Abstract—

The interaction of proteins with DNA underlies all processes of cell functioning. They include DNA transcription, replication, and repair; maintenanc of the chromosome structure, activation and inhibition of the genes by protein transcription factors and protein enzymes involved in chromatin modification; maintenance of the nucleosome structure, the control of gene expression, etc. Transcription factors (TFs) bind to specific sets of DNA sequences, activating or inhibiting gene transcription, and are involved in a variety of signal transmission processes, including changes in cell differentiation, development, and environmental influences. This important role of DNA interactions with transcription factors led to their active study for many years and to the development of different methods to determine binding sites on the DNA matrix and the proteins interacting with them, including footprinting, Southern and Western blot assays, the systematic evolution of ligands via exponential enrichment (SELEX), chromatin immunoprecipitation (ChIP), electrophoretic mobility shift assay (EMSA), surface plasmon resonance (SPR), etc. Each method has advantages and disadvantages. The methods and approaches used to study TF/DNA binding can be divided into in vivo and in vitro. In vivo methods (e.g., ChIP) are used to study the TF/DNA interactions happening under specific conditions, including the tissue type, cells, moment of time, etc. and to scan TF binding sites throughout the genome. In vitro methods are used to study the TF/DNA interaction caused only by the protein and DNA structure to determine the binding site sequences, interaction forces, and characteristics of TF/DNA complexes. The review will list the most widely used in vitro methods for the study of DNA–protein interactions, since there are good reviews for each of them. The footprinting method and the methods to determine the DNA/protein affinity, binding rates, and dissociation of DNA/protein complexes will be discussed in detail.

中文翻译：

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用于研究 DNA-蛋白质相互作用的体外方法

摘要——

蛋白质与 DNA 的相互作用是所有细胞功能过程的基础。它们包括 DNA 转录、复制和修复；通过参与染色质修饰的蛋白质转录因子和蛋白质酶来维持染色体结构、激活和抑制基因；核小体结构的维持，基因表达的控制等。发展和环境影响。DNA 与转录因子相互作用的这一重要作用促使他们进行了多年的积极研究，并开发了不同的方法来确定 DNA 基质上的结合位点以及与它们相互作用的蛋白质，包括足迹法、Southern 和 Western 印迹分析、系统的通过指数富集 (SELEX)、染色质免疫沉淀 (ChIP)、电泳迁移率变化测定 (EMSA)、表面等离子共振 (SPR) 等方法进化配体。每种方法都有优点和缺点。用于研究 TF/DNA 结合的方法和途径可分为体内和体外。体内方法（例如，ChIP）用于研究特定条件下发生的 TF/DNA 相互作用，包括组织类型、细胞、时刻等，并扫描整个基因组中的 TF 结合位点。体外方法用于研究仅由蛋白质和 DNA 结构引起的 TF/DNA 相互作用，以确定 TF/DNA 复合物的结合位点序列、相互作用力和特征。该评论将列出用于研究 DNA-蛋白质相互作用的最广泛使用的体外方法，因为对每种方法都有很好的评论。将详细讨论足迹方法和确定 DNA/蛋白质亲和力、结合率和解离的方法。