Nearest-neighbor parameters for predicting DNA duplex stability in diverse molecular crowding conditions
Saptarshi Ghosh, Shuntaro Takahashi, Tatsuya Ohyama, Tamaki Endoh, Hisae Tateishi‐Karimata, Naoki Sugimoto
Abstract
Significance The intracellular environment is occupied by a high concentration of various types of biomolecules that lead to a situation known as molecular crowding, which affects important biological reactions such as replication and transcription by altering the stability of nucleic acids. Because intracellular crowded conditions are heterogeneous, a general method is needed to predict the stability of nucleic acids in such conditions. Here, we predicted the stability of DNA duplexes under crowded conditions induced by a large amount of a cosolute at a physiological salt concentration using the nearest-neighbor model. We also extended the parameters for predicting DNA stability under conditions imposed by different cosolutes that mimicked a localized intracellular crowded region.