Cooperative nonenzymic base recognition II. thermodynamics of the helix‐coil transition of oligoadenylic + oligouridylic acids

Abstract The properties of oligonucleotide helices of adeuylic‐ and uridylic acid oligomers have been investigated by measurements of hypo‐and hyperchromieity. High ionic strengths favor the formation of triple helices. Thus, the double helix‐coil transition can be studied (without interference by triple helices) only at low ionic‐strength. A “phase diagram” is given representing the T m ‐values of the various transitions at different ionic strengths for the system A(pA) 17 + U(pU) 17 . Oligonucleolides of chain lengths <8 always form both double and triple helices at the nucleotide concentrations required for base pairing. For this reason the double helix‐coil transition without coupling of the triple helix equilibrium can only be measured for chain lengths higher than 7. Melting curves corresponding to this transition have been determined for chain lengths 8, 9, 10, 11, 14 and 18 at different concentrations. An increase in nucleotide concentration leads to an increase in melting temperature. The shorter the chain length the lower the T m ‐value and the broader the helix‐coil transition. The experimental transition curves have been analysed according to a staggering zipper model with consideration of the stacking of the adeuylic acid single strands and the electrostatic repulsion of tlip phosphate charges on opposite strands. The temperature dependence of the nucleation parameter has been accounted for by a slacking factor x . The stacking factor expresses the magnitude of the stacking enthalpy. By curve fitting x was computed to be 0.7, corresponding to a stacking enthalpy of about S kcal/mole. The model described allows the reproduction of the experimental transition curves with relatively high accuracy. In an appendix the thermodynamic parameters of the stacking equilibrium of poly A and of the helix‐coil equilibria of poly A + poly U at neutral pH are calculated (Δ H A = −7.9 kcal/mole for the poly A stacking and Δ H 12 = −10.9 kcal/mole for the formation of the double helix from the randomly coiled single strands). A formula for the configurational entropy of polymers derived by Flory on the basis of a liquid lattice model is adapted to calculate the stacking entropies of adenylic oligomers.