Model for melting transition of twisted DNA in a thermal bath

Omid Farzadian (), Thomas Oikonomou, Mehdi Moradkhani and Saule Zhumambayeva
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Omid Farzadian: Nazarbayev University
Thomas Oikonomou: VinUniversity
Mehdi Moradkhani: Abhar Branch, Islamic Azad University
Saule Zhumambayeva: Astana Medical University

The European Physical Journal B: Condensed Matter and Complex Systems, 2023, vol. 96, issue 2, 1-9

Abstract: Abstract We investigated the melting transition of deoxyribonucleic acid (DNA) embedded in a Langevin fluctuation–dissipation thermal bath. Torsional effects were taken into consideration by introducing a twist angle $$\varphi $$ φ between neighboring base pairs stacked along the molecule backbone. We use the Barbi–Cocco–Payrard model to numerically study the impact of the twist angle on the melting temperature, considering four different sequences composed of 69 base pairs. According to the outcomes of our simulation, for all heterogeneous sequences, an increase in twist angle leads to a linear rise in melting temperature with a positive slope. For angles greater than the so-called equilibrium angle, the DNA chain becomes very rigid against opening and accordingly high temperatures are required to initiate the melting process. We also investigate the opening probability of bubbles, the bubble lifetime profiles and bubble length along the different DNA sequences. Graphical abstract

Date: 2023
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DOI: 10.1140/epjb/s10051-023-00492-4

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