TL;DR
This paper models the conformations of circular DNA as a semi-flexible polymer with self-attraction, analyzing stable states like toroids and racquets, and suggests primary structure influences stability.
Contribution
It introduces a model incorporating sequence-dependent self-attraction and analyzes multiple conformations of circular DNA, providing a state diagram of stability.
Findings
Stable conformations include toroids and racquets.
Conformation stability can be controlled by primary structure.
Model applicable to other semi-flexible polymers.
Abstract
A simple model of a circularly closed dsDNA in a poor solvent is considered as an example of a semi-flexible polymer with self-attraction. To find the ground states, the conformational energy is computed as a sum of the bending and torsional elastic components and the effective self-attraction energy. The model includes a relative orientation or sequence dependence of the effective attraction forces between different pieces of the polymer chain. Two series of conformations are analysed: a multicovered circle (a toroid) and a multifold two-headed racquet. The results are presented as a diagram of state. It is suggested that the stability of particular conformations may be controlled by proper adjustment of the primary structure. Application of the model to other semi-flexible polymers is considered.
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