arXiv:1002.3809v2 [q-bio.BM] 21 Apr 2010 1 Protein-mediated DNA Loop Formation and Breakdown in a Fluctuating Environment Yih-Fan Chen*, 1 J. N. Milstein*, 2, ∗ and Jens-Christian Meiners 2, 3 $^{1}$Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109 $^{2}$Department of Physics, University of Michigan, Ann Arbor, Michigan 48109 $^{3}$LSA Biophysics, University of Michigan, Ann Arbor, Michigan 48109 (Dated: November 12, 2018) 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. Abstract