NDLI: DNA–protein interaction studies: a historical and comparative analysis

Content Provider	Springer Nature : BioMed Central
Author	Ferraz, Ricardo André Campos Lopes, Ana Lúcia Gonçalves da Silva, Jessy Ariana Faria Moreira, Diana Filipa Viana Ferreira, Maria João Nogueira de Almeida Coimbra, Sílvia Vieira
Abstract	DNA–protein interactions are essential for several molecular and cellular mechanisms, such as transcription, transcriptional regulation, DNA modifications, among others. 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–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. 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–binding 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–seq 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–protein interaction study several concerns should be taken and different techniques may need to be considered, since different methods confer different precisions and accuracies.
Related Links	https://plantmethods.biomedcentral.com/counter/pdf/10.1186/s13007-021-00780-z.pdf
Ending Page	21
Page Count	21
Starting Page	1
File Format	HTM / HTML
ISSN	17464811
DOI	10.1186/s13007-021-00780-z
Journal	Plant Methods
Issue Number	1
Volume Number	17
Language	English
Publisher	BioMed Central
Publisher Date	2021-07-23
Access Restriction	Open
Subject Keyword	Plant Sciences Biological Techniques ChIP DNA-footprinting DNA–protein interaction EMSA SELEX SPR
Content Type	Text
Resource Type	Review
Subject	Plant Science Biotechnology Genetics
Journal Impact Factor	4.7/2023
5-Year Journal Impact Factor	5.6/2023

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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