ArticleProceedings of the National Academy of Sciences of the United States of America2010
Specificity landscapes of DNA binding molecules elucidate biological function.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 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.
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Who cites it
65 citing papers in PubMed, 102 citations in OpenAlex.
- NPBIP: predicting binding preferences of uncharacterized nucleic-acid-binding proteins.Bioinformatics (Oxford, England) · 2026Article
- DNA Mechanical Strain Steers Transcription Factor Recognition.Research square · 2026Article
- Defining the DNA Binding Specificity of GRHL2.bioRxiv : the preprint server for biology · 2026Article
- Systematic DNA nicking reveals the structural logic of protein recognition.bioRxiv : the preprint server for biology · 2025Article
- Using synthetic genome readers/regulators to interrogate chromatin processes: A brief review.Methods (San Diego, Calif.) · 2024Review
- Site-Specific Arrangement and Structure Determination of Minor Groove Binding Molecules in Self-Assembled Three-Dimensional DNA Crystals.Journal of the American Chemical Society · 2023Article
- Domain-Selective BET Ligands Yield Next-Generation Synthetic Genome Readers/Regulators with Nonidentical Cellular Functions.Journal of the American Chemical Society · 2023Article
- Hidden modes of DNA binding by human nuclear receptors.Nature communications · 2023Article
- Disease-associated non-coding variants alter NKX2-5 DNA-binding affinity.Biochimica et biophysica acta. Gene regulatory mechanisms · 2023Article
- Flexibility of flanking DNA is a key determinant of transcription factor affinity for the core motif.Biophysical journal · 2022Article
- Simple synthesis of massively parallel RNA microarrays via enzymatic conversion from DNA microarrays.Nature communications · 2022Article
- Sequence-dependent quenching of fluorescein fluorescence on single-stranded and double-stranded DNA.RSC advances · 2022Article
- Inferring primase-DNA specific recognition using a data driven approach.Nucleic acids research · 2021Article
- Getting a handle on chemical probes of chomatin readers.Future medicinal chemistry · 2021Article
- Quantitative analysis of transcription factor binding and expression using calling cards reporter arrays.Nucleic acids research · 2020Article
- The Road Not Taken with Pyrrole-Imidazole Polyamides: Off-Target Effects and Genomic Binding.Biomolecules · 2020Review
- Single position substitution of hairpin pyrrole-imidazole polyamides imparts distinct DNA-binding profiles across the human genome.PloS one · 2020Article
- Nkx2-5 Second Heart Field Target Gene Ccdc117 Regulates DNA Metabolism and Proliferation.Scientific reports · 2019Article
- Flexibility and structure of flanking DNA impact transcription factor affinity for its core motif.Nucleic acids research · 2018Article
- Specificity landscapes unmask submaximal binding site preferences of transcription factors.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
5 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
Abstract
Evaluating the specificity spectra of DNA binding molecules is a nontrivial challenge that hinders the ability to decipher gene regulatory networks or engineer molecules that act on genomes. Here we compare the DNA sequence specificities for different classes of proteins and engineered DNA binding molecules across the entire sequence space. These high-content data are visualized and interpreted using an interactive "specificity landscape" which simultaneously displays the affinity and specificity of a million-plus DNA sequences. Contrary to expectation, specificity landscapes reveal that synthetic DNA ligands match, and often surpass, the specificities of eukaryotic DNA binding proteins. The landscapes also identify differential specificity constraints imposed by diverse structural folds of natural and synthetic DNA binders. Importantly, the sequence context of a binding site significantly influences binding energetics, and utilizing the full contextual information permits greater accuracy in annotating regulatory elements within a given genome. Assigning such context-dependent binding values to every DNA sequence across the genome yields predictive genome-wide binding landscapes (genomescapes). A genomescape of a synthetic DNA binding molecule provided insight into its differential regulatory activity in cultured cells. The approach we describe will accelerate the creation of precision-tailored DNA therapeutics and uncover principles that govern sequence-specificity of DNA binding molecules.
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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.