Yeou Sanghun, Hwang Jihee, Yi Jaehun, Kim Cheolhee, Kim Seong Keun, Lee Nam Ki
Department of Chemistry, Seoul National University 08832 Seoul Republic of Korea
National Science Museum Daejeon 34143 Republic of Korea.
Chem Sci. 2022 Jun 2;13(25):7516-7525. doi: 10.1039/d1sc07115g. eCollection 2022 Jun 29.
Cytosine methylation plays an essential role in many biological processes, such as nucleosome inactivation and regulation of gene expression. The modulation of DNA mechanics may be one of the regulatory mechanisms influenced by cytosine methylation. However, it remains unclear how methylation influences DNA mechanics. Here, we show that methylation has contrasting effects on the bending property of dsDNA depending on DNA curvature. We directly applied bending force on 30 base pairs of dsDNA using a D-shaped DNA nanostructure and measured the degree of bending using single-molecule fluorescence resonance energy transfer without surface immobilization. When dsDNA is weakly bent, methylation increases the stiffness of dsDNA. The stiffness of dsDNA increased by approximately 8% with a single methylation site for 30 bp dsDNA. When dsDNA is highly bent by a strong force, it forms a kink, , a sharp bending of dsDNA. Under strong bending, methylation destabilizes the non-kink form compared with the kink form, which makes dsDNA near the kink region apparently more bendable. However, if the kink region is methylated, the kink form is destabilized, and dsDNA becomes stiffer. As a result, methylation increases the stiffness of weakly bent dsDNA and concurrently can promote kink formation, which may stabilize the nucleosome structure. Our results provide new insight into the effect of methylation, showing that cytosine methylation has opposite effects on DNA mechanics depending on its curvature and methylation location.
胞嘧啶甲基化在许多生物学过程中起着至关重要的作用，如核小体失活和基因表达调控。DNA力学性质的调节可能是受胞嘧啶甲基化影响的调控机制之一。然而，甲基化如何影响DNA力学性质仍不清楚。在这里，我们表明甲基化对双链DNA（dsDNA）的弯曲特性有相反的影响，这取决于DNA的曲率。我们使用D形DNA纳米结构直接对30个碱基对的dsDNA施加弯曲力，并通过单分子荧光共振能量转移测量弯曲程度，且无需表面固定。当dsDNA弱弯曲时，甲基化会增加dsDNA的刚性。对于30 bp的dsDNA，单个甲基化位点可使dsDNA的刚性增加约8%。当dsDNA受到强力高度弯曲时，它会形成一个扭结，即dsDNA的急剧弯曲。在强弯曲下，与扭结形式相比，甲基化会使非扭结形式不稳定，这使得扭结区域附近的dsDNA明显更易弯曲。然而，如果扭结区域被甲基化，扭结形式会变得不稳定，dsDNA会变得更硬。结果，甲基化增加了弱弯曲dsDNA的刚性，同时可以促进扭结形成，这可能会稳定核小体结构。我们的结果为甲基化的作用提供了新的见解，表明胞嘧啶甲基化根据其曲率和甲基化位置对DNA力学性质有相反的影响。
