DNA–protein interaction studies: a historical and comparative analysis

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...

Full description

Saved in:

Bibliographic Details
Published in:	Plant methods Vol. 17; no. 1; pp. 1 - 82
Main Authors:	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
Format:	Journal Article
Language:	English
Published:	London BioMed Central Ltd 23-07-2021 BioMed Central BMC
Subjects:	Amino acids Binding proteins Binding sites ChIP Comparative analysis Deoxyribonucleic acid DNA DNA-binding protein DNA-footprinting DNA–protein interaction EMSA Footprinting Gene expression Gene regulation Genomes In vitro methods and tests Interactomes Investigations Membranes Nucleic acids Protein interaction Proteins Review SELEX Site selection Spectroscopy SPR Transcription Portugal
Online Access:	Get full text
Tags:	Add Tag No Tags, Be the first to tag this record!

Description
Summary:	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.
Bibliography:	ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Feature-3 content type line 23 ObjectType-Review-1
ISSN:	1746-4811 1746-4811
DOI:	10.1186/s13007-021-00780-z