title: The Role of Unconventional Hydrogen Bonds in Determining BII Propensities in B-DNA.
abstract: An accurate understanding of DNA backbone transitions is likely to be the key for elucidating the puzzle of the intricate sequence-dependent mechanical properties that govern most of the biologically relevant functions of the double helix. One factor believed to be important in indirect recognition within protein-DNA complexes is the combined effect of two DNA backbone torsions (ε and ζ) which give rise to the well-known BI/BII conformational equilibrium. In this work we explain the sequence-dependent BII propensity observed in RpY steps (R = purine; Y = pyrimidine) at the tetranucleotide level with the help of a previously undetected C-H···O contact between atoms belonging to adjacent bases. Our results are supported by extensive multimicrosecond molecular dynamics simulations from the Ascona B-DNA Consortium, high-level quantum mechanical calculations, and data mining of the experimental structures deposited in the Protein Data Bank.
authors.affiliation: Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , Baldiri Reixac 10-12, Barcelona 08028, Spain.|Joint BSC-IRB Program in Computational Biology, Institute for Research in Biomedicine , Baldiri Reixac 10-12, Barcelona 08028, Spain.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Balaceanu
authors.affiliation: MMSB, Univ. Lyon I/CNRS UMR 5086, Institut de Biologie et Chimie des Protéines, 7 Passage du Vercors, Lyon 69367, France.|School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham , University Park NG7 2RD, U.K.
authors.forename: Marco
authors.initials: M
authors.lastname: Pasi
authors.affiliation: Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , Baldiri Reixac 10-12, Barcelona 08028, Spain.|Joint BSC-IRB Program in Computational Biology, Institute for Research in Biomedicine , Baldiri Reixac 10-12, Barcelona 08028, Spain.
authors.forename: Pablo D
authors.identifier: http://orcid.org/0000-0002-5927-372X
authors.initials: PD
authors.lastname: Dans
authors.affiliation: Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , Baldiri Reixac 10-12, Barcelona 08028, Spain.|Joint BSC-IRB Program in Computational Biology, Institute for Research in Biomedicine , Baldiri Reixac 10-12, Barcelona 08028, Spain.
authors.forename: Adam
authors.initials: A
authors.lastname: Hospital
authors.affiliation: MMSB, Univ. Lyon I/CNRS UMR 5086, Institut de Biologie et Chimie des Protéines, 7 Passage du Vercors, Lyon 69367, France.
authors.forename: Richard
authors.initials: R
authors.lastname: Lavery
authors.affiliation: Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , Baldiri Reixac 10-12, Barcelona 08028, Spain.|Joint BSC-IRB Program in Computational Biology, Institute for Research in Biomedicine , Baldiri Reixac 10-12, Barcelona 08028, Spain.|Department of Biochemistry and Biomedicine, Faculty of Biology, University of Barcelona . Diagonal 643, Barcelona 08028, Spain.
authors.forename: Modesto
authors.identifier: http://orcid.org/0000-0002-8608-3278
authors.initials: M
authors.lastname: Orozco
mesh_terms: D001483:Base Sequence; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D059371:DNA, B-Form / Q000737:chemistry*; D016208:Databases, Factual; D006859:Hydrogen; D006860:Hydrogen Bonding; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D011687:Purines / Q000737:chemistry; D011743:Pyrimidines / Q000737:chemistry
chemical_list: D059371:DNA, B-Form; D009838:Oligodeoxyribonucleotides; D011687:Purines; D011743:Pyrimidines; D006859:Hydrogen; D004247:DNA; C030986:pyrimidine; C030985:purine