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For many decades scientists tried to unravel how DNA links to proteins, forming complex and vital interactions. However, the high number of techniques developed for the study of these interactions made the choice of the appropriate technique a difficult task. This review intends to provide a historical context and compile the methods that describe DNA\u2013protein interactions according to the purpose of each approach, summarise the respective advantages and disadvantages and give some examples of recent uses for each technique. 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. Considering the DNA\u2013binding proteins characterisation, filter binding assay and EMSA are easy in vitro methods that rapidly identify nucleic acid-protein binding interactions. 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. Concerning binding kinetics and affinities, filter binding assay and EMSA are useful and easy methods, although SPR and spectroscopy techniques are more sensitive. Finally, relatively to genome-wide studies, ChIP\u2013seq is the desired method, given the coverage and resolution of the technique. In conclusion, although some experiments are easier and faster than others, when designing a DNA\u2013protein interaction study several concerns should be taken and different techniques may need to be considered, since different methods confer different precisions and accuracies.<\/jats:p>","DOI":"10.1186\/s13007-021-00780-z","type":"journal-article","created":{"date-parts":[[2021,7,23]],"date-time":"2021-07-23T09:03:10Z","timestamp":1627030990000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":58,"title":["DNA\u2013protein interaction studies: a historical and comparative analysis"],"prefix":"10.1186","volume":"17","author":[{"given":"Ricardo Andr\u00e9 Campos","family":"Ferraz","sequence":"first","affiliation":[]},{"given":"Ana L\u00facia Gon\u00e7alves","family":"Lopes","sequence":"additional","affiliation":[]},{"given":"Jessy Ariana Faria","family":"da Silva","sequence":"additional","affiliation":[]},{"given":"Diana Filipa Viana","family":"Moreira","sequence":"additional","affiliation":[]},{"given":"Maria Jo\u00e3o Nogueira","family":"Ferreira","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9421-2538","authenticated-orcid":false,"given":"S\u00edlvia Vieira","family":"de Almeida Coimbra","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2021,7,23]]},"reference":[{"issue":"4227","key":"780_CR1","doi-asserted-by":"publisher","first-page":"780","DOI":"10.1038\/166780a0","volume":"166","author":"E Stedman","year":"1950","unstructured":"Stedman E, Stedman E. 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