Importance of oligoelectrolyte end effects for the thermodynamics of conformational transitions of nucleic acid oligomers: A grand canonical Monte Carlo analysis

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Abstract
Effects of salt concentration on the stabilities of oligonucleotide helices are analyzed directly in terms of ΔΓN→yN ≡ Γ − ΓNnat, the difference in the salt–nucleotide phosphate preferential interaction coefficients for the denatured state, having yN phosphate charges, and for the native state, having N phosphate charges (y = 1 for hairpin denaturation and y = 0.5 for dimer denaturation). Previous experimental studies of the denaturation of hairpin oligo‐nucleotides (having 18 < N < 44) indicate significant differences between ΔΓN→N and ΔΓ∞, the value determined for the denaturation of the corresponding polynucleotide. These differences are thermodynamic manifestations of the oligoelectrolyte end effect. In contrast, the available data on the denaturation of oligonucleotide dimer helices (N ⩽ 22) imply that differences between ΔΓ∞ and ΔΓN→0.5N, and hence oligoelectrolyte end effects, are small or negligible. To determine the origin of these apparently conflicting implications concerning the importance of oligoelectrolyte end effects, we have calculated the N dependence of ΓN from grand canonical Monte Carlo simulations for an idealized model of the structure and charge distribution of each oligomer conformation. Our calculations are in quantitative agreement with the experimental finding for d(TA) hairpin oligomers that − ΔΓN→N decreases linearly as N−1 increases, and with the extant experimental determinations of ΔΓN→0.5N. These results provide an illustration of how the large electrostatic end effects exhibited by the hairpin denaturation data are masked when ΔΓ∞ is compared with values of ΔΓN→0.5N for short dimer helices (N ⩽ 22). For 0.5N > 24, − ΔΓN→0.5N is predicted to be a linear function of N−1 whose slope has the opposite sign from, and is more salt‐concentration dependent than, the corresponding slope of − ΔΓN→N as a function of N−1. Our calculations also yield predictions about the N dependences of the individual values of ΓN that can be tested by determining Donnan coefficients from membrane dialysis equilibrium experiments. For long enough hairpin and dimer oligonucleotides (yN ⩾ 24), in either native or denatured forms, we predict that the (positive) difference Γ∞ − ΓN increases linearly with increasing N−1. For smaller values of N the difference Γ∞ − ΓN continues to increase with increasing N−1.