Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea.
Nanoscale. 2017 May 18;9(19):6391-6398. doi: 10.1039/c7nr00859g.
The first step in the controlled storage of lengthy DNA molecules is to keep DNA molecules separated while integrated in micrometer-sized space. Herein, we present hybrid Monte Carlo simulations of a histone-complexed DNA (hcDNA) molecule confined in a dense array of nanoposts. Depending on the nanopost dimension, a single, 8.7 kilobase pair hcDNA molecule was either localized and elongated in a single inter-post space surrounded by four nanoposts or spread over several inter-post spaces through passages between two neighboring nanoposts. The conformational change of a hcDNA molecule is interpreted in terms of competitive effects of confinements in the inter-post and passage spaces. We propose that, by elaborately designing nanopost arrays, the competitive confinement effects can be adjusted such that each hcDNA molecule is localized in a single inter-post space, and thereby multiple hcDNA molecules can be physically separated from each other while stored together in the nanopost array.
在对长链 DNA 分子进行控制储存的过程中，首先要将整合在微米级空间内的 DNA 分子分隔开。在此，我们提出了一种在密集纳米柱阵列中受限的组蛋白复合 DNA（hcDNA）分子的混合蒙特卡罗模拟。根据纳米柱的尺寸，单个 8.7 千碱基对的 hcDNA 分子要么定位于由四个纳米柱环绕的单个柱间空间中，并被拉长，要么通过两个相邻纳米柱之间的通道扩展到几个柱间空间中。hcDNA 分子的构象变化可以根据柱间空间和通道空间的限制的竞争效应来解释。我们提出，可以通过精心设计纳米柱阵列来调节竞争限制效应，使得每个 hcDNA 分子都定位于单个柱间空间中，从而可以将多个 hcDNA 分子物理上彼此分离，同时储存在纳米柱阵列中。
