ArticlePloS one2013
An improved SELEX-Seq strategy for characterizing DNA-binding specificity of transcription factor: NF-κB as an example.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed, 34 citations in OpenAlex.
- A Data-Analysis Pipeline for High-Throughput Systematic Evolution of Ligands by Exponential Enrichment (HT-SELEX) in the Characterization of Telomeric Proteins.bioRxiv : the preprint server for biology · 2026Article
- The PrFRS2-PrMYB75a module regulates petal coloration in flare tree peony (Horticulture research · 2026Article
- Teamwork of clustered low-affinity κB sites and accessory factors regulates transcriptional strength of NF-κB RelA dimers.Nucleic acids research · 2025Article
- PAM-adjacent DNA flexibility tunes CRISPR-Cas12a off-target binding.Scientific reports · 2025Article
- Novel Aptamer Strategies in Combating Bacterial Infections: From Diagnostics to Therapeutics.Pharmaceutics · 2024Review
- Therapeutic Interventions into Innate Immune Diseases by Means of Aptamers.Pharmaceutics · 2020Review
- Increased vaccine tolerability and protection via NF-κB modulation.Science advances · 2020Article
- Cancer gene therapy by NF-κB-activated cancer cell-specific expression of CRISPR/Cas9 targeting telomeres.Gene therapy · 2020Article
- AMolecular and cellular biology · 2020Article
- SELEX tool: a novel and convenient gel-based diffusion method for monitoring of aptamer-target binding.Journal of biological engineering · 2020Article
- Inside the Black Box: What Makes SELEX Better?Molecules (Basel, Switzerland) · 2019Review
- Cryptic glucocorticoid receptor-binding sites pervade genomic NF-κB response elements.Nature communications · 2018Article
- NMR monitoring of the SELEX process to confirm enrichment of structured RNA.Scientific reports · 2017Article
- SELMAP - SELEX affinity landscape MAPping of transcription factor binding sites using integrated microfluidics.Scientific reports · 2016Article
- Article
- Elucidating the molecular architecture of adaptation via evolve and resequence experiments.Nature reviews. Genetics · 2015Review
- Single-nucleotide mutation matrix: a new model for predicting the NF-κB DNA binding sites.PloS one · 2014Article
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
SELEX-Seq is now the optimal high-throughput technique for characterizing DNA-binding specificities of transcription factors. In this study, we introduced an improved EMSA-based SELEX-Seq strategy with several advantages. The improvements of this strategy included: (1) using a FAM-labeled probe to track protein-DNA complex in polyacrylamide gel for rapidly recovering the protein-bound dsDNA without relying on traditional radioactive labeling or ethidium bromide staining; (2) monitoring the specificity of SELEX selection by detecting a positive and negative sequence doped into the input DNAs used in each round with PCR amplification; (3) using nested PCR to ensure the specificity of PCR amplification of the selected DNAs after each round; (4) using the nucleotides added at the 5' end of the nested PCR primers as the split barcode to code DNAs from various rounds for multiplexing sequencing samples. The split barcode minimized selection times and thus greatly simplified the current SELEX-Seq procedure. The reliability of the strategy was demonstrated by performing a successful SELEX-Seq of a well-known transcription factor, NF-κB. Therefore, this study provided a useful SELEX-Seq strategy for characterizing DNA-binding specificities of transcription factors.
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