ArticleNucleic acids research2005
Proof of concept for microarray-based detection of DNA-binding oncogenes in cell extracts.
Article in Nucleic acids research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed, 24 citations in OpenAlex.
- DGMP: Identifying Cancer Driver Genes by Jointing DGCN and MLP from Multi-omics Genomic Data.Genomics, proteomics & bioinformatics · 2022Article
- Identification of a binding motif specific to HNF4 by comparative analysis of multiple nuclear receptors.Nucleic acids research · 2012Article
- Protein-binding microarray analysis of tumor suppressor AP2α target gene specificity.PloS one · 2011Article
- A SILAC-based DNA protein interaction screen that identifies candidate binding proteins to functional DNA elements.Genome research · 2009Article
- Quantifying DNA-protein binding specificities by using oligonucleotide mass tags and mass spectroscopy.Proceedings of the National Academy of Sciences of the United States of America · 2007Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The function of DNA-binding proteins is controlled not just by their abundance, but mainly at the level of their activity in terms of their interactions with DNA and protein targets. Moreover, the affinity of such transcription factors to their target sequences is often controlled by co-factors and/or modifications that are not easily assessed from biological samples. Here, we describe a scalable method for monitoring protein-DNA interactions on a microarray surface. This approach was designed to determine the DNA-binding activity of proteins in crude cell extracts, complementing conventional expression profiling arrays. Enzymatic labeling of DNA enables direct normalization of the protein binding to the microarray, allowing the estimation of relative binding affinities. Using DNA sequences covering a range of affinities, we show that the new microarray-based method yields binding strength estimates similar to low-throughput gel mobility-shift assays. The microarray is also of high sensitivity, as it allows the detection of a rare DNA-binding protein from breast cancer cells, the human tumor suppressor AP-2. This approach thus mediates precise and robust assessment of the activity of DNA-binding proteins and takes present DNA-binding assays to a high throughput level.
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Registered trials
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