Kinetic pathways of DNA melting with long- and short-range interactions

Abstract

We investigate kinetic pathways of the DNA melting transition using modified versions of the Poland–Scheraga (PS) and Peyrard–Dauxois–Bishop (PDB) models. The models have been generalized to include variable-range energetic interactions. Using Monte Carlo and Brownian dynamic simulations on the PS and PDB models, respectively, we find that while both models exhibit metastability for a variety of ranges, only the modified PS model with short-range interactions gives compact nucleating droplets. In contrast, the nearest-neighbor PDB model exhibits a critical configuration where most bases are unbound. For both the PS and PDB models, we find that increasing the range of interaction allows the system to be brought close to a pseudospinodal where the susceptibility diverges. We calculate the exponent γ characterizing this divergence using simulations and a self-consistent mean field theory. Near the pseudospinodal, the nucleating droplet in both models is diffuse and grows from the center in contrast to droplets predicted by classical nucleation theory. Finally, we show that including a heterogeneous sequence of bases does not significantly alter these qualitative results and discuss the implications for biological DNA.