title: Understanding the sequence-dependence of DNA groove dimensions: implications for DNA interactions.
abstract: BACKGROUND
  The B-DNA major and minor groove dimensions are crucial for DNA-protein interactions. It has long been thought that the groove dimensions depend on the DNA sequence, however this relationship has remained elusive. Here, our aim is to elucidate how the DNA sequence intrinsically shapes the grooves.
  
  
  RESULTS
  The present study is based on the analysis of datasets of free and protein-bound DNA crystal structures, and from a compilation of NMR (31)P chemical shifts measured on free DNA in solution on a broad range of representative sequences. The (31)P chemical shifts can be interpreted in terms of the BI↔BII backbone conformations and dynamics. The grooves width and depth of free and protein-bound DNA are found to be clearly related to the BI/BII backbone conformational states. The DNA propensity to undergo BI↔BII backbone transitions is highly sequence-dependent and can be quantified at the dinucleotide level. This dual relationship, between DNA sequence and backbone behavior on one hand, and backbone behavior and groove dimensions on the other hand, allows to decipher the link between DNA sequence and groove dimensions. It also firmly establishes that proteins take advantage of the intrinsic DNA groove properties.
  
  
  CONCLUSIONS
  The study provides a general framework explaining how the DNA sequence shapes the groove dimensions in free and protein-bound DNA, with far-reaching implications for DNA-protein indirect readout in both specific and non specific interactions.
authors.affiliation: Laboratoire de Physique Théorique et Modélisation, UMR-8089, Centre National de la Recherche Scientifique et Université de Cergy-Pontoise, Cergy-Pontoise, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Oguey
authors.forename: Nicolas
authors.initials: N
authors.lastname: Foloppe
authors.forename: Brigitte
authors.initials: B
authors.lastname: Hartmann
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D018360:Crystallography, X-Ray / Q000379:methods; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D008956:Models, Chemical; D008958:Models, Molecular; D008968:Molecular Conformation; D009690:Nucleic Acid Conformation; D009711:Nucleotides / Q000737:chemistry; D010759:Phosphorus Isotopes / Q000737:chemistry; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry
chemical_list: D009711:Nucleotides; D010759:Phosphorus Isotopes; D011506:Proteins; D004247:DNA