Transcription-driven twin supercoiling of a DNA loop: A Brownian dynamics study

Abstract

The torque generated by RNA polymerase as it tracks along double-stranded DNA can potentially induce long-range structural deformations integral to mechanisms of biological significance in both prokaryotes and eukaryotes. In this paper, we introduce a dynamic computer model for investigating this phenomenon. Duplex DNA is represented as a chain of hydrodynamic beads interacting through potentials of linearly elastic stretching, bending, and twisting, as well as excluded volume. The chain, linear when relaxed, is looped to form two open but topologically constrained subdomains. This permits the dynamic introduction of torsional stress via a centrally applied torque. We simulate by Brownian dynamics the 100 μs response of a 477-base pair B-DNA template to the localized torque generated by the prokaryotic transcription ensemble. Following a sharp rise at early times, the distributed twist assumes a nearly constant value in both subdomains, and a succession of supercoiling deformations occurs as superhelical stress is increasingly partitioned to writhe. The magnitude of writhe surpasses that of twist before also leveling off when the structure reaches mechanical equilibrium with the torsional load. Superhelicity is simultaneously right handed in one subdomain and left handed in the other, as predicted by the “transcription-induced twin-supercoiled-domain” model [L. F. Liu and J. C. Wang, Proc. Natl. Acad. Sci. U.S.A. 84, 7024 (1987)]. The properties of the chain at the onset of writhing agree well with predictions from theory, and the generated stress is ample for driving secondary structural transitions in physiological DNA.

Human Topoisomerase IIα Rapidly Relaxes Positively Supercoiled DNA

“…DNA buckling (i.e. the transition to non-B form structures) was not observed in these experiments below a value of ϩ0.058 (69). Therefore, we believe that the positively supercoiled substrates used in our DNA relaxation assays ( Ϸ ϩ0.035 to ϩ0.039) should be free of unusual non-B structures.…”

“…However, single molecule experiments suggest that DNA ahead of tracking systems can reach a value as high as ϩ0.110 (69). DNA buckling (i.e.…”

Transcription-Coupled DNA Supercoiling in Escherichia Coli: Mechanisms and Biological Functions

“…At a critical point, energetically, it is more feasible for the DNA molecule to rotate around its own helix axis to produce a positively supercoiled domain in front of the RNA polymerase and a negatively supercoiled domain behind it. These two transient supercoiled domains may be relaxed by DNA topoisomerases or cancel each other by diffusion Mielke et al, 2004;Nelson, 1999;Tsao et al, 1989;.…”

“…For instance, Nelson demonstrated that small natural bends in the DNA helix backbone was able to increase a few thousand fold of torsional stress even in a linear unanchored DNA (Nelson, 1999), this torsional force is sufficient to generate a positively supercoiled domain in front of the RNA polymerase and a negatively supercoiled domain behind it (Nelson, 1999). Another case is a Brownian dynamic study conducted by Mielke et al (Mielke et al, 2004). These studies clearly demonstrated that a transcribing RNA polymerase alone is able to drive the formation of positively and negatively domains in a naked plasmid DNA template.…”

“…It has been demonstrated that increased viscosity was able to significantly induce the DNA supercoiling in a defined protein system , which supports the view that in vivo situation is more complicated than the dilute aqueous solution. Recently, several groups re-investigated the induced torsional stress by a transcribing RNA polymerase, they showed that even in a dilute aqueous solution, the torsional force of RNA polymerase was sufficient to generate the twin-supercoileddomains (Nelson, 1999;Mielke et al, 2004). For instance, Nelson demonstrated that small natural bends in the DNA helix backbone was able to increase a few thousand fold of torsional stress even in a linear unanchored DNA (Nelson, 1999), this torsional force is sufficient to generate a positively supercoiled domain in front of the RNA polymerase and a negatively supercoiled domain behind it (Nelson, 1999).…”