Biological and Environmental Science and Engineering Division , King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900 , Saudi Arabia.
Department of Biomolecular Engineering, Graduate School of Engineering , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8603 , Japan.
ACS Nano. 2019 Jul 23;13(7):8155-8168. doi: 10.1021/acsnano.9b03259. Epub 2019 Jun 25.
Histones are basic protein monomers capable of interacting with DNA, providing the mechanism of DNA compaction inside the cell nucleus. The well-ordered assembly process of histone and DNA is a potential candidate as the approach for building DNA-protein nanostructures. Here, utilizing the sequence-independent histone-DNA interaction, we present an approach to self-assemble histones and single-stranded DNA (ssDNA) to form well-defined histone-DNA (sHD) nanoparticles and their multidimensional cross-linked complexes (cHD). By using various molecular biology and microscopy techniques, we elucidate the structure of these complexes, and we show that they are formed at carefully controlled conditions of temperature, ionic strength, concentration, and incubation time. We also demonstrate using a set of ssDNA molecular rulers and a geometric accommodation model that the assembly of sHD and cHD particles proceeds with precise geometry so that the number of ssDNA in these particles can be programmed by the length of ssDNA. We further show that the formation of cHD amplifies the effect of the length of ssDNA on the self-assembly, allowing for distinguishing ssDNA of different lengths at single nucleotide resolution. We envision that our geometry-directed approach of self-assembling histone-DNA nanostructures and the fundamental insights can serve as a structural platform to advance building precisely ordered DNA-protein nanostructures.
组蛋白是一种能够与 DNA 相互作用的基本蛋白质单体，为细胞核内 DNA 紧缩提供了机制。组蛋白和 DNA 的有序组装过程是构建 DNA-蛋白质纳米结构的潜在候选方法。在这里，我们利用序列非依赖性的组蛋白-DNA 相互作用，提出了一种自组装组蛋白和单链 DNA（ssDNA）以形成明确定义的组蛋白-DNA（sHD）纳米颗粒及其多维交联复合物（cHD）的方法。通过使用各种分子生物学和显微镜技术，我们阐明了这些复合物的结构，并表明它们是在精心控制的温度、离子强度、浓度和孵育时间条件下形成的。我们还使用一组 ssDNA 分子标尺和一个几何容纳模型表明，sHD 和 cHD 颗粒的组装具有精确的几何形状，因此这些颗粒中的 ssDNA 数量可以通过 ssDNA 的长度来编程。我们进一步表明，cHD 的形成放大了 ssDNA 长度对自组装的影响，允许以单核苷酸分辨率区分不同长度的 ssDNA。我们设想，我们的基于几何形状的自组装组蛋白-DNA 纳米结构的方法和基本见解可以作为推进精确有序 DNA-蛋白质纳米结构构建的结构平台。
