Directing the motion of molecules/colloids in any specific direction is of great interest in many applications of chemistry, physics, and biological sciences, where regulated positioning or transportation of materials is highly desired. Using Brownian dynamics simulations of coarse-grained models of a long, double-stranded DNA molecule and positively charged nanoparticles, we observed that the motion of a single nanoparticle bound to and wrapped by the DNA molecule can be directed along a gradient of DNA local flexibility. The flexibility gradient is constructed along a 0.8 kilobase-pair DNA molecule such that local persistence length decreases gradually from 50 nm to 40 nm, mimicking a gradual change in sequence-dependent flexibility. Nanoparticles roll over a long DNA molecule from less flexible regions towards more flexible ones as a result of the decreasing energetic cost of DNA bending and wrapping. In addition, the rolling becomes slightly accelerated as the positive charge of nanoparticles decreases due to a lower free energy barrier of DNA detachment from charged nanoparticle for processive rolling. This study suggests that the variation in DNA local flexibility can be utilized in constructing and manipulating supramolecular assemblies of DNA molecules and nanoparticles in structural DNA nanotechnology.

中文翻译：

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带正电荷的纳米粒子在长DNA分子上沿着柔性梯度方向滚动†

在化学，物理学和生物科学的许多应用中，对分子/胶体的任何特定方向的运动进行引导都引起了极大的兴趣，在这些应用中，人们非常希望对材料进行有规律的定位或运输。使用长双链DNA分子和带正电的纳米粒子的粗粒度模型的布朗动力学模拟，我们观察到与DNA分子结合并包裹的单个纳米粒子的运动可以沿DNA局部柔性的梯度定向。柔性梯度是沿着0.8 kb的碱基对DNA分子构建的，因此局部持久性长度从50 nm逐渐减小到40 nm，从而模仿了序列依赖性柔性的逐渐变化。由于减少了DNA弯曲和包裹的能量成本，纳米颗粒将一个较长的DNA分子从较不柔软的区域滚动到较柔软的区域。另外，由于DNA从带电荷的纳米颗粒上脱离的自由能垒较低，因此随着纳米颗粒的正电荷减少，轧制变得略有加速，从而进行连续轧制。这项研究表明，DNA局部柔性的变化可用于构建和操纵结构DNA纳米技术中的DNA分子和纳米粒子的超分子组装。