ArticleNucleic acids research2018
Experimental maps of DNA structure at nucleotide resolution distinguish intrinsic from protein-induced DNA deformations.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Readout of intrinsic and induced DNA shape by homeodomain transcription factor complexes.Biophysical journal · 2026Article
- Systematic Comparison of Atomistic Force Fields for the Mechanical Properties of Double-Stranded DNA.Journal of chemical theory and computation · 2024Article
- DNA binding specificity of all four Saccharomyces cerevisiae forkhead transcription factors.Nucleic acids research · 2023Article
- Insights into DNA solvation found in protein-DNA structures.Biophysical journal · 2022Review
- Flexibility of flanking DNA is a key determinant of transcription factor affinity for the core motif.Biophysical journal · 2022Article
- Article
- Landscape of DNA binding signatures of myocyte enhancer factor-2B reveals a unique interplay of base and shape readout.Nucleic acids research · 2020Article
- TFBSshape: an expanded motif database for DNA shape features of transcription factor binding sites.Nucleic acids research · 2020Article
- New insights into protein-DNA binding specificity from hydrogen bond based comparative study.Nucleic acids research · 2019Article
- A New Generation of Minor-Groove-Binding-Heterocyclic Diamidines That Recognize G·C Base Pairs in an AT Sequence Context.Molecules (Basel, Switzerland) · 2019Review
- Compound Shape Effects in Minor Groove Binding Affinity and Specificity for Mixed Sequence DNA.Journal of the American Chemical Society · 2018Article
- Intrinsic DNA Shape Accounts for Affinity Differences between Hox-Cofactor Binding Sites.Cell reports · 2018Article
- Beyond the double helix: DNA structural diversity and the PDB.The Journal of biological chemistryReview
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Authors and funding
8 authors.
Funding
Abstract
Recognition of DNA by proteins depends on DNA sequence and structure. Often unanswered is whether the structure of naked DNA persists in a protein-DNA complex, or whether protein binding changes DNA shape. While X-ray structures of protein-DNA complexes are numerous, the structure of naked cognate DNA is seldom available experimentally. We present here an experimental and computational analysis pipeline that uses hydroxyl radical cleavage to map, at single-nucleotide resolution, DNA minor groove width, a recognition feature widely exploited by proteins. For 11 protein-DNA complexes, we compared experimental maps of naked DNA minor groove width with minor groove width measured from X-ray co-crystal structures. Seven sites had similar minor groove widths as naked DNA and when bound to protein. For four sites, part of the DNA in the complex had the same structure as naked DNA, and part changed structure upon protein binding. We compared the experimental map with minor groove patterns of DNA predicted by two computational approaches, DNAshape and ORChID2, and found good but not perfect concordance with both. This experimental approach will be useful in mapping structures of DNA sequences for which high-resolution structural data are unavailable. This approach allows probing of protein family-dependent readout mechanisms.
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