ArticleNature2020
DNA mismatches reveal conformational penalties in protein-DNA recognition.
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In one paragraph
Article in Nature, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers.
0numbers the graph read from it
0cells of the map it votes in
73citing papers in PubMed
7.1field-weighted citation impact, top 2% of its field
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
73 citing papers in PubMed, 146 citations in OpenAlex.
- Reciprocal, methylation-dependent binding of Zfp57 and Gzf1 safeguards Dlk1-Dio3 imprinting during developmental reprogramming.Nature communications · 2026Article
- Unraveling single-molecule reactions via multiplexed in-situ DNA sequencing.Nature communications · 2026Article
- Molecular basis of UV lesion binding and repair inhibition by ETS-family transcription factors.Nucleic acids research · 2026Article
- High-throughput characterization of transcription factors that modulate UV damage formation and repair at single-nucleotide resolution.Nature communications · 2026Article
- Mapping DNA glycosylase binding across lesion sequence contexts reveals extended sequence and structural recognition logic.Nature communications · 2026Article
- Searching for sequence features that control DNA cyclizability.PNAS nexus · 2026Article
- DNA Mechanical Strain Steers Transcription Factor Recognition.Research square · 2026Article
- Graph-based deep learning approach for high-throughput protein-DNA interaction scoring.Acta pharmacologica Sinica · 2026Article
- Article
- Article
- DNA methylation shapes transcription factor binding beyond canonical CpG contexts.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- High-throughput characterization of transcription factors that modulate UV damage formation and repair at single-nucleotide resolution.Research square · 2025Article
- Article
- Effects of flanking regions on DNA i-motif folding and stability.Nucleic acids research · 2025Article
- AlkD's Conformational Dynamics Regulated by Protein-DNA Interactions for Effective Target Recognition.The journal of physical chemistry letters · 2025Article
- Proteome-Wide Identification ofAnalytical chemistry · 2025Article
- Article
- Systematic DNA nicking reveals the structural logic of protein recognition.bioRxiv : the preprint server for biology · 2025Article
- An Insight into Cancer Cells and Disease Progression Through the Lens of Mathematical Modeling.Current issues in molecular biology · 2025Review
- Kinetic Dissection of Proton-Coupled Conformational Transitions in Nucleic Acids by Integrating pH-Dependent NMR and Chemical Modifications.Journal of the American Chemical Society · 2025Article
13 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
15 authors at 4 institutions in 3 countries.
Ariel AfekCenter for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC, USA.ORCID http://orcid.org/0000-0001-8584-9879
Honglue ShiDepartment of Chemistry, Duke University, Durham, NC, USA.ORCID http://orcid.org/0000-0003-3847-1652
Atul RangaduraiDepartment of Biochemistry, Duke University School of Medicine, Durham, NC, USA.
Harshit SahayCenter for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC, USA.ORCID http://orcid.org/0000-0001-7955-6527
Alon SenitzkiDepartment of Biology, Technion-Israel Institute of Technology, Haifa, Israel.
Suela XhaniDepartment of Chemistry, Georgia State University, Atlanta, GA, USA.
Mimi FangDepartment of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
Raul SalinasDepartment of Biochemistry, Duke University School of Medicine, Durham, NC, USA.
Zachery MielkoCenter for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC, USA.ORCID http://orcid.org/0000-0002-1935-9203
Miles A PufallDepartment of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.ORCID http://orcid.org/0000-0002-7022-6916
Gregory M K PoonDepartment of Chemistry, Georgia State University, Atlanta, GA, USA.ORCID http://orcid.org/0000-0001-5107-9458
Tali E HaranDepartment of Biology, Technion-Israel Institute of Technology, Haifa, Israel.ORCID http://orcid.org/0000-0002-9700-3392
Maria A SchumacherDepartment of Biochemistry, Duke University School of Medicine, Durham, NC, USA.
Hashim M Al-HashimiDepartment of Chemistry, Duke University, Durham, NC, USA. hashim.al.hashimi@duke.edu.ORCID http://orcid.org/0000-0003-0681-1747
Raluca GordânCenter for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC, USA. raluca.gordan@duke.edu.ORCID http://orcid.org/0000-0002-6404-6556
Duke University · USGeorgia State University · USTechnion – Israel Institute of Technology · ILUniversity of Iowa · US
Funding
User Training and OutreachP30GM124169 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI PAUL David ADAMS, Gregory L Hura · 2017 to 2026
$28.6MRole of DNA structural dynamics in mutagenesis and oncogenesisR01GM089846 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Hashim M Al-Hashimi · 2010 to 2026
$5.2MDeciphering fundamental biological processes involving protein-nucleic acid interactions at the molecular levelR35GM130290 · NIGMS · DUKE UNIVERSITY · PI Maria Schumacher · 2019 to 2026
$4.9MEliminating Critical Systematic Errors In Structural Biology With Next-Generation SimulationR01GM124149 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI HOLTON, JAMES M · 2017 to 2024
$2.5MNew methods for quantitative modeling of protein-DNA interactionsR01GM117106 · NIGMS · DUKE UNIVERSITY · PI GORDAN, RALUCA · 2015 to 2019
$1.8MThe role of transcription factor proteins in mutagenesis at regulatory sitesR01GM135658 · NIGMS · DUKE UNIVERSITY · PI GORDAN, RALUCA · 2020 to 2023
$1.3MPilatus 6mS10OD021832 · OD · UNIVERSITY OF CALIFORNIA BERKELEY · PI ADAMS, PAUL DAVID · 2016 to 2016
$980kA cellular osmotic pressure sensorR21GM137160 · NIGMS · GEORGIA STATE UNIVERSITY · PI POON, GREGORY MAN KAI · 2020 to 2021
$428kHoward Hughes Medical InstituteNIGMS NIH HHS P30 GM124169NIGMS NIH HHS R01 GM089846NIGMS NIH HHS R01 GM117106NIGMS NIH HHS R01 GM124149NIGMS NIH HHS R01 GM135658NIGMS NIH HHS R21 GM137160NIGMS NIH HHS R35 GM130290NIH HHS S10 OD021832
Abstract
Transcription factors recognize specific genomic sequences to regulate complex gene-expression programs. Although it is well-established that transcription factors bind to specific DNA sequences using a combination of base readout and shape recognition, some fundamental aspects of protein-DNA binding remain poorly understood
Indexed as
Molecular ConformationArabidopsis ProteinsBase PairingBinding SitesCrystallography, X-RayDNA-Binding ProteinsHumansModels, MolecularMutationNuclear Magnetic Resonance, BiomolecularNucleic Acid HeteroduplexesProtein BindingSaccharomyces cerevisiae ProteinsThermodynamicsTranscription FactorsArabidopsis ProteinsDNA-Binding ProteinsNucleic Acid HeteroduplexesSaccharomyces cerevisiae ProteinsTranscription Factors
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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.