# New Insights into the Geometry and Topology of DNA Replication Intermediates

## TL;DR

This paper uses simulations to study how DNA replication intermediates change shape and manage stress during replication.

## Contribution

The first molecular dynamics simulations of partially replicated DNA molecules at different replication stages are presented.

## Key findings

- Deproteinization allows superhelical stress to distribute between replicated and unreplicated DNA regions.
- Five components of superhelical stress and four types of collision events were identified in replicating DNA molecules.
- Collision events' chirality and topological sign correlate with replication fork progression.

## Abstract

The topological and conformational properties of DNA replication intermediates change after deproteinization. We present the first molecular dynamics simulations of partially replicated molecules at both early and late stages of the DNA replication process. Deproteinization facilitates the distribution of superhelical stress between unreplicated and replicated regions to reach a thermodynamic equilibrium. Our simulations identified five components of superhelical stress and four types of collision events in replicating molecules. The topological sign and chirality of collision events were correlated with the progression of DNA replication.

The regulation of superhelical stress, mediated by the combined action of topoisomerases and fork rotation, is crucial for DNA replication. The conformational changes during DNA replication are still experimentally challenging, mainly due to the rapid kinetics of the replication process. Here, we present the first molecular dynamics simulations of partially replicated circular DNA molecules, with stalled replication forks at both early and late stages of DNA replication. These simulations allowed us to map the distribution of superhelical stress after deproteinization. We propose a five-component model that determines the linking number difference of replication intermediates. At a thermodynamic equilibrium, the contribution of these five components was correlated to the progress of the replication forks. Additionally, we identified four types of segment collision events in replication intermediates, characterized by their geometric properties, including chirality and topological sign. The distribution of these collision events between the early and late stages of DNA replication provides new insights into the coordinated function of topoisomerases, warranting further discussion.