Twist-writhe partitioning in a coarse-grained DNA minicircle model

Area of Science:

• Biophysics
• Computational Biology
• Molecular Biology

Background:

• DNA supercoiling is crucial for genomic processes.
• Understanding supercoil formation in minicircles is essential for DNA packaging and replication.
• Previous studies have explored DNA supercoiling, but long-chain dynamics remain challenging to simulate.

Purpose of the Study:

• To systematically investigate supercoil formation in DNA minicircles using molecular dynamics.
• To analyze the partitioning of linking number into twist and writhe as a function of chain length and excess linking number.
• To develop and validate a coarse-grained model for simulating long DNA chains with preserved structural properties.

Main Methods:

• Molecular-dynamics simulations of a two-bead coarse-grained DNA model.
• Parameter extraction from full-atomistic simulations via Boltzmann inversion.
• Analysis of twist/writhe partitioning in DNA minicircles of varying lengths and linking numbers.

Main Results:

• Observed an asymmetric supercoiling transition consistent with experimental findings.
• Demonstrated that twist/writhe partitioning is non-trivially dependent on chain length and excess linking number.
• Found that beyond the supercoiling transition, DNA chains of approximately one persistence length equally partition linking number into twist and writhe.
• Showed that longer DNA chains increasingly absorb linking number into writhe.

Conclusions:

• The study provides insights into the complex interplay of chain length, linking number, twist, and writhe in DNA minicircle supercoiling.
• The developed coarse-grained model allows for the simulation of DNA dynamics at lengths and timescales previously inaccessible.
• Results contribute to a deeper understanding of DNA structural transitions and their implications in biological systems.