Frykholm Karolin, Nyberg Lena K, Westerlund Fredrik
Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
Integr Biol (Camb). 2017 Aug 14;9(8):650-661. doi: 10.1039/c7ib00085e.
DNA-protein interactions are at the core of the cellular machinery and single molecule methods have revolutionized the possibilities to study, and our understanding of these interactions on the molecular level. Nanofluidic channels have been extensively used for studying single DNA molecules during the last twelve years and in this review, we discuss how this experimental platform has been extended to studies of DNA-protein interactions. We first present how the design of the device can be tailored for the specific DNA-protein system studied and how the channels can be passivated to avoid non-specific binding of proteins. We then focus on describing the different kinds of DNA-interacting proteins that have been studied in nanofluidic devices, including proteins that compact DNA and proteins that form filaments on DNA. Our main objective is to highlight the diverse functionalities of DNA-protein systems that have been characterized using nanofluidic structures and hence demonstrate the versatility of these experimental tools. We finally discuss potential future directions studies of DNA-protein complexes in nanochannels might take, including specific DNA-protein systems that are difficult to analyze with traditional techniques, devices with increased complexity, and fully integrated lab-on-a-chip devices for analysis of material extracted from (single) cells.
DNA-蛋白质相互作用是细胞机制的核心，单分子方法彻底改变了研究这些相互作用的可能性，以及我们在分子水平上对它们的理解。在过去的十二年里，纳米流体通道已被广泛用于研究单个DNA分子。在这篇综述中，我们讨论了这个实验平台是如何扩展到DNA-蛋白质相互作用研究中的。我们首先介绍如何根据所研究的特定DNA-蛋白质系统定制设备的设计，以及如何对通道进行钝化处理以避免蛋白质的非特异性结合。然后，我们重点描述在纳米流体装置中研究的不同类型与DNA相互作用的蛋白质，包括使DNA压缩的蛋白质和在DNA上形成细丝的蛋白质。我们的主要目的是突出使用纳米流体结构表征的DNA-蛋白质系统的多样功能，从而展示这些实验工具的多功能性。我们最后讨论了纳米通道中DNA-蛋白质复合物未来潜在的研究方向，包括用传统技术难以分析的特定DNA-蛋白质系统、复杂度增加的设备，以及用于分析从（单个）细胞中提取材料的完全集成的芯片实验室设备。
