Mass-Tuned Initial Excited-State Structural Dynamics of DNA Nucleobases from UV Resonance Raman Spectroscopy: 5-Deuterouracil

Abstract

5-Deuterouracil (5-d-U) is an analogue of uracil (RNA) and thymine (DNA), which differ only in the mass of their 5-substituent. Previous work has shown that the initial excited-state structural dynamics primarily lie along C5C6 bond lengthening in thymine, while these dynamics primarily lie along C5 and C6 pyramidalization in uracil. To test whether the 5-substituent mass determines these dynamics, the resonance Raman spectra of 5-d-U, with a 5-substituent mass intermediate between uracil and thymine, is measured at wavelengths throughout its 262 nm absorption band. The resulting spectrum of 5-d-U is intermediate between that of thymine and uracil, indicating both bond-lengthening and pyramidalization motions in the excited state. Self-consistent analysis of the resonance Raman excitation profiles and absorption spectra show that the initial excited-state structural dynamics of 5-d-U are indeed intermediate between those of thymine and uracil, supporting the mass-tuning model of initial excited-state structural dynamics in DNA and RNA pyrimidine nucleobases.

Initial Excited-State Structural Dynamics of 6-Substituted Uracil Derivatives: Femtosecond Angle and Bond Lengthening Dynamics in Pyrimidine Nucleobase Photochemistry

“…However, an unexpectedly upward trend is observed in the 1235 cm −1 mode, which causes a poorer fit to the experimental RREP of this normal mode. The shape of this resonance Raman cross-section excitation profile may be due to resonance with [21], γ(C2N3) [11], ring def 6 [10], γ(C4O10) [9], γ(C5H11) [8] the higher electronic transition. Further experimentation is necessary to characterize the UV resonance Raman excitation profiles in the 1235 cm −1 mode of both molecules at higher energies.…”

“…The general implementation of these equations for absorption and resonance Raman spectroscopy have been described in detail previously. [4][5][6][7][8][9][10][11][12][13][14]16,17 The vibrational mode assignments described in Tables 1 and 2 were obtained by DFT computation at the B3LYP/6-311G(d,p) level of theory, with the default gradients implemented in the Gaussian09 18 package performed on the initial planar C s structures of uracil and 6-MeU in the diketo tautomer form. The isotope effect was calculated for 6-d-U from the uracil frequencies, which are not scaled.…”

“…However, the 6-d-U spectrum in Figure 4 (B) exhibits more uracil-like spectral behavior, particularly in the 1230 and 1600 cm −1 spectral regions. 7,8 However, two peaks are observed for uracil, 5-d-U and 6-d-U in the 1600−1666 cm −1 region, but only a single peak in this region attributed to C5C6 stretch, is seen for 5-MeU and 6-MeU. The very similar integrated peak intensities of the 1600 cm −1 bands in 5-MeU and 6-MeU predict that the C5−C6 stretch or the bond lengthening coordinate is similarly affected by the presence of a CH 3 group on C5 or C6.…”

Resonance Raman Intensities Demonstrate that C5 Substituents Affect the Initial Excited‐State Structural Dynamics of Uracil More than C6 Substituents

“…The methods used for converting the resonance Raman intensities into differential cross sections have been described previously . The experimental resonance Raman differential cross sections of sulfate used for the calculations were 3.30×10 −12 , 2.87×10 −12 , 2.42×10 −12 , and 2.05×10 −12 Å 2 molecule −1 sr −1 at λ =250, 257, 266, and 275 nm, respectively …”

“…The initial excited‐state structural dynamics of nucleobases with short‐lived excited‐states can be obtained by using resonance Raman intensities, absorption spectra, and a self‐consistent time‐dependent wavepacket formalism. Such an analysis has been performed on numerous uracil derivatives in an attempt to elucidate photochemical mechanisms in DNA components. Previous elucidation of the initial excited‐state structural dynamics of C5‐and C6‐methylated uracil derivatives have shown that methyl substitution increases the initial excited‐state structural dynamics along the C5−C6 bond‐lengthening coordinate .…”