![]() The studies usually performed were either from a purely chemical perspective, analysing the structure of the complex formed, or from a transcriptomic level, investigating if a certain protein does bind to a particular DNA or gene and the interference of this interaction in gene expression, existing great intersection between both approaches. This interaction is responsible for essential molecular and cellular mechanisms, such as transcription, transcriptional regulation, recombination, replication, DNA repair, viral infection, DNA packing and DNA modifications. Since then, scientists have not abandoned this research field, having unravelled many details about the crucial interaction between proteins and DNA. In the early beginning of these studies, even before the publication of the DNA molecular structure, Stedman and Stedman already referred to histones as potential regulators of the DNA biological activity. For many decades and representing a big segment of the molecular biology research conducted, scientists tried to unravel how DNA links to proteins, forming complex and vital interactions. It has been known since the second half of the last century that the binding of a protein to a DNA molecule has a very important role in the function of a living cell and in life’s sustainability itself. In conclusion, although some experiments are easier and faster than others, when designing a DNA–protein interaction study several concerns should be taken and different techniques may need to be considered, since different methods confer different precisions and accuracies. Finally, relatively to genome-wide studies, ChIP–seq is the desired method, given the coverage and resolution of the technique. Concerning binding kinetics and affinities, filter binding assay and EMSA are useful and easy methods, although SPR and spectroscopy techniques are more sensitive. To find DNA-binding sites, DNA-footprinting is indeed an easier, faster and reliable approach, however, techniques involving base analogues and base-site selection are more precise. Considering the DNA–binding proteins characterisation, filter binding assay and EMSA are easy in vitro methods that rapidly identify nucleic acid-protein binding interactions. The final aim of this work is to help in deciding which technique to perform according to the objectives and capacities of each research team. ![]() This review intends to provide a historical context and compile the methods that describe DNA–protein interactions according to the purpose of each approach, summarise the respective advantages and disadvantages and give some examples of recent uses for each technique. However, the high number of techniques developed for the study of these interactions made the choice of the appropriate technique a difficult task. For many decades scientists tried to unravel how DNA links to proteins, forming complex and vital interactions. ![]() DNA–protein interactions are essential for several molecular and cellular mechanisms, such as transcription, transcriptional regulation, DNA modifications, among others. ![]()
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