Protein-mediated DNA Loop Formation and Breakdown in a Fluctuating Environment

TL;DR

This study investigates how fluctuating forces influence DNA loop formation and breakdown, revealing that noise can enhance loop formation but regulatory mechanisms may remain robust due to noise cancellation effects.

Contribution

The paper provides single-molecule measurements of DNA looping under artificial fluctuating forces, highlighting the impact of cellular-like noise on DNA regulation mechanisms.

Findings

Noise of a fraction of k_B T enhances loop formation.

Regulatory schemes using mechanical tension can be robust despite noise.

DNA loop formation is significantly affected by environmental fluctuations.

Abstract

Living cells provide a fluctuating, out-of-equilibrium environment in which genes must coordinate cellular function. DNA looping, which is a common means of regulating transcription, is very much a stochastic process; the loops arise from the thermal motion of the DNA and other fluctuations of the cellular environment. We present single-molecule measurements of DNA loop formation and breakdown when an artificial fluctuating force, applied to mimic a fluctuating cellular environment, is imposed on the DNA. We show that loop formation is greatly enhanced in the presence of noise of only a fraction of $k_B T$, yet find that hypothetical regulatory schemes that employ mechanical tension in the DNA--as a sensitive switch to control transcription--can be surprisingly robust due to a fortuitous cancellation of noise effects.