Elucidating the Role\nof Groove Hydration on Stability\nand Functions of Biased DNA Duplexes in Cell-Like Chemical Environments

Hydration plays a key role in the structure-specific\nstabilization\nof biomolecules such as nucleic acids. The hydration patterns of biased\nDNA sequences in the genome, such as GC-repetitive and AT-repetitive\nregions, are unique to their duplex grooves. As these regions are\ncrucial for maintaining genomic homeostasis and preventing diseases\nsuch as cancer and neurodegenerative disorders, the effects of hydration\non their stability and functions must be quantitatively analyzed in\nchemical environments that resemble intracellular conditions. In this\nstudy, we systematically investigated duplex formation of biased sequences\nin cell-like molecularly crowded environments to quantify the effects\nof groove hydration on their thermodynamics. The interaction of crowders\nwith water molecules in the grooves was found to provide excess stabilization\nto biased DNAs than to unbiased DNAs, as estimated from the nearest-neighbor\nprediction model. These hydration effects are sequence-specific and\ndepend on the cation type and cosolute size. Introduction of the “hydration\nparameters” into the nearest-neighbor model quantifying the\neffect of groove hydration remarkably enhanced the prediction accuracy\nfor biased DNA stability in crowded environments. Hydration parameters\ncan aid in elucidating the roles of biased sequences in cells such\nas cation-dependent quadruplex formation in cancer-related genes and\nregulation of replication initiation by intracellular crowding fluctuations.\nAdditionally, these parameters can predict the free energy changes\nduring the binding of protein to DNA grooves. Overall, our findings\ncan help in realizing and predicting the functions of biased DNAs\nin cells controlled by variable chemical environments.