Stability prediction of canonical and non-canonical structures of nucleic acids in various molecular environments and cells,Chemical Society Reviews

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Stability prediction of canonical and non-canonical structures of nucleic acids in various molecular environments and cells
Chemical Society Reviews ( IF 40.4 ) Pub Date : 2020-10-13 , DOI: 10.1039/d0cs00594k
Shuntaro Takahashi _{1,

2,

3,

4} , Naoki Sugimoto _{1,

2,

3,

4,

5}

Affiliation

Nucleic acids (DNA and RNA) dynamically fold and unfold to exert their functions in cells. These folding and unfolding behaviours are also the basis for various technical applications. To understand the biological mechanism of nucleic acid function, and design active materials using nucleic acids, biophysical approaches based on thermodynamics are very useful. Methods for predicting the stability of canonical duplexes of nucleic acids have been extensively investigated for more than half a century and are now widely used. However, such predictions are not always accurate under various solution conditions, particularly cellular conditions, as the concentrations of cations and cosolutes under intracellular conditions, named as molecular crowding, differ from those under standard experimental conditions. Moreover, the crowding condition in cells is spatiotemporally variable. Furthermore, non-canonical structures such as triplex and tetraplex exist in cells and play important roles in gene expression. Therefore, a prediction method reflecting the cellular conditions must be established to determine the stability of various nuclei acid structures. This article reviews the biophysicochemical background of predicting nucleic acid stability and recent advances in the prediction of this stability under cellular conditions.

中文翻译：

各种分子环境和细胞中核酸的规范和非规范结构的稳定性预测

核酸（DNA和RNA）动态折叠和展开以在细胞中发挥其功能。这些折叠和展开行为也是各种技术应用的基础。为了理解核酸功能的生物学机制，并使用核酸设计活性物质，基于热力学的生物物理方法非常有用。预测核酸经典双链体稳定性的方法已经进行了半个多世纪的研究，现已广泛使用。但是，这种预测在各种溶液条件下，尤其是在细胞条件下，并不总是准确的，因为在细胞内条件下（称为分子拥挤）的阳离子和共溶质的浓度与标准实验条件下的不同。此外，细胞中的拥挤状况是时空可变的。此外，细胞中存在非规范结构，例如三链体和四链体，并在基因表达中起重要作用。因此，必须建立一种反映细胞状况的预测方法来确定各种核酸结构的稳定性。本文综述了预测核酸稳定性的生物物理化学背景以及在细胞条件下预测这种稳定性的最新进展。

更新日期：2020-11-03

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