FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan.
FIRST (Graduate School of Frontiers of Innovative Research in Science and Technology), Konan University, 7-1-20 minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan.
J Am Chem Soc. 2024 Nov 27;146(47):32479-32497. doi: 10.1021/jacs.4c09388. Epub 2024 Nov 6.
Hydration plays a key role in the structure-specific stabilization of biomolecules such as nucleic acids. The hydration patterns of biased DNA sequences in the genome, such as GC-repetitive and AT-repetitive regions, are unique to their duplex grooves. As these regions are crucial for maintaining genomic homeostasis and preventing diseases such as cancer and neurodegenerative disorders, the effects of hydration on their stability and functions must be quantitatively analyzed in chemical environments that resemble intracellular conditions. In this study, we systematically investigated duplex formation of biased sequences in cell-like molecularly crowded environments to quantify the effects of groove hydration on their thermodynamics. The interaction of crowders with water molecules in the grooves was found to provide excess stabilization to biased DNAs than to unbiased DNAs, as estimated from the nearest-neighbor prediction model. These hydration effects are sequence-specific and depend on the cation type and cosolute size. Introduction of the "hydration parameters" into the nearest-neighbor model quantifying the effect of groove hydration remarkably enhanced the prediction accuracy for biased DNA stability in crowded environments. Hydration parameters can aid in elucidating the roles of biased sequences in cells such as cation-dependent quadruplex formation in cancer-related genes and regulation of replication initiation by intracellular crowding fluctuations. Additionally, these parameters can predict the free energy changes during the binding of protein to DNA grooves. Overall, our findings can help in realizing and predicting the functions of biased DNAs in cells controlled by variable chemical environments.
水合作用在生物分子（如核酸）的结构特异性稳定中起着关键作用。基因组中偏向性 DNA 序列（如 GC 重复和 AT 重复区域）的水合模式是其双链凹槽所特有的。由于这些区域对于维持基因组的动态平衡以及预防癌症和神经退行性疾病等疾病至关重要，因此必须在类似于细胞内条件的化学环境中定量分析水合作用对其稳定性和功能的影响。在这项研究中，我们系统地研究了细胞样分子拥挤环境中偏向性序列的双链形成，以定量分析凹槽水合作用对其热力学的影响。从最近邻预测模型估计，与非偏向性 DNA 相比，与水合作用相关的拥挤物与凹槽中的水分子相互作用为偏向性 DNA 提供了额外的稳定性。这些水合作用效应是序列特异性的，并且取决于阳离子类型和共溶质大小。将“水合参数”引入到量化凹槽水合作用影响的最近邻模型中，显著提高了在拥挤环境中预测偏向性 DNA 稳定性的准确性。水合参数可以帮助阐明偏向性序列在细胞中的作用，例如与癌症相关基因中的阳离子依赖性四链体形成和细胞内拥挤波动对复制起始的调节。此外，这些参数可以预测蛋白质与 DNA 凹槽结合过程中的自由能变化。总体而言，我们的研究结果可以帮助理解和预测受可变化学环境控制的偏向性 DNA 在细胞中的功能。
