Femtonewton Entropic Forces Can Control the Formation of Protein-Mediated DNA Loops

We show that minuscule entropic forces, on the order of 100 fN, can prevent the formation of DNA loops—a ubiquitous means of regulating the expression of genes. We observe a tenfold decrease in the rate of LacI-mediated DNA loop formation when a tension of 200 fN is applied to the substrate DNA, biasing the thermal fluctuations that drive loop formation and breakdown events. Conversely, once looped, the DNA-protein complex is insensitive to applied force. Our measurements are in excellent agreement with a simple polymer model of loop formation in DNA, and show that an antiparallel topology is the preferred LacI-DNA loop conformation for a generic loop-forming construct.

Figure 1

(a) Tethered DNA is trapped in the linear region of an optical potential (dashed line indicates laser focus). The figure also represents a kinetic model of DNA looping. (b) Raw experimental recording of LacI-mediated DNA looping. The looped or unlooped threshold is chosen at the minimum between the two state distributions displayed in a histogram of the binned data.

Figure 2

Cumulative probability distributions of the observed durations that the DNA molecule remains in the looped and unlooped state under increasing force conditions (left to right). The data of (a) the looped state and (b) the unlooped state are fit to the single exponential function and a biexponential function, respectively.

Figure 3

Measured values for $k_{-}$ (△), $k_{+}$ (◇), $k_L$ (■), and $k_U$ (○) (see Table ). The looping rate $k_L$ is fit by the theoretical predictions for the antiparallel (solid line) and parallel (dashed line) topologies illustrated in the insert.