Controlled microfluidic switching in arbitrary time-sequences with low drag

Abstract

The ability to test the response of cells and proteins to a changing biochemical environment is of interest for studies of fundamental cell physiology and molecular interactions. In a common experimental scheme the cells or molecules of interest are attached to a surface and the composition of the surrounding fluid is changed. It is desirable to be able to switch several different biochemical reagents in any arbitrary order, and to keep the flow velocity low enough so that the cells and molecules remain attached and can be expected to retain their function. Here we develop a device with these capabilities, using U-shaped access channels. We use total-internal reflection fluorescence microscopy to characterize the time-dependent change in concentration during switching of solutions near the device surface. Well-defined fluid interfaces are formed in the immediate vicinity of the surface ensuring distinct switching events. We show that the experimental data agrees well with Taylor-Aris theory in its range of validity. In addition, we find that well-defined interfaces are achieved also in the immediate vicinity of the surface, where analytic approaches and numerical models become inaccurate. Assisted by finite-element modelling, the details of our device were designed for use with a specific artificial protein motor, but the key results are general and can be applied to a wide range of biochemical studies in which switching is important.

Motor properties from persistence: a linear molecular walker lacking spatial and temporal asymmetry

“…The binding sites for repressors on DNA have palindromic sequences, hence the DNA track will be symmetric. Using a microfluidic device to temporally change the concentration of ligands [33], the binding and unbinding of modules A and B to the track can be orchestrated in arbitrary temporal order.…”

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

“…Based on the modeling results above and their comparison to existing experiments, we establish the following requirements for a nanofluidic device to control and characterize IW: the device needs to provide for (i) NCs of 100-200 nm diameter to confine the DNA in quasi-linear conformation; [20][21][22][23][24][25] (ii) the ability to switch the DNA's chemical environment (buffer) in a specific, cyclical order; 34,35 (iii) the ability to minimize or apply a defined, constant load force on the DNA (crucially, this means that buffer switching must be possible without the use of hydrodynamic flow in the NCs), (iv) the ability to functionalize the NC's inner walls for ligandgated DNA binding, and (v) the capability to monitor IW in real time using epifluorescence microscopy. Based on the modeling results above and their comparison to existing experiments, we establish the following requirements for a nanofluidic device to control and characterize IW: the device needs to provide for (i) NCs of 100-200 nm diameter to confine the DNA in quasi-linear conformation; [20][21][22][23][24][25] (ii) the ability to switch the DNA's chemical environment (buffer) in a specific, cyclical order; 34,35 (iii) the ability to minimize or apply a defined, constant load force on the DNA (crucially, this means that buffer switching must be possible without the use of hydrodynamic flow in the NCs), (iv) the ability to functionalize the NC's inner walls for ligandgated DNA binding, and (v) the capability to monitor IW in real time using epifluorescence microscopy.…”

“…We use a two-layered design. 34 There is an inlet/outlet pair for each of the four buffers to minimize diffusive mixing between switching events in the microfluidics. 3A).…”

“…The bottom layer consists of a set of parallel NCs (300 µm-long half cylinders with radius 100 nm) that start and end at microfluidic side channels (Fig. Fluids can be switched on a time scale of 0.1-1 s. 34 In order to be able to control the pressure drop along each NC, the device allows us to flow the buffer through the side channels at the same time as through the center channels, for example to establish the same longitudinal pressure drop along the center and side channels, eliminating any pressure drop along each NC. The side channels are used to load the NCs with DNA, and for the control of pressure along the NCs.…”

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

“…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.…”