Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea.
J Am Chem Soc. 2022 Jul 27;144(29):13137-13145. doi: 10.1021/jacs.2c02466. Epub 2022 Jul 15.
Z-DNA, a noncanonical helical structure of double-stranded DNA (dsDNA), plays pivotal roles in various biological processes, including transcription regulation. Mechanical stresses on dsDNA, such as twisting and stretching, help to form Z-DNA. However, the effect of DNA bending, one of the most common dsDNA deformations, on Z-DNA formation is utterly unknown. Here, we show that DNA bending induces the formation of Z-DNA, that is, more Z-DNA is formed as the bending force becomes stronger. We regulated the bending force on dsDNA by using D-shaped DNA nanostructures. The B-Z transition was observed by single-molecule fluorescence resonance energy transfer. We found that as the bending force became stronger, Z-DNA was formed at lower Mg concentrations. When dsDNA contained cytosine methylations, the B-Z transition occurred at 78 mM Mg (midpoint) in the absence of the bending force. However, the B-Z transition occurred at a 28-fold lower Mg concentration (2.8 mM) in the presence of the bending force. Monte Carlo simulation suggested that the B-Z transition stabilizes the bent form via the formation of the B-Z junction with base extrusion, which effectively releases the bending stress on DNA. Our results clearly show that the bending force facilitates the B-Z transition under physiological salt conditions.
Z-DNA，一种双链 DNA（dsDNA）的非规范螺旋结构，在包括转录调控在内的多种生物学过程中发挥着关键作用。dsDNA 上的机械应力，如扭曲和拉伸，有助于形成 Z-DNA。然而，DNA 弯曲（dsDNA 最常见的变形之一）对 Z-DNA 形成的影响却完全未知。在这里，我们表明 DNA 弯曲会诱导 Z-DNA 的形成，即随着弯曲力的增强，形成的 Z-DNA 更多。我们使用 D 形 DNA 纳米结构来调节 dsDNA 上的弯曲力。通过单分子荧光共振能量转移观察 B-Z 转变。我们发现，随着弯曲力的增强，Z-DNA 在更低的 Mg 浓度下形成。当 dsDNA 含有胞嘧啶甲基化时，在不存在弯曲力的情况下，B-Z 转变发生在 78 mM Mg（中点）处。然而，在存在弯曲力的情况下，B-Z 转变发生在 28 倍更低的 Mg 浓度（2.8 mM）处。蒙特卡罗模拟表明，B-Z 转变通过碱基外推形成 B-Z 连接来稳定弯曲形式，这有效地释放了 DNA 上的弯曲应力。我们的结果清楚地表明，在生理盐条件下，弯曲力有助于 B-Z 转变。
