Molecular and thermodynamic properties of d(A+-G)10, a single-stranded nucleic acid helix without paired or stacked bases

Abstract

Previously (Dolinnaya & Fresco, 1992), on the basis of an analysis of UV absorption and CD properties as a function of temperature and pH, the secondary structure of the deoxyoligonucleotide d(A(+)-G)10 was hypothesized to be helical and intramolecular in origin, being stabilized not by stacked bases or hydrogen-bonded base pairs but instead by ionic bonds between positively charged adenine residues and distal negatively charged phosphates. Several other properties are now shown to be consistent with this unusual type of structure. The molecular weight determined for d(A(+)-G)10 by sedimentation equilibrium is that of the single strand, and consistent with this, there is no molecular weight change on helix disruption. Formation of the d(A(+)-G)10 helix is accompanied by cooperative uptake of nine protons, corresponding to nine adenine residues that can form ionic bonds with all the available distal phosphates, i.e., the n+1 or the n+2 phosphates. The thermodynamic parameters of this helical structure obtained from both van't Hoff analysis of the melting of the structure and calorimetric measurements are in keeping with the ionic properties of the proposed structure. So are the dependence of its stability on pH and ionic strength, and also on oligomer length when compared with the behavior of d(A(+)-G)6. The possible role of this type of secondary structure in protein recognition of the single-stranded homopurine element of H-DNA is evaluated.