THz spectra and corresponding vibrational modes of DNA base pair cocrystals and polynucleotides
Abstract
The generalized energy-based fragmentation (GEBF) approach has been applied to study the THz spectra and vibrational modes of base pair cocrystals under periodic boundary conditions (denoted as PBC-GEBF). Results of vibrational mode reveal that hydrogen bonds play a pivotal role in the pairing process of base crystals, where most Nsbnd H and Csbnd H bonds stretch to some extent. We also found that hydrogen bonds of a self-made A:T cocrystal completely break in a transition from liquid to the solid state, while self-made C:G cocrystal is different and easier to form a cocrystal, as confirmed by X-ray diffraction (XRD) and terahertz (THz) spectra. Furthermore, we have studied DNA polynucleotides (in both A and B forms) found that the vibrational modes changed a lot during the process of their forming double strand. Despite the key role played by hydrogen bonds, the key contribution originates from collective motions of the main skeleton. A comparative study of the spectra of some stranded fragments suggests that different sequences or forms have similar spectra in THz band. They distinguish from each other mainly in the low-frequency regions, especially below 1 THz. This study would make great contributions to the molecular dynamics model based DNA long-chain structure simulation in the future study.
- Publication:
-
Spectrochimica Acta Part A: Molecular Spectroscopy
- Pub Date:
- July 2018
- DOI:
- 10.1016/j.saa.2018.04.024
- Bibcode:
- 2018AcSpA.200..195W
- Keywords:
-
- DNA base pair crystal;
- Polyncleotides;
- THz spectrum;
- Vibrational mode;
- Generalized energy-based fragmentation (GEBF)