Sevier, S. A. | Search bioRxiv

bioRxiv2019

Mechanical Properties of DNA Replication

Central to the function of cellular life is the reading, storage and replication of DNA. Due to the helical structure of DNA, a complicated topological braiding of new strands follows the duplication of the old strands. Even though this was discovered over 60 years ago, the mathematical and physical questions this presents have largely gone unaddressed. In this letter we construct a simple idealized model of DNA replication using only the most basic mathematical and mechanical elements of DNA replication. The aim of this is to reveal the mechanical balance of braided, replicated DNA against the twist of unreplicated DNA at the heart of the replication process. The addition of topoisomerase action is included presenting a balancing force offering a glimpse into the ways in which cells maintain this balance. Additionally the physical basis for recently observed replication/replication and replication/transcription conflicts are examined showing how gene orientation and size can impact DNA replication.

biophysics↗

bioRxiv2018

Properties of Gene Expression and Chromatin Structure with Mechanically Regulated Transcription

The mechanical properties of transcription have emerged as central elements in our understanding of gene expression. Recent work has been done introducing a simple description of the basic physical elements of transcription where RNA elongation, RNA polymerase (RNAP) rotation and DNA supercoiling are coupled [1]. Here we generalize this framework to accommodate the behavior of many RNAPs operating on multiple genes on a shared piece of DNA. The resulting framework is combined with well-established stochastic processes of transcription resulting in a model which characterizes the impact of the mechanical properties of transcription on gene expression and DNA structure. Transcriptional bursting readily emerges as a common phenomenon with origins in the geometric nature of the genetic system and results in the bounding of gene expression statistics. Properties of a multiple gene system are examined with special attention paid to role that genome composition (gene orientation, size, and intergenic distance) plays in the ability of genes to transcribe. The role of transcription in shaping DNA structure is examined and the possibility of transcription driven domain formation is discussed.\n\nPACS numbers:

biophysics↗