Anti-cooperative interactions in single-strand oligomers of deoxyriboadenylic acid.

Abstract

AbstractOptical rotatory dispersion measurements were made on the deoxyribo nucleotides d(pA)2, d(pA)4, d(pA)6 and poly(deoxyriboadenylic acid) at neutral pH over the temperature range 5–80°C. and were compared to similar data for the analogous oligoriboadenylic acids. The data were interpreted in terms of a temperature‐dependent stacking of the bases in the single‐strand deoxyribo oligomers. The thermal transition curves show an inverted chain‐length dependence compared to the ribo oligomer curves. These results are explained by a theory of anti‐cooperative interaction, where the nucleation parameter σ is >1. The theory, based on a one‐dimensional Ising model involving both attractive nearest‐neighbor and repulsive next‐nearest‐neighbor interactions, predicts the inverse chain length dependence and agrees rather well with the experimental data. At and above the transition temperature, the deoxyribo polymer is seen to consist of isolated stacked base pairs separated by at least one unit of random coil, there being only a very small probability for the existence of sequences of stacked residues longer than one. The partition function is seen to undergo an irregular behavior as a function of chain length because of the anti‐cooperative phenomenon. It is necessary to use an enthalpy of stacking of −5.0 kcal./mole in order to fit the experimental data with the theory. This value, 1.5 kcal./mole more positive than the ΔH found for the ribo oligomers, is reasonable, since the 2′ hydroxyl group would be expected to stabilize the stacking interaction in the ribo oligomers. Various kinds of distribution functions are calculated and plotted graphically for this theoretical model. A physical rationale is presented for the use of a repulsive next‐nearest‐neighbor term in this theory for the deoxyribo oligomers.