Self-complementary oligoribonucleotides: Adenylic acid-uridylic acid block copolymers

A series of block oligonucleotides of adenylic and uridylic acid of the form (Ap)_m(Up)_n-1, where m and n vary individually from 3 to 7, have been prepared. Individual oligonucleotides were shown to form bimolecular helical complexes in solution when m ≥ n but when m < n multichain aggregates containing some triple-stranded helical regions form. Ultraviolet spectra, concentration dependence of T_m, hypochromicity on melting and sedimentation coefficients provided the evidence for these conclusions. Even with non-complementary bases inserted between the adenylic and uridylic acid blocks no single chain, hairpin helices were observed. For m = n the concentration and temperature dependence of association was consistent with a dimer-monomer equilibrium. The concentration dependence of T_m yielded enthalpy changes per base pair, ΔH₁, that increased from -6.4 kcal./mole for (Ap)₄(Up)₃U to -7.6 kcal./mole for (Ap)₇(Up)₆U. The slope of the thermal dissociation curve at midpoint yielded average values of only -5.5 kcal./ mole. Plots of 1 T_m, versus, 1 N, where N = m + n, were linear. However, the apparent variation of ΔH₁ had to be introduced in order to obtain values of β that were comparable to other estimates. The chain-length dependence of ΔH₁ presumably arises from end effects and/or from variations in the stacking energy of the adenylic acid sequences at the different temperature ranges over which different chain-length dimers dissociated.