A. Yu. Sosorev, O. D. Paraschuk, A. A. Trubitsyn, N. O. Dubinets, I. V. Chicherin, D. Yu. Paraschuk
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引用次数: 0
Abstract
The degree of DNA compaction in various regions of the cell nucleus determines whether the corresponding genes should be expressed and other crucial cellular processes, such as DNA replication and repair, should occur. Therefore, the development of approaches to the experimental assessment of DNA compactness in cell nuclei, as well as its indicator, dynamic disorder which determines the degree of thermal fluctuation in the position and mutual orientation of molecular fragments, is highly relevant. In this paper, using single-stranded guanine and cytosine oligonucleotides, as well as their double-stranded combination as an example, it is shown that dynamic disorder in DNA can be assessed based on low-frequency Raman scattering (RS) spectroscopy data. For the first time, Raman spectra of oligonucleotides have been measured over a wide frequency range, including the low-frequency (10–200 cm\({}^{-1}\)) and high-frequency (200–2000 cm\({}^{-1}\)) regions. It was found that the low-frequency Raman intensity is maximal in single-stranded oligocytosine and minimal in the double-stranded oligonucleotide, which is in full agreement with the magnitude of dynamic disorder estimated from molecular dynamics simulations. The obtained results indicate the promising application of low-frequency Raman spectroscopy for assessing dynamic disorder and DNA compactness. The use of such a technique is expected to contribute to the understanding of key cellular processes and the physical mechanisms that underlie them, which is necessary for the development of advanced methods in molecular biophysics and cell biology.
摘要 细胞核各区域 DNA 的致密程度决定了相应基因是否表达以及 DNA 复制和修复等其他关键细胞过程是否发生。因此，开发实验评估细胞核中 DNA 紧密度的方法及其指标--动态无序度（动态无序度决定分子片段位置和相互取向的热波动程度）--具有重要意义。本文以单链鸟嘌呤和胞嘧啶寡核苷酸以及它们的双链组合为例，说明可以根据低频拉曼散射（RS）光谱数据评估 DNA 的动态无序度。该研究首次在较宽的频率范围内测量了寡核苷酸的拉曼光谱，包括低频（10-200 cm\({}^{-1}\) ）和高频（200-2000 cm\({}^{-1}\) ）区域。研究发现，低频拉曼强度在单链寡核苷酸中最大，而在双链寡核苷酸中最小，这与分子动力学模拟估计的动态无序程度完全一致。这些结果表明，低频拉曼光谱在评估动态无序度和 DNA 紧密度方面的应用前景广阔。这种技术的使用有望促进对关键细胞过程及其物理机制的理解，这对于分子生物物理学和细胞生物学先进方法的发展是必要的。
期刊介绍：
Moscow University Physics Bulletin publishes original papers (reviews, articles, and brief communications) in the following fields of experimental and theoretical physics: theoretical and mathematical physics; physics of nuclei and elementary particles; radiophysics, electronics, acoustics; optics and spectroscopy; laser physics; condensed matter physics; chemical physics, physical kinetics, and plasma physics; biophysics and medical physics; astronomy, astrophysics, and cosmology; physics of the Earth’s, atmosphere, and hydrosphere.
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