphoton probing of molecular dynamics

“…We therefore regard single-photon probing abetter method for a systematic investigation of underlying molecular dynamics. Although high-harmonic sources have only been used on conceptually simple molecules [8][9][10][11][12][13] so far, appli cation of SPI on more complex systems such as nucleobases, base pairs, and base-pair models [36] will be possible.…”