The influence of anharmonic and solvent effects on the theoretical vibrational spectra of the guanine–cytosine base pairs in Watson–Crick and Hoogsteen configurations

Abstract

The theoretical IR and Raman spectra of the guanine-cytosine DNA base pairs in Watson-Crick and Hoogsteen configurations were computed using DFT method with M06-2X meta-hybrid GGA exchange-correlation functional, including the anharmonic corrections and solvent effects. The results for harmonic frequencies and their anharmonic corrections were compared with our previously calculated values obtained with the B3PW91 hybrid GGA functional. Significant differences were obtained for the anharmonic corrections calculated with the two different DFT functionals, especially for the stretching modes, while the corresponding harmonic frequencies did not differ considerable. For the Hoogtseen case the H⁺ vibration between the G-C base pair can be characterized as an asymmetric Duffing oscillator and therefore unrealistic anharmonic corrections for normal modes where this proton vibration is involved have been obtained. The spectral modification due to the anharmonic corrections, solvent effects and the influence of sugar-phosphate group for the Watson-Crick and Hoogsteen base pair configurations, respectively, were also discussed. For the Watson-Crick case also the influence of the stacking interaction on the theoretical IR and Raman spectra was analyzed. Including the anharmonic correction in our normal mode analysis is essential if one wants to obtain correct assignments of the theoretical frequency values as compared with the experimental spectra.

Robust IR‐based detection of stable and fractionally populated G‐C+ and A‐T Hoogsteen base pairs in duplex DNA

“…This prompted a few studies 105--107 that investigated the effects of anharmonicity on the vibrational density of states of Watson-Crick and Hoogsteen bps. These anharmonic corrections 105,106 to the potential provided better predictions of the Raman experimental value for the Hoogsteen protonated cytosine at 1260 cm −1 and which we observe at 1280 cm −1 in the IR measurements. The anharmonic corrections were particularly important for the G-C + Hoogsteen bp modes involving the extra proton.…”

“…The anharmonic corrections were particularly important for the G-C + Hoogsteen bp modes involving the extra proton. Additionally, these studies [105,106] list several high-frequency IR modes (between 1740 and 1770 cm À1 , depending on the potential used) due to carbonyl stretching and N-H bending modes that are not observed in our experimental spectra. In addition, these theoretical studies did not predict the change in position of the cytosine ring mode which we observe at around 1540 cm À1 in Hoogsteen (1530 cm À1 in Watson-Crick).…”

“…Previous studies have performed theoretical investigations of the Raman [104][105][106][107] and IR spectra [106,107] of G-C + Hoogsteen bps [107]. Early calculations [104] typically found shifts in the opposite direction to those observed in experiment.…”

“…Early calculations [104] typically found shifts in the opposite direction to those observed in experiment. This prompted a few studies [105][106][107] that investigated the effects of anharmonicity on the vibrational density of states of Watson-Crick and Hoogsteen bps. These anharmonic corrections [105,106] to the potential provided better predictions of the Raman experimental value for the Hoogsteen-protonated cytosine at 1260 cm À1 and which we observe at 1280 cm À1 in the IR measurements.…”

Fingerprints of Both Watson–Crick and Hoogsteen Isomers of the Isolated (Cytosine-Guanine)H+ Pair

“…However, rare tautomers and specific protonation sites within the pairs are hardly detectable by the biological machinery, and very complicated and time-consuming experiments such as X-ray crystal diffraction or NMR nuclear relaxation experiments have been used to structurally characterize these species. In addition, many theoretical efforts have been done to understand these phenomena, ,,,, which need benchmark gas-phase experimental data to prove their validity and universality.…”