First-passage probability: a test for DNA Hamiltonian parameters

Abstract

A method is proposed to select the suitable sets of potential parameters for a one-dimensional mesoscopic Hamiltonian model, first introduced to describe the DNA melting transition and later extended to investigate thermodynamic and dynamical properties of nucleic acids. The DNA base pair fluctuations are considered as time dependent trajectories whose initial condition sets the no crossing constraint enforced in the path integral for the first-passage probability. Performing the path integration at room temperature, relations are established between the cutoff on the amplitude of the base pair fluctuations and the model parameters. In particular, a suitable range of values for the non-linear stacking parameter has been proposed while the effect of the stiffness constant on the first-passage probability has been highlighted. The formalism here developed may be applied to compute the lifetime of open base pairs in three-dimensional helical models for DNA molecules.