ArticleJournal of molecular biology2009
Signatures of protein-DNA recognition in free DNA binding sites.
Article in Journal of molecular biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Structural and mechanistic insights into the Artemis endonuclease and strategies for its inhibition.Nucleic acids research · 2021Article
- The RNA Polymerase α Subunit Recognizes the DNA Shape of the Upstream Promoter Element.Biochemistry · 2020Article
- Experimental maps of DNA structure at nucleotide resolution distinguish intrinsic from protein-induced DNA deformations.Nucleic acids research · 2018Article
- Expanding the repertoire of DNA shape features for genome-scale studies of transcription factor binding.Nucleic acids research · 2017Article
- DNAproDB: an interactive tool for structural analysis of DNA-protein complexes.Nucleic acids research · 2017Article
- 5-Formylcytosine alters the structure of the DNA double helix.Nature structural & molecular biology · 2015Article
- Specific minor groove solvation is a crucial determinant of DNA binding site recognition.Nucleic acids research · 2014Article
- cgDNA: a software package for the prediction of sequence-dependent coarse-grain free energies of B-form DNA.Nucleic acids research · 2014Article
- μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA.Nucleic acids research · 2014Article
- Structure of catabolite activator protein with cobalt(II) and sulfate.Acta crystallographica. Section F, Structural biology communications · 2014Article
- DNA dynamics and single-molecule biology.Chemical reviews · 2014Review
- Bioinformatic analysis of the protein/DNA interface.Nucleic acids research · 2014Article
- Improved predictions of transcription factor binding sites using physicochemical features of DNA.Nucleic acids research · 2012Article
- Article
- DNA shape, genetic codes, and evolution.Current opinion in structural biology · 2011Review
- Bifacial nucleoside as a surrogate for both T and A in duplex DNA.Journal of the American Chemical Society · 2011Article
- The shape of the DNA minor groove directs binding by the DNA-bending protein Fis.Genes & development · 2010Article
- Origins of specificity in protein-DNA recognition.Annual review of biochemistry · 2010Review
- A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA.Nucleic acids research · 2010Article
- Article
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5 authors.
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Abstract
One obstacle to achieving complete understanding of the principles underlying sequence-dependent recognition of DNA is the paucity of structural data for DNA recognition sequences in their free (unbound) state. Here, we carried out crystallization screening of 50 DNA duplexes containing cognate protein binding sites and obtained new crystal structures of free DNA binding sites for three distinct modes of DNA recognition: anti-parallel beta strands (MetR), helix-turn-helix motif + hinge helices (PurR), and zinc fingers (Zif268). Structural changes between free and protein-bound DNA are manifested differently in each case. The new DNA structures reveal that distinctive sequence-dependent DNA geometry dominates recognition by MetR, protein-induced bending of DNA dictates recognition by PurR, and deformability of DNA along the A-B continuum is important in recognition by Zif268. Together, our findings show that crystal structures of free DNA binding sites provide new information about the nature of protein-DNA interactions and thus lend insights towards a structural code for DNA recognition.
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