POLYNUCLEOTIDES .22. ALPHA-DNA, A SINGLE-STRANDED SECONDARY STRUCTURESTABILIZED 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 stac king and pairing, and is maintained by hydrogen and ionic bonds betwee n 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, interact ing with the n - 1 backbone phosphates (with electronegative oxygens), somewhat like the -C=O-H-N-longitudinal interactions in a protein alp ha-helix. Moreover, the intervening dG side-chain residues are extrahe lical, as are amino acid side chains of an alpha-helix.