**A Review on the Thermodynamics of Denaturation Transition of DNA Duplex Oligomers in the Context of Nearest-Neighbor Models**

João C. O. Guerra

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http://dx.doi.org/10.5772/62574

#### **Abstract**

In this review, we show that additive physical properties of DNA double strands can be written in terms of eight (polymeric) irreducible parameters. This results in self-consis‐ tency relations constraining the 10 duplex dimer contributions. Studies of thermodynam‐ ic stability of duplex oligomers are feasible, adding extra degrees of freedom, and this is performed, initially, considering the influence of end parameters on the thermodynamic stability of oligomers. Hence, we connect a statistical mechanics approach to the nearestneighbor (NN) approach in the framework of the two-state model. This provides one cor‐ relation between end effects and initiation phenomena. Because of that, inside the framework of the NN modeling, the role played by end effects could not be so well de‐ fined. Thus, we propose a new model that permits to provide the nucleation free ener‐ gies. The power of this model is relating the nucleation free energy to the mean composition of the chain, permitting to obtain a good estimate for the free energy associ‐ ated only to the Watson–Crick base pairings.

**Keywords:** Thermodynamics of DNA duplex oligomers, Initiation free energy, Nuclea‐ tion free energy, Irreducible parameters for free energy
