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Low-frequency vibrations of water molecules in DNA minor groove
The European Physical Journal E ( IF 1.8 ) Pub Date : 2021-06-24 , DOI: 10.1140/epje/s10189-021-00080-3
T L Bubon 1 , S M Perepelytsya 1
Affiliation  

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\(^{-1}\) 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



中文翻译:

DNA小沟中水分子的低频振动

DNA 周围的水分子形成水合壳,在双螺旋的不同区域具有不同的结构和动力学特征。在 DNA 小沟中,水分子高度有序,在 AT 核苷酸序列的情况下,观察到水合脊的形成。在目前的研究中,研究了水合脊椎的振动,以建立 DNA 低频光谱中水分子的平移振动模式(水脊振动)。使用已开发的现象学模型和为 DNA 片段 CGCGAATTCGCG 的不同核苷酸确定的参数,已获得水化脊椎的振动频率在 185 ± 20 cm \(^{-1}\)取决于核苷酸的类型。获得的频率与大量水分子的平移振动处于同一区域。为了从存在于大量水中的那些模式中选择水脊振动模式,分析了具有不同核苷酸含量的 DNA 的动力学,并估计了重水的可能影响。DNA小沟水合脊中水振动模式的确定特征表明,这种模式可以在实验光谱中观察到

更新日期:2021-06-24
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