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Alpha-DNA, a single-stranded secondary structure stabilized by ionic and hydrogen bonds: d(A(+)-G)n.

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.