Resonance Hyper-Raman Spectroscopy of Nucleotides and Polynucleotides

Abstract

We applied 532 nm-excited two-photon resonance hyper-Raman (RHR) spectroscopy to nucleotides (dA, dG, dT, and dC) to obtain fundamental knowledge about their spectral patterns. The RHR spectrum of each nucleotide exhibited various modes of the purine and pyrimidine rings, showing the ability to acquire the structural information on the chromophore. The band positions of the RHR spectrum and the 266 nm-excited onephoton UV-resonance Raman (UVRR) spectrum were identical, while the intensity patterns differed. The peak assignments of the RHR bands were given by analogy to the UVRR spectrum. In examining the polynucleotides, which form a double-stranded helix through intermolecular hydrogen bonds, some RHR bands were found to be available as structural markers. Moreover, several overtone and combination bands were detected above 2000 cm −1 . The frequencies of dA and dG were accounted for by considering the involvement of the vibration of dA at 1579 cm −1 and that of dG at 1482 cm −1 , respectively. Multiple vibronically active modes were seen for dT and dC. HR spectroscopy offers unique information on the fundamental, combination, and overtone modes of dA and dG, of which the multiple electronic states are involved in the resonance process.

Characterization of Secondary Structures of Model Polypeptides in Solutions with Hyper-Raman Spectroscopy

“…Both HR and IR signals arise from odd orders of electric dipole moment, indicating that HR spectra show similarity to IR absorption spectra rather than visible Raman spectra. [22][23][24][25]28,29 The reported FT-IR spectra of PLL α-helix and the undefined conformation in aqueous solutions, with the quantitative subtraction of the contribution of water to spectra, show only the amide I and II bands around 1650 and 1550 cm −1 , respectively. 58 In the FT-IR spectra, the amide I band is stronger than the amide II band in both the α-helix and the undefined conformation, different from our HR spectra.…”

“…Furthermore, CD spectroscopy has been applied to distinguish minor secondary structures such as the 3 10 - and π-helices by decomposing relatively broad bands in the UV region. , Similarly, vibrational spectroscopy can also characterize those from fine structures in vibrational spectra . CD spectroscopy and vibrational spectroscopy are intrinsically different; the former is based on electronic transitions, , while the latter is about vibrational modes of chemical bonds, including additional information on vibronic couplings under electronic preresonant or resonant conditions like UVRR spectroscopy. , As a vibrational spectroscopic technique providing complementary information on molecular vibrations, hyper-Raman (HR) spectroscopy has been recently applied to biomolecules, including N -methylacetamide (NMA), amino acids and proteins, , and nucleotides and polynucleotides . HR spectroscopy gives unique spectral features different from Raman and IR spectra because of the distinct selection rules. ,− We have recently reported the HR spectra of NMA as a model molecule for the peptide backbone.…”

“…19,20 As a vibrational spectroscopic technique providing complementary information on molecular vibrations, hyper-Raman (HR) spectroscopy has been recently applied to biomolecules, including N-methylacetamide (NMA), 22 amino acids and proteins, 23,24 and nucleotides and polynucleotides. 25 HR spectroscopy gives unique spectral features different from Raman and IR spectra because of the distinct selection rules. 22,26−29 We have recently reported the HR spectra of NMA as a model molecule for the peptide backbone.…”

TMAO perturbs intermolecular vibrational motions of water revealed by low-frequency modes

“…Hyper-Raman (HR) spectroscopy has been recently applied to water and small organic molecules in solutions as a vibrational spectroscopic technique complementary to conventional IR and Raman spectroscopies. [38][39][40][41][42][43] In particular, HR spectroscopy has the advantage of observing signals in the low-frequency region in addition to the bending and stretching vibrational motions of water molecules, 38 while IR spectroscopy has difficulties measuring the whole spectral region, including the low-frequency region. Low-frequency signals of water and aqueous solutions directly reflect information on the intramolecular hydrogen bond formation and collective motions of water, 38 closely correlated with the initiation of rearrangement dynamics of the hydrogen bonding network.…”