title: Alpha-DNA, a single-stranded secondary structure stabilized by ionic and hydrogen bonds: d(A(+)-G)n.
abstract: A novel nucleic acid secondary structure, exemplified by d(A(+)-G)10, is formed by an intramolecular, cooperative, acid-induced, coil-->helix transition. The helix is apparently left-handed, lacks base stacking and pairing, and is maintained by hydrogen and ionic bonds between dA+ "side-chain" residues (with electropositive hydrogens -N6H2, -N1+H) and the phosphodiester backbone. Modeling indicates that those dA+ residues lie approximately parallel to the helix axis, interacting with the n-1 backbone phosphates (with electronegative oxygens), somewhat like the -C=O...H-N- longitudinal interactions in a protein alpha-helix. Moreover, the intervening dG side-chain residues are extrahelical, as are amino acid side chains of an alpha-helix.
authors.affiliation: Department of Molecular Biology, Princeton University, New Jersey 08544-1014, USA.
authors.forename: M C
authors.initials: MC
authors.lastname: Shiber
authors.forename: L
authors.initials: L
authors.lastname: Lavelle
authors.forename: J A
authors.initials: JA
authors.lastname: Fossella
authors.forename: J R
authors.initials: JR
authors.lastname: Fresco
mesh_terms: D000818:Animals; D004277:DNA, Single-Stranded / Q000737:chemistry*; D006801:Humans; D006860:Hydrogen Bonding; D007477:Ions; D008958:Models, Molecular; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D011089:Polydeoxyribonucleotides / Q000737:chemistry
chemical_list: D004277:DNA, Single-Stranded; D007477:Ions; D011089:Polydeoxyribonucleotides