The Free Energy of Nucleosomal DNA Based on the Landau Model and Topology

Abstract

The free energy of nucleosomal DNA plays a key role in the formation of nucleosomes in eukaryotes. Some work on the free energy of nucleosomal DNA have been carried out in experiments. However, the relationships between the free energy of nucleosomal DNA and its conformation, especially its topology, remain unclear in theory. By combining the Landau theory, the Hopfion model and experimental data, we find that the free energy of nucleosomal DNA is at the lower level. With the help of the energy minimum principle, we conclude that nucleosomal DNA stays in a stable state. Moreover, we discover that small perturbations on nucleosomal DNA have little effect on its free energy. This implies that nucleosomal DNA has a certain redundancy in order to stay stable. This explains why nucleosomal DNA will not change significantly due to small perturbations.

Keywords

• nucleosome core particle
• DNA free energy
• minimum free energy principle
• Landau theory
• Hopfion model