title: Protein-mediated DNA loop formation and breakdown in a fluctuating environment.
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.
authors.affiliation: Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA.
authors.forename: Yih-Fan
authors.initials: YF
authors.lastname: Chen
authors.forename: J N
authors.initials: JN
authors.lastname: Milstein
authors.forename: Jens-Christian
authors.initials: JC
authors.lastname: Meiners
mesh_terms: D001696:Biomechanical Phenomena; D004247:DNA / Q000737:chemistry* / Q000378:metabolism* / Q000502:physiology; D005786:Gene Expression Regulation; D008954:Models, Biological; D009038:Motion; D009690:Nucleic Acid Conformation; D011506:Proteins / Q000378:metabolism*; D013269:Stochastic Processes; D013696:Temperature; D013816:Thermodynamics
chemical_list: D011506:Proteins; D004247:DNA