ReviewAnnual review of biochemistry2010
Origins of specificity in protein-DNA recognition.
Review in Annual review of biochemistry, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 518 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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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
518 citing papers in PubMed, 921 citations in OpenAlex.
- Single-molecule imaging reveals DNA shape read-out by the INO80 chromatin remodeler.Nature communications · 2026Article
- Review
- Readout of intrinsic and induced DNA shape by homeodomain transcription factor complexes.Biophysical journal · 2026Article
- Nonconsensus flanking sequence of hundreds of base pairs around in vivo binding sites: statistical beacons for transcription factor scanning.Nucleic acids research · 2026Article
- Structural basis of AtCas9 recognition of PAM mutants in underwound DNA topology.Nature structural & molecular biology · 2026Article
- The transcriptional repressor PheR regulates uptake and catabolism of phenanthrene in Sphingobium sp. SHPJ-2.The Journal of biological chemistry · 2026Article
- hexABC seeking the physical code of DNA.Nature communications · 2026Article
- Cis- and Trans-Regulatory Factors Independently Shape Phenotypic Heterogeneity of Retinitis Pigmentosa.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Direct amidinium-phosphate interactions guide AT-selective DNA binding by a potent antileishmanial drug.Communications chemistry · 2026Article
- Human cathelicidin peptide LL-37 compacts nucleic acids and alters neutrophil extracellular trap structure.Scientific reports · 2026Article
- DNA Mechanical Strain Steers Transcription Factor Recognition.Research square · 2026Article
- Thermodynamics of Indirect Readout in Cre-bioRxiv : the preprint server for biology · 2026Article
- Protein loops are major contributors to DNA strand separation and high-fidelity substrate recognition for DNA methyltransferase CcrM.The Journal of biological chemistry · 2026Article
- VGLL4-driven TEAD4 multimerization orchestrates DNA binding and YAP recruitment.Nature communications · 2026Article
- Article
- Sequence-based modeling of low-affinity transcription factor-DNA binding through deep learning.NAR genomics and bioinformatics · 2026Article
- Functional analysis of major detoxification gene superfamilies driving flubendiamide resistance in South Indian Tuta absoluta field populations.Scientific reports · 2026Article
- Investigation of Regulation and Binding Patterns of the Human Cathelicidin Peptide LL-37 in Complexation with Nucleic Acids, and its Impact on Neutrophil Extracellular Traps.bioRxiv : the preprint server for biology · 2026Article
- The virulence regulator Rv3425 mediates stress adaptation and promotes intracellular survival of Mycobacterium tuberculosis avirulent strain.Archives of microbiology · 2026Article
- Inferring DNA Kinkability from Biased MD Simulations.Journal of chemical theory and computation · 2026Article
458 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
Specific interactions between proteins and DNA are fundamental to many biological processes. In this review, we provide a revised view of protein-DNA interactions that emphasizes the importance of the three-dimensional structures of both macromolecules. We divide protein-DNA interactions into two categories: those when the protein recognizes the unique chemical signatures of the DNA bases (base readout) and those when the protein recognizes a sequence-dependent DNA shape (shape readout). We further divide base readout into those interactions that occur in the major groove from those that occur in the minor groove. Analogously, the readout of the DNA shape is subdivided into global shape recognition (for example, when the DNA helix exhibits an overall bend) and local shape recognition (for example, when a base pair step is kinked or a region of the minor groove is narrow). Based on the >1500 structures of protein-DNA complexes now available in the Protein Data Bank, we argue that individual DNA-binding proteins combine multiple readout mechanisms to achieve DNA-binding specificity. Specificity that distinguishes between families frequently involves base readout in the major groove, whereas shape readout is often exploited for higher resolution specificity, to distinguish between members within the same DNA-binding protein family.
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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.