ArticleNucleic acids research2005
Combining SELEX with quantitative assays to rapidly obtain accurate models of protein-DNA interactions.
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 32 papers.
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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.
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Who cites it
32 citing papers in PubMed.
- Deep Learning-Based Classification of Histone-DNA Interactions Using Drying Droplet Patterns.Small science · 2024Article
- A deterministic code for transcription factor-DNA recognition through computation of binding interfaces.NAR genomics and bioinformatics · 2022Article
- Aptamer nucleotide analog drug conjugates in the targeting therapy of cancers.Frontiers in cell and developmental biology · 2022Review
- I-Block: a simple Escherichia coli-based assay for studying sequence-specific DNA binding of proteins.Nucleic acids research · 2020Article
- Quantitative profiling of BATF family proteins/JUNB/IRF hetero-trimers using Spec-seq.BMC molecular biology · 2018Article
- Quantum annealing versus classical machine learning applied to a simplified computational biology problem.NPJ quantum information · 2018Article
- Potential Diagnostic and Therapeutic Applications of Oligonucleotide Aptamers in Breast Cancer.International journal of molecular sciences · 2017Review
- Inherent limitations of probabilistic models for protein-DNA binding specificity.PLoS computational biology · 2017Article
- Generation of Internal-Image Functional Aptamers of Okadaic Acid via Magnetic-Bead SELEX.Marine drugs · 2015Article
- Aptamers and Their Significant Role in Cancer Therapy and Diagnosis.Biomedicines · 2015Review
- Nucleic Acid Aptamers: An Emerging Tool for Biotechnology and Biomedical Sensing.Sensors (Basel, Switzerland) · 2015Review
- Shapely DNA attracts the right partner.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Spec-seq: determining protein-DNA-binding specificity by sequencing.Briefings in functional genomics · 2015Review
- Aptamers: active targeting ligands for cancer diagnosis and therapy.Theranostics · 2015Review
- High-resolution specificity from DNA sequencing highlights alternative modes of Lac repressor binding.Genetics · 2014Article
- New Technologies Provide Quantum Changes in the Scale, Speed, and Success of SELEX Methods and Aptamer Characterization.Molecular therapy. Nucleic acids · 2014Article
- Discrimination between thermodynamic models of cis-regulation using transcription factor occupancy data.Nucleic acids research · 2014Article
- Mechanisms by which transcription factors gain access to target sequence elements in chromatin.Current opinion in genetics & development · 2013Review
- Multiplexed microcolumn-based process for efficient selection of RNA aptamers.Analytical chemistry · 2013Article
- An improved SELEX-Seq strategy for characterizing DNA-binding specificity of transcription factor: NF-κB as an example.PloS one · 2013Article
Corrections and comments
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2 authors.
Funding
Abstract
Models for the specificity of DNA-binding transcription factors are often based on small amounts of qualitative data and therefore have limited accuracy. In this study we demonstrate a simple and efficient method of affinity chromatography-SELEX followed by a quantitative binding (QuMFRA) assay to rapidly collect the data necessary for more accurate models. Using the zinc finger protein EGR as an e.g. we show that many bindings sites can be obtained efficiently with affinity chromatography-SELEX, but those sequences alone provide a weight matrix model with limited accuracy. Using a QuMFRA assay to determine the quantitative relative affinity for only a subset of the sequences obtained by SELEX leads to a much more accurate model. Application of this method to variants of a transcription factor would allow us to generate a large collection of quantitative data for modeling protein-DNA interactions that could facilitate the determination of recognition codes for different transcription factor families.
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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.