Fluidic switching in nanochannels for the control of Inchworm: a synthetic biomolecular motor with a power stroke

Abstract

Synthetic molecular motors typically take nanometer-scale steps through rectification of thermal motion. Here we propose Inchworm, a DNA-based motor that employs a pronounced power stroke to take micrometer-scale steps on a time scale of seconds, and we design, fabricate, and analyze the nanofluidic device needed to operate the motor. Inchworm is a kbp-long, double-stranded DNA confined inside a nanochannel in a stretched configuration. Motor stepping is achieved through externally controlled changes in salt concentration (changing the DNA's extension), coordinated with ligand-gated binding of the DNA's ends to the functionalized nanochannel surface. Brownian dynamics simulations predict that Inchworm's stall force is determined by its entropic spring constant and is ∼ 0.1 pN. Operation of the motor requires periodic cycling of four different buffers surrounding the DNA inside a nanochannel, while keeping constant the hydrodynamic load force on the DNA. We present a two-layer fluidic device incorporating 100 nm-radius nanochannels that are connected through a few-nm-wide slit to a microfluidic system used for in situ buffer exchanges, either diffusionally (zero flow) or with controlled hydrodynamic flow. Combining experiment with finite-element modeling, we demonstrate the device's key performance features and experimentally establish achievable Inchworm stepping times of the order of seconds or faster.

The bar-hinge motor: a synthetic protein design exploiting conformational switching to achieve directional motility

“…The small fluctuations in angle are due to the large but finite bending energy (V ang-h =V ang-b =1000 k B T) and to the range of the track binding potential (d b =1.5 nm). The BHM0 is next switched to the V conformation with θ 0 ∼74°in ligand pulse II with only foot B bound to the track; the distribution in hinge angles shown in the graph results from thermal fluctuations related to the form of bending potential of equation (6). The BHM0 remains in the V conformation, C 2 , but with much smaller angular variation when both feet are bound in ligand pulse III.…”

“…We investigated the behaviour of the BHM by simulating its motion using a coarse-grained minimal model in conjunction with three-dimensional overdamped Langevin dynamics [5,6]. Figure 3(d) shows the coarsegrained model used in our simulations.…”

“…However, biological motors are predominantly protein-based. This has inspired efforts to design and synthesize directional molecular motors from protein-based components [4][5][6][7]. However, these protein-based concepts would achieve their motion only from diffusion, and lack a means to incorporate conformational change to stimulate directed motion.…”

“…We then describe a proposed experimental realization of the BHM using a combination of components from our previous nanomotor concepts. These include coiled-coil domains for structurally near-rigid components [4], ligand-gated DNAbinding protein domains [4][5][6]9], and a DNA track with corresponding binding sites [4,5,9]. To these we add a conformational switching moiety such as the photo-switchable molecule azobenzene [10].…”

“…This track can be synthesized from DNA using the same methods as for the Tumbleweed motor track [9]. Clocked control of the ligand environment can be achieved through microfluidics [6,30] making it possible to synchronize the light switching of the azobenzene with the flow of specific ligand states through a computerized system that controls both simultaneously. Figure 3(c) shows a rendering of the proposed structure for the BHM construct and its track.…”