Programme

P.18 -- Poster, ANSWCCMS-2023

Date: Tuesday, 7 November 2023

Time: 13:00 - 14:30

Energetic preference and topological constraint effects on the formation of DNA twisted toroidal bundles

Nhung T. T. Nguyen (1), Anh T. Ngo (2), and Trinh X. Hoang (3)

(1) Graduate University of Science and Technology, VAST, Hanoi, Vietnam (2) Chemical Engineering Department, University of Illinois Chicago, Illinois, USA (3) Institute of Physics, Vietnam Academy of Science and Technology, Hanoi, Vietnam

DNA toroids are compact torus-shaped bundles formed by one or multiple DNA molecules being condensed from the solution due to various condensing agents. It has been shown that the DNA toroidal bundles are twisted. However, the global conformations of DNA inside these bundles are still not well understood. In this study, we investigate this issue by solving different models for the toroidal bundles and performing replica-exchange molecular dynamics (REMD) simulations for self-attractive stiff polymers of various chain lengths. We find that a moderate degree of twisting is energetically favorable for toroidal bundles. The simulations show that the ground states of the stiff polymers are twisted toroidal bundles with the average twist degrees close to those predicted by the theoretical model. Constant-temperature simulations show that twisted toroidal bundles can be formed through successive processes of nucleation, growth, quick tightening, and slow tightening of the toroid. The two last processes facilitate the polymer threading through the toroid’s hole enabling the twisted bundle formation. The simulations also find twisted toroidal bundles with a sharp U-shaped region in the polymer conformation. It is suggested that this U-shaped region makes the formation of twisted bundles easier by effectively reducing the polymer length. This effect can be equivalent to having multiple chains in the toroid.

Presenter: Nguyen Thi Thuy Nhung

Presentation file: