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首页> 外文期刊>The journal of physical chemistry, A. Molecules, spectroscopy, kinetics, environment, & general theory >Terahertz Absorption of DNA Decamer Duplex
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Terahertz Absorption of DNA Decamer Duplex

机译：DNA Decamer Duplex的太赫兹吸收

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摘要

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.
机译：这项工作结合了实验和理论方法来研究由序列低聚物5'-CCGGCGCCGG-3'形成的DNA的太赫兹吸收光谱。这种自我互补的DNA decamer的三维结构已得到充分研究，使我们能够直接识别与特定构象相关的低频声子模式并进行全面的计算机模拟。两种建模技术，即正常模式分析和具有显式溶剂分子的纳秒分子动力学，被用来提取低频振动模式，并以此为基础计算吸收光谱。使用太赫兹傅里叶变换红外光谱法在10-25 cm〜（-1）的频率范围内测量DNA decamer在水溶液中的吸收光谱。观察到多个良好解析和可再现的共振模式。当计算和比较实验光谱时，基于分子动力学模拟的光谱与基于正常模式分析的光谱具有更好的相关性。这些结果证明在这种短的DNA双链体中存在大量的活跃的低频声子模式。

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