Nearest-neighbor parameters for predicting DNA duplex stability in diverse molecular crowding conditions

Proceedings of the National Academy of Sciences of the United States of America
Saptarshi GhoshNaoki Sugimoto

Abstract

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 nearest-neighbor 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 nearest-neighbor parameters in the crowding condition. The determined parameters were shown to predict the thermodynamic parameters (∆H°, ∆S°, and ∆G°37) and melting temperatures (Tm) 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 val...Continue Reading

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Citations

Sep 16, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Shuntaro TakahashiNaoki Sugimoto
Feb 17, 2021·Accounts of Chemical Research·Shuntaro Takahashi, Naoki Sugimoto
Jul 18, 2020·International Journal of Biological Macromolecules·Andrea De PieriDimitrios I Zeugolis
Mar 31, 2021·Topics in Current Chemistry·Saki Matsumoto, Naoki Sugimoto
Jul 11, 2021·Nucleic Acids Research·Hisae Tateishi-Karimata, Naoki Sugimoto
Oct 20, 2020·Journal of the American Chemical Society·Jim-Marcel KnopRoland Winter
Feb 2, 2022·ChemPlusChem·Xiaohui DingDayong Yang

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