DNA dimer correlations reflect in vivo conditions and discriminate among nearest-neighbor base pair free energy parameter measures

The stability of the DNA duplex depends on its sequence rather than on its composition (the relative proportions of the four nucleotides or bases A, C, G and T). This fact was recognized since the eighties by several authors. They calculated the duplex relative stability and temperature-dependent behavior (ΔG, ΔH) for the ten different pairwise interactions. Even accepting that the experimental conditions and theoretical assumptions in these reports differ, one should expect little disagreement if their results were to reflect the same natural phenomenon. Unfortunately, this is not the case: The discrepancies among different teams are beyond acceptable experimental errors. Thermodynamics allows to relate DNA dimer frequencies with in vivo DNA interactions. In this paper we follow this approach and settle out the controversy by finding the parameter set consistent with intra-cellular DNA local free energy distribution.