Helix untwisting and bubble formation in circular DNA

TL;DR

This paper introduces a mesoscopic model for circular DNA that predicts helix untwisting, bubble formation, and sequence-specific properties across temperatures using path integral simulations.

Contribution

It presents a novel computational approach incorporating twisting and bending degrees of freedom to analyze circular DNA conformations.

Findings

Predicts helical repeat and bubble sizes for specific sequences.

Identifies energetically favorable conformations as temperature varies.

Provides insights into DNA behavior in mammalian cells.

Abstract

The base pair fluctuations and helix untwisting are examined for a circular molecule. A realistic mesoscopic model including twisting degrees of freedom and bending of the molecular axis is proposed. The computational method, based on path integral techniques, simulates a distribution of topoisomers with various twist numbers and finds the energetically most favorable molecular conformation as a function of temperature. The method can predict helical repeat, openings loci and bubble sizes for specific sequences in a broad temperature range. Some results are presented for a short DNA circle recently identified in mammalian cells.