Co-operative non-enzymic base recognition: I. Thermodynamics of the helix-coil transition of oligoriboadenylic acids at acidic pH

Abstract

The hypochromicity of oligoriboadenylic acids (pA) n was measured at acidic pH as a function of temperature for chain lengths up to 10. At high nucleotide concentrations and a pH of 3.2 co-operative helix-coil transitions could be observed down to the tetranucleotide. The helix-coil transition can be described satisfactorily by an all-or-none model. Using such a model the analysis of melting curves yielded enthalpy changes, which depend on the chain length. With increasing nucleotide concentrations the melting curves are shifted to higher temperatures. From this concentration dependence, enthalpy changes were calculated, which agree quite well with the first set of values. In a more accurate treatment, partly bonded structures have to be considered. Corresponding corrections of the experimental transition enthalpies were applied according to the staggering zipper model. The chain length dependence of the enthalpy changes can be explained by two different effects: first, the stabilization of the double helix is mainly due to stacking interactions between adjacent base pairs. This results in transition enthalpies increasing with chain length if calculated per base pair. The second effect comes from differences in the degree of stacking of the single strands. Longer nucleotides melt at higher temperatures, where the degree of stacking is smaller. Another correction has to be introduced because of the protonation reaction. Analysis of the chain-length dependence of the melting temperature ( T m) leads to the conclusion that the nucleation parameter β is connected with a positive enthalpy difference; this is equivalent to the conclusion that the stability constant for a first base pair, β s, is associated with an enthalpy difference close to zero. These results show that the stacking between adjacent base pairs is the main source of stabilisation and that the enthalpy of base pairing in the co-operative model is mainly given by the enthalpy of stacking. This enthalpy difference, i.e. the enthalpy of base-pair formation adjacent to an already existing stack from randomly coiled single strands is found to be −11.8 ± 0.6 kcal./mole.