10] Extracting thermodynamic data from equilibrium melting curves for oligonucleotide order-disorder transitions

Abstract

This chapter presents general forms of the equations required to extract thermodynamic data from equilibrium transition curves on oligomeric and polymeric nucleic acids of any molecularity. The reason that the equations and protocols are general, they also can be used to characterize thermodynamically equilibrium processes in systems other than nucleic acids. This work reviews how the reduced forms of the general equations have been used by many investigators to evaluate mono-and bimolecular transitions and then explains how these equations can be generalized to calculate thermodynamic parameters from common experimental observables for transitions of higher molecutarities. The strengths and weaknesses of each method of data analysis are emphasized, so that investigators can select the approach most appropriate for their experimental circumstances. This work also describes how to analyze calorimetric heat capacity curves and non-calorimetric differentiated melting curves to extract both model-independent and model-dependent thermodynamic data for transitions of any molecularity. The general equations and methods of analysis described should be of that are investigating association and dissociation processes in nucleic acids that exhibit molecularities greater than 2.