Nearest-neighbor parameters for predicting DNA duplex stability in diverse molecular crowding conditions
Nearest-neighbor parameters for predicting DNA duplex stability in diverse molecular crowding conditions
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DOI：
10.1073/pnas.1920886117
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发表时间：
2020-06-23
影响因子：
11.1
通讯作者：
Sugimoto, Naoki
中科院分区：
文献类型：
--
作者：
Ghosh, Saptarshi;Takahashi, Shuntaro;Sugimoto, Naoki
细胞内环境是拥挤和异质的。尽管核酸双链体在稀溶液中的热力学稳定性是可以预测的，但在特定的细胞内条件下预测这种稳定性的方法尚不存在。我们最近的研究表明，自互补DNA的近邻模型在聚乙二醇量为40%、平均分子质量为200(PEG200)的100 mM氯化钠溶液中是有效的。在这里，我们确定了在相同拥挤条件下DNA双链形成的最近邻参数，以预测细胞内环境中DNA双链的热力学。在拥挤条件下，核苷酸的优先水化是近邻参数的关键因素。所确定的参数对拥挤条件下DNA二聚体的热力学参数(Delta H度、Delta S度和Delta G度(37))和熔融温度(T-m)的预测具有显著的准确性。此外，根据双链体稳定性与共溶体溶液水活度的关系，提出了一种预测短DNA双链在不同共溶体中稳定性的通用方法。本文描述的方法对于研究特定细胞内拥挤条件下发生的生物过程以及基于DNA的生物技术在拥挤环境中的应用将是有价值的。
The intracellular environment is crowded and heterogeneous. Although the thermodynamic stability of nucleic acid duplexes is predictable in dilute solutions, methods of predicting such stability under specific intracellular conditions are not yet available. We recently showed that the nearest-neighbor model for self-complementary DNA is valid under molecular crowding condition of 40% polyethylene glycol with an average molecular weight of 200 (PEG 200) in 100 mM NaCl. Here, we determined nearestneighbor parameters for DNA duplex formation under the same crowding condition to predict the thermodynamics of DNA duplexes in the intracellular environment. Preferential hydration of the nucleotides was found to be the key factor for nearestneighbor parameters in the crowding condition. The determined parameters were shown to predict the thermodynamic parameters (Delta H degrees, Delta S degrees, and Delta G degrees(37)) and melting temperatures (T-m) of the DNA duplexes in the crowding condition with significant accuracy. Moreover, we proposed a general method for predicting the stability of short DNA duplexes in different cosolutes based on the relationship between duplex stability and the water activity of the cosolute solution. The method described herein would be valuable for investigating biological processes that occur under specific intracellular crowded conditions and for the application of DNA-based biotechnologies in crowded environments.