Fracture fabrication of a multi-scale channel device that efficiently captures and linearizes DNA from dilute solutions

Abstract

This paper describes a simple technique for patterning channels on elastomeric substrates, at two distinct scales of depth, through the use of controlled fracture. Control of channel depth is achieved by the careful use of different layers of PDMS, where the thickness and material properties of each layer, as well as the position of the layers relative to one another, dictate the depth of the channels formed. The system created in this work consists of a single 'deep' channel, whose width can be adjusted between the micron- and the nano-scale by the controlled application or removal of a uniaxial strain, and an array of 'shallow' nano-scale channels oriented perpendicular to the 'deep' channel. The utility of this system is demonstrated through the successful capture and linearization of DNA from a dilute solution by executing a two-step 'concentrate-then-linearize' procedure. When the 'deep' channel is in its open state and a voltage is applied across the channel network, an overlapping electric double layer forms within the 'shallow' channel array. This overlapping electric double layer was used to prevent passage of DNA into the 'shallow' channels when the DNA molecules migrate into the junctional region by electrophoresis. Release of the applied strain then allows the 'deep' channel to return to its closed state, reducing the cross-sectional area of this channel from the micro- to the nano-scale. The resulting hydrodynamic flow and nano-confinement effects then combine to efficiently uncoil and trap the DNA in its linearized form. By adopting this strategy, we were able to overcome the entropic barriers associated with capturing and linearizing DNA derived from a dilute solution.

Figure 1

Schematic of DNA migration and squeezing system. (A) A single ‘deep’ channel and multiple perpendicularly-oriented ‘shallow’ channels. Each fracture-formed structure originates, and terminates, within a reservoir so that ‘shallow’ channels effectively connect the blunt-tip reservoirs, while the ‘deep’ channel connects the sharp-tip reservoirs. A photograph of the device is provided for reference (Right). In its operation, (B) the ‘deep’ channel is transitioned from a closed to an open-state through the application of a uniaxial strain along an axis perpendicular to the ‘deep’ channel itself. When in its open state, (C) DNA introduced via one of the sharp-tip reservoirs will migrate and become localized at the juncture between the ‘deep’ channel and its intersecting ‘shallow’ channels through exclusion-enrichment effect. (D) The subsequent release of the previously-applied uniaxial strain then allows the ‘deep’ channel to return to its closed-state, and in doing so, generates hydrodynamic flow within the channel sufficient to linearize the trapped DNA molecule.

Figure 2

A diagram of the stepwise fabrication process used for the fabrication of the described crisscrossing channel system. (A) Two pairs of symmetrical micro-features were first cast within the h-PDMS/PDMS bilayer assembly from a pre-patterned SU-8 mold. (B) A single crack was then formed in the h-PDMS layer. This crack extended between the mirrored V-notch tips by the controlled application of uniaxial strain, and was capable of being (C) ‘healed’ (closed and bonded through van der Waals forces) upon release of the applied strain. (D) The two-layer assembly was then covered by a tape mask so that only the surface region between the blunt-tip features (measuring approximately 1.0 × 0.3 mm) was exposed. This enabled the (E) selective plasma-treatment of this region, producing a SL-h-PDMS nano-layer on the surface of the h-PDMS layer. (F) Multiple nano-cracks were then produced in the SL-h-PDMS layer when the assembly was subjected to a second uniaxial strain applied in a direction perpendicular to that of the previously applied strain. The resulting cracks were then sealed by plasma bonding the cracked-surface to a PDMS membrane, forming (G) a single ‘deep’ channel in the h-PDMS layer and multiple orthogonally-oriented ‘shallow’ channels in the SL-h-PDMS layer.

Figure 3

Application of the ‘deep’/’shallow’ channel system for capturing and elongating single DNA molecules. (A) A schematic illustrating the ion concentration polarization and DNA migration generated within the ‘deep’/’shallow’ channel junction under an applied electric field. (B) Changes in the cross-sectional dimensions of the ‘deep’ channel in response to a sustained applied strain. (C) An illustration of the multiple steps involved in DNA concentration, trapping, and linearization in the ‘deep’ channel. As the ‘deep’ channel narrows, a hydrodynamic squeezing flow is generated. The coincident application of a hydrodynamic squeezing flow and nano-confinement induce and maintain DNA elongation. The yellow dashed-line represents the ‘shallow’ nano-scale channel region. Scale bar is 5 μm. (D) A plot of the frequency distribution of the lengths of elongated λ-DNA in the closed ‘deep’ channel.