Fluidic Switching in Nanochannels for the Control of a Synthetic DNA-based Motor

Processive molecular motors are thought to utilize a ``power stroke'' whereby chemical changes are converted into conformational changes, facilitating forward motion. We have developed a concept for a synthetic molecular motor, the Inchworm (IW), which harnesses salt-induced changes in DNA conformation$^{1}$ to achieve power strokes. To implement IW we must switch between four solutions (of varied salt concentration) surrounding DNA confined in a nanochannel (NC) while monitoring its response. We have developed NCs of radii 100-400 nm, with 10-20 nm wide top-slits for buffer exchange via diffusion from adjacent microfluidic channels$^{2}$. NCs are made in SiO$_{2}$ to allow for imaging through the substrate. To cycle through four buffers specifically designed microchannels are used$^{3}$. We measure changes in intensity when fluids containing fluorescent molecules are switched, with and without a pressure difference over the NCs. By fitting this data we extract effective diffusivity of molecules and determine fluid velocities, information that is crucial for evaluating IW performance. \\[4pt] [1] W.Reisner et al., PRL 2007, 99, 058302;\\[0pt] [2] M.Graczyk et al., J. Vac. Sci. {\&} Technol. B 2012, 30, 6;\\[0pt] [3] C.S.Niman et al., Lab Chip 2013, 13, 2389