论文标题
DNA双螺旋的小凹槽中水分子的低频振动
Low-frequency vibrations of water molecules in minor groove of the DNA double helix
论文作者
论文摘要
DNA双螺旋的水合壳中结构化水分子的动力学对于理解许多生物学机制至关重要。特别是，本研究的目的是在DNA小凹槽中形成的水脊柱的振动动力学。在开发的现象学模型的框架内，基于DNA构象振动的方法，H键拉伸的模式，骨干振动和水转换振动。根据核苷酸序列的不同，水分子翻译振动的计算频率从167到205 cm $^{ - 1} $不等。水振动的模式高于DNA内部构象振动的模式。计算出的水振动频率已与DNA的实验低频振动光谱有足够的一致性。在DNA的振动光谱的同一区域中观察到所获得的水振动模式，这是大量相中水分子的翻译振动。为了区分DNA小凹槽中的水分子的振动与大量水中的水分子的振动，还考虑了用重水的DNA动力学。结果表明，在重水的情况下，振动的频率约为10 cm $^{ - 1} $，可以在实验中使用，以识别DNA小凹槽中水合的水振动模式。
The dynamics of the structured water molecules in the hydration shell of the DNA double helix is of paramount importance for the understanding of many biological mechanisms. In particular, the vibrational dynamics of a water spine that is formed in the DNA minor groove is the aim of the present study. Within the framework of the developed phenomenological model, based on the approach of DNA conformational vibrations, the modes of H-bond stretching, backbone vibrations, and water translational vibrations have been established. The calculated frequencies of translation vibrations of water molecules vary from 167 to 205 cm$^{-1}$ depending on the nucleotide sequence. The mode of water vibrations higher than the modes of internal conformational vibrations of DNA. The calculated frequencies of water vibrations have shown a sufficient agreement with the experimental low-frequency vibrational spectra of DNA. The obtained modes of water vibrations are observed in the same region of the vibrational spectra of DNA as translation vibrations of water molecules in the bulk phase. To distinguish the vibrations of water molecules in the DNA minor groove from those in the bulk water, the dynamics of DNA with heavy water was also considered. The results have shown that in the case of heavy water the frequencies of vibrations decrease for about 10 cm$^{-1}$ that may be used in the experiment to identify the mode of water vibrations in the spine of hydration in DNA minor groove.
