First experimental tests of the Peyrard-Bishop model applied to the melting of very short DNAs

The melting curves of short heterogeneous DNA chains in solution are calculated on the basis of statistical thermodynamics and compared to experiments. The computation of the partition function is based on the Peyrard-Bishop hamiltonian, which has already been adopted in the theoretical description of the melting of long DNA chains. In the case of short chains it is necessary to consider not only the breaking of the hydrogen bonds between single base pairs, but also the complete dissociation of the two strands forming the double helix. There is a need for a theory of the melting of short DNA chains (oligonucleotides). The melting is the highly cooperative thermal disruption of the hydrogen bonds between complementary bases in the double helix, as usually monitored by the UV absorption increment due to the unstacking of the separated bases [1]. At the equilibrium melting temperature half of the bonds are disrupted. Synthetic oligonucleotides of a fixed length and base pairs sequence have been used for a long time as model systems for the study of the structural and thermodynamical properties of the longer and more complex natural forms of DNA [2]. Many studies have shown the effects of both sequence and solvent composition on the melting curves of oligonucleotides in solution [3]. More recently particular attention has been given to the study of sequence specific effects on the thermal stability of a variety of specially designed oligonucleotides, due to their importance in the exploitation of molecular biological techniques in gene therapy [4] and genome mapping [5]. Predictive information has been gained through an extensive thermodynamical investigation on the melting behavior of oligonucleotides, based on the computation of the Gibbs free energy, Author to whom correspondence should be addressed. E-mail:[email protected]