Theoretical model of transcription based on torsional mechanics of DNA template

TL;DR

This paper presents a simple physical model of DNA transcription mechanics, analyzing how DNA supercoiling and enzyme rotation interact during gene expression, with implications for understanding the physical basis of transcription regulation.

Contribution

It introduces a novel theoretical model linking DNA torsional mechanics, RNA synthesis, and enzyme rotation, advancing understanding of transcription physical behavior.

Findings

Rotation during early transcription is mainly released by RNAP rotation.

Intermediate transcription involves both supercoiling and RNAP rotation.

Approaching DNA twisting limits, RNAP rotation dominates rotation release.

Abstract

Transcription is the first step of gene expression, in which a particular segment of DNA is copied to RNA by the enzyme RNA polymerase (RNAP). Despite many details of the complex interactions between DNA and RNA synthesis disclosed experimentally, much of physical behavior of transcription remains largely unknown. Understanding torsional mechanics of DNA and RNAP together with its nascent RNA and RNA-bound proteins in transcription maybe the first step towards deciphering the mechanism of gene expression. In this study, based on the balance between viscous drag on RNA synthesis and torque resulted from untranscribed supercoiled DNA template, a simple model is presented to describe mechanical properties of transcription. With this model, the rotation and supercoiling density of the untranscribed DNA template are discussed in detail. Two particular cases of transcription are considered, transcription with constant velocity and transcription with torque dependent velocity. Our results show that, during the initial stage of transcription, rotation originated from the transcribed part of DNA template is mainly released by the rotation of RNAP synthesis. During the intermediate stage, the rotation is usually released by both the supercoiling of the untranscribed part of DNA template and the rotation of RNAP synthesis, with proportion depending on the friction coefficient in environment and the length of nascent RNA. However, with the approaching to the upper limit of twisting of the untranscribed DNA template, the rotation resulted from transcription will then be mainly released by the rotation of RNAP synthesis.