Initial excited-state structural dynamics of 2′-deoxyadenosine

Abstract

Purine nucleobases (adenosine and guanosine) are prone to spontaneous breaking of the nucleosidic bond to form abasic sites in both DNA and RNA. However, the purines also undergo photochemical reactions, including oxidation and cycloaddition, to form damage sites, albeit at lower photochemical quantum yields than the pyrimidines. In this study, we use ultraviolet resonance Raman spectroscopy to measure the initial excited-state structural dynamics in the nucleoside, 2′-deoxyadenosine. The resonance Raman-derived initial excited-state structural dynamics throughout the 260 nm La excited electronic state of adenine are found to be smaller in the nucleoside than in the previously reported 9-methyladenine nucleobase derivative, consistent with what is found for the pyrimidines thymine and uracil. Interestingly, resonance-enhanced vibrational modes in this electronic state also contain internal coordinates localized on the sugar, which may represent a different energy dissipation mechanism than in the pyrimidine nucleosides. The results will be discussed in terms of the initial excited-state photophysics and photochemistry of DNA and RNA.

Initial Excited-State Structural Dynamics of dT and dA Oligonucleotide Homopentamers Using Resonance Raman Spectroscopy

“…The slopes of the excited-state potential energy surface at Franck–Condon geometry (β/ℏ) in cm –1 were obtained by fitting the experimental cross sections and absorption spectrum with the following parameters in eqs and : temperature, T = 298 K, zero–zero energy, E 0 = 36 000 cm –1 , Gaussian homogeneous line width, Γ G = 1750 cm –1 , inhomogeneous line width, θ = 1500 cm –1 , transition length, M = 0.88 Å, and Brownian oscillator line shape, κ = Λ/ D = 0.1. The mode assignments are from ref . Uncertainties in the parameters are estimated to be ±10%, based on the ±10% uncertainty in the intensities of strong Raman modes and ±20% uncertainty in weaker Raman modes.…”

“… a The parameters for 2′-deoxyadenosine were obtained from ref . b The parameters for thymidine were obtained from ref . Uncertainties in the parameters are estimated to be ±10%, based on the ±10% uncertainty in the intensities of strong Raman modes and ±20% uncertainty in weaker Raman modes. …”

“…Unfortunately, no vibrational assignments have been carried out for any of the homopentamers. However, the vibrational assignments and resonance Raman studies are reported for the nucleotide monomers. ,,,, Therefore, those reported vibrational mode assignments are used in further discussion. Though there were studies on the Raman signature of genomic DNA, those studies only show that the intensity and frequencies are sensitive to base sequences; they do not provide any insight into the excited-state structural dynamics.…”

“…There have been several resonance Raman studies on DNA and DNA components. − Loppnow and co-workers have successfully used resonance Raman spectroscopy to understand the initial excited-state structural dynamics of the different nucleobases and their derivatives. ,− ,,− ,− In thymine, the observed resonance Raman intensities suggest that C5C6 bond elongation is the primary structural dynamics. This bond elongation and the pyramidalization of C5 and C6, the other significant excited-state structural dynamics, are consistent with the thymine photochemistry. , In contrast, the C5H and C6H bending modes are the most intense modes in uracil, where the photohydrate is the major photoproduct .…”

“…The resonance Raman intensities of 2′-deoxyguanosine and 2′deoxyadenosine also show that initial excited-state structural dynamics occur primarily along the photochemically active coordinates. 34,53 Resonance Raman studies on cytosine suggests that only about one-third of the reorganization energy is along vibrational modes that are photochemically active. 42 All these studies show that there is a pronounced difference in the initial excited-state structural dynamics between the nucleobases that are reflected in their photoproduct formation and quantum yields.…”