Transcription on Tangled DNA

Abstract

Bending and torsional deformations of DNA often occur in vivo and are important for various biological functions in the cell. In particular, DNA supercoiling (a combination of bending and torsional stresses within DNA) plays a central role in regulating gene expression. Recent experimental studies of short circular DNA fragments suggest that combined DNA torsional and bending stresses strongly impact transcription by RNA polymerase (RNAP). However, despite phenomenological observations establishing a relationship between DNA supercoiling and transcription kinetics, many details of the structure-function relationship between RNAP and DNA template mechanics remain unclear. We aim to understand how supercoiled DNA affects the structure of DNA-bound RNA polymerase, with the goal of specifically identifying protein domains that are sensitive to mechanically stressed DNA templates. Massively parallel molecular dynamics simulations are performed to describe the interaction of bacteriophage T7-RNAP with three DNA minicircles possessing qualitatively distinct states of torsional stress: underwound, overwound, and relaxed. The simulations reveal the topologies of the minicircles in complex with T7-RNAP and the structural details of bent and twisted protein-bound DNA. We observe remarkable differences between the conformations of T7-RNAP in complex with undertwisted, overtwisted and relaxed minicircle templates. In particular, on overtwisted DNA, T7-RNAP is capable of transitioning from the classical elongation complex structure into a stable intermediate that resembles the structure immediately preceding elongation. This finding suggests a structural mechanism by which transcription elongation may be hindered on bent and overtwisted DNA templates.