A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics

Abstract

A unified view of polymer, dumbbell, and oligonucleotide nearest-neighbor (NN) thermodynamics is presented. DNA NN DeltaG degrees 37 parameters from seven laboratories are presented in the same format so that careful comparisons can be made. The seven studies used data from natural polymers, synthetic polymers, oligonucleotide dumbbells, and oligonucleotide duplexes to derive NN parameters; used different methods of data analysis; used different salt concentrations; and presented the NN thermodynamics in different formats. As a result of these differences, there has been much confusion regarding the NN thermodynamics of DNA polymers and oligomers. Herein I show that six of the studies are actually in remarkable agreement with one another and explanations are provided in cases where discrepancies remain. Further, a single set of parameters, derived from 108 oligonucleotide duplexes, adequately describes polymer and oligomer thermodynamics. Empirical salt dependencies are also derived for oligonucleotides and polymers.

Figure 1

Application of the unified nearest neighbor parameters (Table 1) and Eq. 1 to predict ΔG°₃₇. Each arrow points to the middle of one of the NN dimers. The duplex CGTTGA⋅TCAACG is non-self-complementary and thus ΔG°(sym) is zero.

Figure 2

Experimental vs. predicted NN ΔG°₃₇ parameters (Table 1) of three polymer studies (7, 10, 17). •, NN data of Gotoh and Tagashira (7); ▪, NN data of Vologodskii et al. (10); ▴, NN data of Delcourt and Blake (17). Predictions are based on the unified oligonucleotide parameters (22) with the salt concentration extrapolated according to Eq. 9. The linear least-squares regression line is shown (y = 1.101 × +0.115; R² = 0.961). The standard deviation from the regression line is 0.12 kcal/mol.