Fluctuations cutoff in a 1D Hamiltonian model for DNA

Abstract

Considering a one dimensional mesoscopic model for DNA, we focus on the upper bound for the base pair fluctuations, a relevant parameter in computer simulations for which contrasting estimates have been reported. Noticing that the free energy of the model can be obtained analytically in the thermodynamic limit, we derive a relation for the fluctuations upper bound in terms of temperature and elastic force constant of the stacking potential. At room temperature, the fluctuation cutoff is constrained to values ∼ 2˚A in fair agreement with the threshold above which hydrogen bonds break and base pairs dissociate.