ArticleACS chemical biology2011
A map of minor groove shape and electrostatic potential from hydroxyl radical cleavage patterns of DNA.
Article in ACS chemical biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed.
- Quantitative and systematic NMR measurements of sequence-dependent A-T Hoogsteen dynamics uncovers unique conformational specificity in the DNA double helix.bioRxiv : the preprint server for biology · 2024Article
- Novel Amidine Derivative K1586 Sensitizes Colorectal Cancer Cells to Ionizing Radiation by Inducing Chk1 Instability.International journal of molecular sciences · 2024Article
- Synthesis and Biophysical and Biological Studies ofJournal of medicinal chemistry · 2023Article
- Hidden modes of DNA binding by human nuclear receptors.Nature communications · 2023Article
- Computational Assessment of the Expression-modulating Potential for Non-coding Variants.Genomics, proteomics & bioinformatics · 2023Article
- Binding to the DNA Minor Groove by Heterocyclic Dications: from AT Specific to GC Recognition Compounds.Current protocols · 2023Review
- Structural basis of Streptomyces transcription activation by zinc uptake regulator.Nucleic acids research · 2022Article
- Learning the Regulatory Code of Gene Expression.Frontiers in molecular biosciences · 2021Review
- Multiple plasmid origin-of-transfer regions might aid the spread of antimicrobial resistance to human pathogens.MicrobiologyOpen · 2020Article
- Review
- A New Generation of Minor-Groove-Binding-Heterocyclic Diamidines That Recognize G·C Base Pairs in an AT Sequence Context.Molecules (Basel, Switzerland) · 2019Review
- Flexibility and structure of flanking DNA impact transcription factor affinity for its core motif.Nucleic acids research · 2018Article
- Compound Shape Effects in Minor Groove Binding Affinity and Specificity for Mixed Sequence DNA.Journal of the American Chemical Society · 2018Article
- Structural interpretation of DNA-protein hydroxyl-radical footprinting experiments with high resolution using HYDROID.Nature protocols · 2018Article
- Intrinsic DNA Shape Accounts for Affinity Differences between Hox-Cofactor Binding Sites.Cell reports · 2018Article
- Experimental maps of DNA structure at nucleotide resolution distinguish intrinsic from protein-induced DNA deformations.Nucleic acids research · 2018Article
- Recent Advances on the Machine Learning Methods in Identifying DNA Replication Origins in Eukaryotic Genomics.Frontiers in genetics · 2018Review
- Genome-wide prediction of minor-groove electrostatic potential enables biophysical modeling of protein-DNA binding.Nucleic acids research · 2017Article
- Molecular basis of CENP-C association with the CENP-A nucleosome at yeast centromeres.Genes & development · 2017Article
- Hydroxyl-radical footprinting combined with molecular modeling identifies unique features of DNA conformation and nucleosome positioning.Nucleic acids research · 2017Article
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Authors and funding
8 authors.
Funding
Abstract
DNA shape variation and the associated variation in minor groove electrostatic potential are widely exploited by proteins for DNA recognition. Here we show that the hydroxyl radical cleavage pattern is a quantitative measure of DNA backbone solvent accessibility, minor groove width, and minor groove electrostatic potential, at single nucleotide resolution. We introduce maps of DNA shape and electrostatic potential as tools for understanding how proteins recognize binding sites in a genome. These maps reveal periodic structural signals in yeast and Drosophila genomic DNA sequences that are associated with positioned nucleosomes.
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