ReviewPlant methods2021
DNA-protein interaction studies: a historical and comparative analysis.
Review in Plant methods, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
25 citing papers in PubMed.
- Advancing bioinformatics with language models: components, applications, and perspectives.Briefings in bioinformatics · 2026Review
- A rapid test for protein-DNA interactions.Nucleic acids research · 2026Article
- Refined ChIP-Seq Protocol for High-Quality Chromatin Profiling in Solid Tissues Using the Complete Genomics/MGI Sequencing Platform.Current protocols · 2025Article
- ArnR binds a [4Fe-4S] cluster and indirectly senses anaerobicity in Corynebacteria.Metallomics : integrated biometal science · 2025Article
- Experimental approaches to investigate biophysical interactions between homeodomain transcription factors and DNA.Biochimica et biophysica acta. Gene regulatory mechanisms · 2025Review
- Development of an FBP-based bioluminescence reporter system for investigating transcriptional regulation in plants.Plant communications · 2025Article
- Concise Overview of Methodologies Employed in the Study of Bacterial DNA Replication.International journal of molecular sciences · 2025Review
- WSHNN: A Weakly Supervised Hybrid Neural Network for the Identification of DNA-protein Binding Sites.Current computer-aided drug design · 2025Article
- Advances in Language-Model-Informed Protein-Nucleic Acid Binding Site Prediction.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Spatial proximity and gene function: a new dimension in prokaryotic gene association network analysis with 3D-GeneNet.Briefings in bioinformatics · 2024Article
- Three Prime Repair Exonuclease 1 preferentially degrades the integration-incompetent HIV-1 DNA through favorable kinetics, thermodynamic, structural and conformational properties.bioRxiv : the preprint server for biology · 2024Article
- Harnessing regulatory networks in Actinobacteria for natural product discovery.Journal of industrial microbiology & biotechnology · 2024Review
- Recent advances in exploring transcriptional regulatory landscape of crops.Frontiers in plant science · 2024Review
- Protein-DNA binding sites prediction based on pre-trained protein language model and contrastive learning.Briefings in bioinformatics · 2023Article
- Review
- Modeling protein-nucleic acid complexes with extremely large conformational changes using Flex-LZerD.Proteomics · 2023Article
- Building an improved transcription factor-centered yeast one hybrid system to identify DNA motifs bound by protein comprehensively.BMC plant biology · 2023Article
- Mass Spectrometry for Assessing Protein-Nucleic Acid Interactions.Analytical chemistry · 2023Review
- Regulatory mechanism ofFrontiers in plant science · 2023Article
- Deciphering Macromolecular Interactions Involved in Abiotic Stress Signaling: A Review of Bioinformatics Analysis.Methods in molecular biology (Clifton, N.J.) · 2023Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.