Molecular dynamics of DNA and nucleosomes in solution studied by fast-scanning atomic force microscopy

Nucleosome is a fundamental structural unit of chromatin, and the exposure from or occlusion into chromatin of genomic DNA is closely related to the regulation of gene expression. In this study, we analyzed the molecular dynamics of poly-nucleosomal arrays in solution by fast-scanning atomic force microscopy (AFM) to obtain a visual glimpse of nucleosome dynamics on chromatin fiber at single molecule level. The influence of the high-speed scanning probe on nucleosome dynamics can be neglected since bending elastic energy of DNA molecule showed similar probability distributions at different scan rates. In the sequential images of poly-nucleosomal arrays, the sliding of the nucleosome core particle and the dissociation of histone particle were visualized. The sliding showed limited fluctuation within similar to 50 nm along the DNA strand. The histone dissociation occurs by at least two distinct ways: a dissociation of histone octamer or sequential dissociations of tetramers. These observations help us to develop the molecular mechanisms of nucleosome dynamics and also demonstrate the ability of fast-scanning AFM for the analysis of dynamic protein-DNA interaction in sub-seconds time scale. (C) 2010 Elsevier B.V. All rights reserved.

核小体是染色质的基本结构单位，基因组DNA从染色质上的暴露或被其遮蔽与基因表达的调控密切相关。在本研究中，我们通过快速扫描原子力显微镜（AFM）分析了溶液中多核小体阵列的分子动力学，以便在单分子水平上直观了解染色质纤维上核小体的动力学。由于DNA分子的弯曲弹性能在不同扫描速率下呈现相似的概率分布，高速扫描探针对核小体动力学的影响可忽略不计。在多核小体阵列的连续图像中，核小体核心颗粒的滑动以及组蛋白颗粒的解离得以可视化。这种滑动沿DNA链在约50纳米范围内呈现有限的波动。组蛋白解离至少通过两种不同的方式发生：组蛋白八聚体的解离或四聚体的连续解离。这些观察结果有助于我们阐明核小体动力学的分子机制，同时也证明了快速扫描原子力显微镜在亚秒级时间尺度上分析动态蛋白质 - DNA相互作用的能力。（C）2010爱思唯尔有限公司。保留所有权利。