A model for the single stranded random coil form of polydeoxyadenylic acid from minimum energy conformations of the dimeric subunit

The minimum energy conformations of dApdA have been examined for their suitability as buildings blocks of the single stranded coil form of polynucleotides. Calculations of the characteristic ratio C {reversed tilde} = 〈r_o〉² /nl² were made for a polymer generated from all the low energy conformers, as well as for selected combinations. A polymer composed of a conformer with ω', ω = t^*,g⁺ ,(skewed) ψ =t, C-(2′)-endo type pucker, in combination with the 'B' form, has a C {reversed tilde} equal to that observed in coils of apurinic acid (6) when the fraction of 'B' form conformers is ∼ 25% and ∼ 91%. The t^*,g⁺ conformer is the second lowest energy form in the C-(2′)-endo puckering domain, following the 'B' form.