Genes operate within a crowded cellular environment that is constantly interacting with the encoding DNA through various proteins that bind along its contour. We are only be- ginning to understand how chromosomal packing, and a crowded and constantly fluctuating cellular interior affects genetic regulation [1]; however, the cytoskeleton of eukaryotes already provides a startling example of the dynamic effects of the intracellular medium on cellular function [2]. The cytoskeleton is often considered an active polymeric gel, since its dynamic organization is driven by ATP hydrolysis, and is known to generate mechanical stress and shear forces. These active properties give rise to non-equilibrium effects such as the gener- ation of an “effective temperature” that can drive processes of embedded elements beyond the levels of thermal activation. Recently, force fluctuations an order of magnitude larger than thermal fluctuations have been measured within the cytoskeleton [3]. Such findings remind us that the cellular interior is very much an active, non-equilibrium medium, the effects of which need to be given careful consideration in the context of gene expression as well. 

A regulatory mechanism that is potentially acutely sensitive to environmental noise is the fluctuation driven formation of protein-mediated DNA loops. In genomic DNA, this is a ubiquitous motif for the transcriptional control of gene expression [4]. The lac operon, which is responsible for efficiently metabolizing lactose in E. coli bacteria, provides a canonical example of DNA looping. A lac repressor-mediated DNA loop is formed when tetrameric LacI protein simultaneously binds to two lac operator sites and is crucial for the repressive regulation of lac genes [5]. Thermal fluctuations, which generate tiny entropic forces on the order of only k$_{B}$T/l$_{p}$ ≈ 80 fN, where l$_{p}$ = 50 nm is the persistence length [6], are sufficient to form loops within the DNA, making the association rate of loops extremely sensitive to tension along the DNA molecule [7]. 

To explore the effects of environmental fluctuations on protein-mediated DNA loops, a 1316 bp dsDNA molecule with two primary lac operators spaced 305 bp apart was tethered to a coverslip and then attached to an 800 nm polystyrene microsphere. The microsphere was then trapped within the linear region of the optical potential of a focused laser beam allowing us to apply a well defined tension to the DNA. Details of our axial-constant force optical tweezers as well as a discussion of the DNA preparation can be found in [8]. Ten- sion in the DNA was calibrated to include both the applied optical force, which is linearly proportional to the laser intensity modulated by an acousto-optic modulator (AOM), and 

