Thermodynamics of oligo(A)N·2poly(U)∞ from the dependence of the temperature of the helix–coil transition on oligomer concentration

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Abstract
On the basis of elementary two‐state, ideal solution thermocynamics, a modified expression for the melting of oligo. polynucleotide helices is derived which is applicable to variations in TmN and/or oligomer concentration, Cm with oligomer length, N: ΔHr is the enthalpy per helix residue, i.e., per base‐pair or base‐triplet, Vrf is the thermodynamic “available” or “reaction” volume, in liters/mole of helical residues; and n is the number of polynucleotide strands, e.g., n = 2 for oligo (A)N·2 poly(U)∞. Some earlier treatments have engendered confusion in the interpretation of the “reaction volume,” but with the derivation herein, the entropic origin and physical significance of Vrf is unequivocal.The following approximation was arrived at for the reduction expected in the configurational entropy, ΔSrconf, ∞, for (A)∞·2(U)∞, when the poly(A), strand is substituted for by an equivalent strand of contiguous oligo(A)N,′s: This adjustment of ΔSrconf, ∞ represents the source of the coefficient to 1/Tm∞ in expression (I). The expectation that ΔSrconf, N < ΔSrconf, ∞ is due to the effect of releasing normal internucleotide configurational restrictions every Nth residue in one‐third of the strands of the (A)N·2(U)∞ helix.Although the reduction in ΔSrconf, ∞ (II) may seem small (i.e., only 5.5% for the tetramer), its effect on the magnitude of Vrf in expression (I) is exponential. Thus, without these considerations the quantitative applicability of earlier expressions is questionable.By examining the variation in TmN with cm for a single N, all assumptions, required for evaluating Vrf or the entropic effects of discontinuities in the (A)N strand are avoided in the determination of a reliable enthalpy. We have therefore examined the system and obtained a ΔHr = 12.58 ± 0.08 kcal per mole (A)·2(U) base‐triplets between 5 and 2.5°C. That this value for ΔHr is in such excellent agreement with all calorimetric values reported for (A)∞·2(U)∞ suggests that the enthalpy for reaction(III) is not significantly affected by disconnections in the backbone of (A)4·2(U)∞. From (I), Vrf = 6.0 × 10−4 1/mole or 1 Å 3per helical residue. ΔHr°, corrected for residual single‐strand stacking in (A)4, is in excellent agreement with that found earlier for (A)1·2(U)∞. A residual heat capacity of 90 kcal(±20) per mole (A)·2(U) base‐triplets per °C is deduced from the decrease of ΔHr° with temperature.