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

Yih-Fan Chen, J. N. Milstein, and Jens-Christian Meiners

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 kBT, 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.

DOI