Sharp DNA denaturation in a helicoidal mesoscopic model

• Published in: Chemical physics letters 2020-09, Vol.755, p.137781, Article 137781
• Main Authors: Rodrigues Leal, Mateus, Weber, Gerald
• Format: Article
• Language: English
• Subjects: DNA stability; Mesoscopic models; Peyrard Bishop model
• ISSN: 0009-2614; 1873-4448
• DOI: 10.1016/j.cplett.2020.137781

[Display omitted] •A new 1D DNA Hamiltonian with twist angle dependence was obtained from a 3D model.•We show the validity of the new Hamiltonian in the regime of small angles.•Resulting melting transition are found to be very sharp, even first-order like in the limit of long sequences, without the need of additional non-linear potentials.•Model parameters are compatible with other microscopic models and hydrogen bond parameters are of the same order of magnitude than those from ab-initio calculations. The Peyrard-Bishop DNA model describes the molecular interactions with simple potentials which allow efficient calculations of melting temperatures. However, it is based on a Hamiltonian that does not consider the helical twist or any other relevant molecular dimensions. Here, we start from a more realistic 3D model and work out several approximations to arrive at a new non-linear 1D Hamiltonian with a twist angle dependence. Our approximations were numerically compared to full 3D calculations, and established its validity in the regime of small angles. For long DNA sequences we obtain sharp, first-order-like melting, transitions.