title: DNA conformations and their sequence preferences.
abstract: The geometry of the phosphodiester backbone was analyzed for 7739 dinucleotides from 447 selected crystal structures of naked and complexed DNA. Ten torsion angles of a near-dinucleotide unit have been studied by combining Fourier averaging and clustering. Besides the known variants of the A-, B- and Z-DNA forms, we have also identified combined A + B backbone-deformed conformers, e.g. with alpha/gamma switches, and a few conformers with a syn orientation of bases occurring e.g. in G-quadruplex structures. A plethora of A- and B-like conformers show a close relationship between the A- and B-form double helices. A comparison of the populations of the conformers occurring in naked and complexed DNA has revealed a significant broadening of the DNA conformational space in the complexes, but the conformers still remain within the limits defined by the A- and B- forms. Possible sequence preferences, important for sequence-dependent recognition, have been assessed for the main A and B conformers by means of statistical goodness-of-fit tests. The structural properties of the backbone in quadruplexes, junctions and histone-core particles are discussed in further detail.
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, CZ-166 10 Prague, Czech Republic.
authors.forename: Daniel
authors.initials: D
authors.lastname: Svozil
authors.forename: Jan
authors.initials: J
authors.lastname: Kalina
authors.forename: Marek
authors.initials: M
authors.lastname: Omelka
authors.forename: Bohdan
authors.initials: B
authors.lastname: Schneider
mesh_terms: D001483:Base Sequence; D003596:Cytosine / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D044704:DNA, A-Form / Q000737:chemistry; D045566:DNA, Cruciform / Q000737:chemistry; D004268:DNA-Binding Proteins / Q000737:chemistry; D003854:Deoxyribonucleotides / Q000737:chemistry; D054856:G-Quadruplexes; D008024:Ligands; D009690:Nucleic Acid Conformation; D009707:Nucleosomes / Q000737:chemistry; D012313:RNA / Q000737:chemistry
chemical_list: D044704:DNA, A-Form; D045566:DNA, Cruciform; D004268:DNA-Binding Proteins; D003854:Deoxyribonucleotides; D008024:Ligands; D009707:Nucleosomes; D012313:RNA; D003596:Cytosine; D004247:DNA