title: Twist versus nonlinear stacking in short DNA molecules.
abstract: The denaturation of the double helix is a template for fundamental biological functions such as replication and transcription involving the formation of local fluctuational openings. The denaturation transition is studied for heterogeneous short sequences of DNA, i.e. ~100 base pairs, in the framework of a mesoscopic Hamiltonian model which accounts for the helicoidal geometry of the molecule. The theoretical background for the application of the path integral formalism to predictive analysis of the molecule thermodynamical properties is discussed. The base pair displacements with respect to the ground state are treated as paths whose temperature dependent amplitudes are governed by the thermal wavelength. The ensemble of base pairs paths is selected, at any temperature, consistently with both the model potential and the second law of thermodynamics. The partition function incorporates the effects of the base pair thermal fluctuations which become stronger close to the denaturation. The transition appears as a gradual phenomenon starting from the molecule segments rich in adenine-thymine base pairs. Computing the equilibrium thermodynamics, we focus on the interplay between twisting of the complementary strands around the molecule axis and nonlinear stacking potential: it is shown that the latter affects the melting profiles only if the rotational degrees of freedom are included in the Hamiltonian. The use of ladder Hamiltonian models for the DNA complementary strands in the pre-melting regime is questioned.
authors.affiliation: School of Science and Technology - CNISM, University of Camerino, I-62032 Camerino, Italy. Electronic address: marco.zoli@unicam.it.
authors.forename: Marco
authors.initials: M
authors.lastname: Zoli
mesh_terms: D004247:DNA / Q000737:chemistry*; D008956:Models, Chemical; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D013816:Thermodynamics
chemical_list: D004247:DNA
keywords: Base pair fluctuations; DNA denaturation; Nonlinear potentials; Path integral method; Twisting of DNA strands