Twist versus nonlinear stacking in short DNA molecules

DOI10.1016/J.JTBI.2014.03.031MaRDI QIDQ2415531zbMATH OpenOpenAlexWikidataFDO

Authors Marco Zoli

Publication date 23 May 2019

Published in Journal of Theoretical Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1310.3985

zbMATH Keywords

base pair fluctuationsDNA denaturationnonlinear potentialspath integral methodtwisting of DNA strands

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40)

Abstract: The denaturation of the double helix is a template for fundamental biological functions such as replication and transcription involving the formation of local fluctuational openings. The denaturation transition is studied for heterogeneous short sequences of DNA, i.e. $sim100$ base pairs, in the framework of a mesoscopic Hamiltonian model which accounts for the helicoidal geometry of the molecule. The theoretical background for the application of the path integral formalism to predictive analysis of the molecule thermodynamical properties is discussed. The base pair displacements with respect to the ground state are treated as paths whose temperature dependent amplitudes are governed by the thermal wavelength. The ensemble of base pairs paths is selected, at any temperature, consistently with both the model potential and the second law of thermodynamics. The partition function incorporates the effects of the base pair thermal fluctuations which become stronger close to the denaturation. The transition appears as a gradual phenomenon starting from the molecule segments rich in adenine-thymine base pairs. Computing the equilibrium thermodynamics, we focus on the interplay between twisting of the complementary strands around the molecule axis and nonlinear stacking potential: it is shown that the latter affects the melting profiles only if the rotational degrees of freedom are included in the Hamiltonian. The use of ladder Hamiltonian models for the DNA complementary strands in the pre-melting regime is questioned.

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Cited in

(7)

• Thermodynamics of a nonlinear model for DNA denaturation
• A duplex DNA model with regular inter-base-pair hydrogen bonds
• Distribution of base pair alternations in a periodic DNA chain: application of Pólya counting to a physical system
• Twisting short dsDNA with applied tension
• Writhe of DNA induced by a terminal twist
• NON-HARMONIC DNA BENDING ELASTICITY IS REVEALED BY STATISTICS OF DNA MINICIRCLE SHAPES
• Torsion and entropy driven denaturation of DNA

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