Single molecule tug-of-war and the entropic recoiling of DNA from micro- to nanofluidic interfaces

We built two microchannels bridged by a nanoslit to observe tug-of-war of single DNA molecules through micro/nano/micro fluidic interfaces (Fig. 1a), and to observe single DNA molecules retraction in nanoslit caused by confinement-induced entropic recoiling forces (Fig 1b). The dimension of nanoslits is of 50 nm in depth, 10 μm in width, and 4 μm in length; the depth of microchannel is 2 μm.  By applying electric field, one end of DNA polymer may be moved through a nanoslit where two free ends of DNA straddle two micro/nano interfaces and form a tug-of-war scenario as field is off. Due to opposing entropic recoiling forces along a DNA polymer at two micro/nano interfaces, the tug of war between two ends of a DNA polymer across a nanoslit could last from seconds to minutes, and then retract from one micro regime to another (Fig 2).

Figure 1. Schematic of motions of a DNA polymer in a fluidic environment composed of two micro channels bridged by a nanoslit. (a) DNA tug of war across a nanoslit. (b) DNA retracts from one microchannel to another

Figure 2. Single DNA molecule tug of war through a nanoslit. (a) DNA fluctuates in microchannel. (b) DNA is driven in a 50 nm nanoslit by single 0.8 V/cm pulse as one end of DNA reaches another side of the nanoslit, (c) DNA tug of war may last from seconds to minutes as field is off, (d) one end of DNA is losing the tug of war and pulling into the nanoslit. (e) DNA retracts from one end of the nanoslit to the other. (f) DNA retracts fully out of the nanoslit

We also develop a theoretical model to describe the dynamics of a DNA molecule trapped in a Nanoslit in a Tug-of-War scenario. The model allows us to determine the ratio between the recoiling force due to the confinement and the elastic force inside the slit.

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