The effect of solvent dynamics on the low frequency collective motions of DNA in solution and unoriented films

Low-frequency vibrations of water molecules in DNA minor groove

Water molecules around the DNA form the hydration shell having different structural and dynamical features in different regions of the double helix. In the DNA minor groove, water molecules are highly ordered and in the case of AT nucleotide sequence, the formation of a hydration spine is observed. In the present research, the vibrations of the hydration spine have been studied to establish the mode of translational vibrations of water molecules in the DNA low-frequency spectra (water-spine vibrations). Using the developed phenomenological model with the parameters determined for different nucleotides of the DNA fragment CGCGAATTCGCG, the frequencies of vibrations of the hydration spine have been obtained within 185 ± 20 cm[Formula: see text] depending on type of nucleotide. The obtained frequencies are in the same region as the translational vibrations of water molecules in the bulk. To select the mode of water-spine vibrations from those modes that are present in the bulk water, the dynamics of DNA with different nucleotide contents has been analyzed, and the possible influence of heavy water has been estimated. The determined features of the mode of water vibrations in the hydration spine of DNA minor groove indicate that this mode may be observed in the experimental spectra.

Terahertz absorption of DNA decamer duplex

This work combines experimental and theoretical approaches to investigate terahertz absorption spectra of the DNA formed by the sequence oligomer 5'-CCGGCGCCGG-3'. The three-dimensional structure of this self-complimentary DNA decamer has been well-studied, permitting us to perform direct identification of the low-frequency phonon modes associated with specific conformation and to conduct comprehensive computer simulations. Two modeling techniques, normal-mode analysis and nanosecond molecular dynamics with explicit solvent molecules, were employed to extract the low-frequency vibrational modes based on which the absorption spectra were calculated. The absorption spectra of the DNA decamer in aqueous solution were measured in the frequency range 10-25 cm(-1) using the terahertz Fourier transform infrared spectroscopy. Multiple well-resolved and reproducible resonance modes were observed. When calculated and experimental spectra were compared, the spectrum based on molecular dynamics simulations showed a better correlation with the experimental spectra than the one based on normal-mode analysis. These results demonstrate that there exist a considerable number of active low-frequency phonon modes in this short DNA duplex.

Analysis of low-frequency phonons in guanosine dihydrate based on molecular dynamics simulations

Fourier analysis, using the atomic trajectory calculated by molecular dynamics simulation at 300 K, is applied to the study of low-frequency phonons of guanine dihydrate. The vibrational modes of guanine bases are analyzed, and the optically active modes associated with the guanine moieties are extracted. There are a few significant peaks in the low-frequency region. A possible assignment of the Raman active mode near 27 cm(-1), whose origin would be common to the S-mode of DNA double helices, is discussed.