Supplementary Methods

Transcription

1 Supplementary Methods Generation of nanocrack patterns: PDMS (Sylgard 184, Dow Corning) base and curing agent were mixed at a weight ratio of 10:1. Degassed PDMS prepolymer was cast against a photolithographically-prepared SU8 (SU8-50, MicroChem Corp.) mold and cured at 60 C for 4 hours to produce PDMS substrates with recessed inlet and outlet microchannel features. The substrates were then cleaned with scotch tape and treated with oxygen plasma for 4 minutes in a bench-top plasma etcher (Plasma Prep II, SPI Supplies). Vacuum pressure and operation current used for plasma treatment were 150 mtorr and 30 ma, respectively. Subsequently, the oxidized PDMS surface was stretched to a strain of 5 ~ 10 % for 10 seconds by an electronically controlled stretcher (ST140, STREX Inc.) to create nanocracks. Fabrication of nanochannel molds: the PDMS surface with nanocracks was silanized with (tridecafluoro-1,1,2,2-tetrahydrooctyl)-1-trichlorosilane for 1.5 hours in a vacuum desiccator. Nanochannel molds were prepared by casting an epoxy resin (Epo-tek, Dow Corning) against the silanized nanocrack patterns, as shown below. Photo-curing of an epoxy resin was performed for 1.5 hours in a custom-built UV exposure chamber. 1

2 Fabrication of sealed elastomeric nanochannels: PDMS nanochannels were fabricated by curing PDMS prepolymer with a base-to-curing agent ratio of 3:1 against the epoxy master at 60 C for 4 hours. The cured PDMS substrates were peeled off the mold and further incubated at 150 C overnight to ensure complete cross-linking. Reservoirs for the inlet and outlet microchannels were created by punching holes through the channel PDMS slabs using blunt syringe needles with sharpened edges. The PDMS substrate having negative relief patterns of nanochannels was treated with oxygen plasma for 1 minute at a vacuum pressure of 300 mtorr and sealed against a flat 3:1 PDMS slab oxidized under the same plasma treatment conditions to generate enclosed elastomeric nanochannels. Application of compressive stress to nanochannels: as depicted in the schematic shown below, uniform compressive forces were imposed on the nanochannels by putting rectangular weights on a simple custom-designed glass plate sitting on top of a channel-containing PDMS substrate. The magnitude of compressive forces applied to the nanochannels was varied by changing the number of weights. 2

3 Preparation of DNA samples: λ-phage DNA was obtained from New England Bio Laboratory and stained with the intercalating dye YOYO-1 at the concentration of 10 base pairs/1 dye molecule. DNA was then diluted to 50 pg/µl in 10X Tris-borate EDTA (TBE) buffer. β-mercaptoethanol (5 % v/v) was added to prevent photobleaching of the DNA molecules and electroosmotic flows were suppressed by the high concentration of TBE buffer. Preparation of fluorescent acrylamide solution: the acrylamide monomer solution was prepared by using the commercial ReproGel system purchased from Amersham Pharmacia. A solution containing 200 µl of acrylamide/bisacrylamide monomers was mixed with 300 µl of photoinitiator solution. Sodium periodate (NaIO 4 ) was added at the concentration of 10 mm as a scavenger of oxygen that tends to inhibit photopolymerization. Finally, 120 µl of the solution was mixed with 1 µl of fluorescein (0.2 mg/ml in DI water) and evacuated for 2 hours immediately before use in the nanochannels. Finite-element model for numerical simulations: finite-element calculations were performed to study the energy of the nanochannel system as bonding proceeds. When two surfaces are in proximity to each other, whether they bond or not depends on the difference in total energy between the bonded and unbonded states. This energy is the difference between the elastic energy of deformation associated with the bonding, and the surface energy released by mating the two surfaces. U total = U elastic U surface energy The symmetry of the nanochannel problem was taken advantage of in creation of the finite-element mesh. A quarter-model of the geometry (corresponding to experimental AFM measurements) was used with appropriate symmetric boundary conditions as illustrated in the mesh diagram shown below. 3

4 Plane-strain hyperelastic finite-element analyses were run using the finite-element package ABAQUS. At many intermediate extents of bonding (c/a), the deformation energy, U elastic, was calculated as c 1 P( x) h( x) dx, the integral over the length of 0 2 closure (c) of the load necessary to close the nanochannel times the height of the nanochannel. At the same intervals, the surface energy released, U surface energy, was calculated as 2cγ. Equipment and settings: We used a CCD camera (Hamamatsu ORCA-ER) mounted on an epi-fluorescence microscope (Nikon TE-300) and SimplePCI 5.2 (Compix Inc.) as an image acquisition device and software. Image depth was 8 bit for all images presented in the manuscript. Figure 1: the sequential micrographs showing the accumulation of fluorescein at the outlet microchannel and the image of fluorescein flows through nanochannels in Figure 4

5 1a were taken using a 20X objective (Nikon Plan Fluorite, NA = 0.45). Peak excitation and emission wavelengths for fluorescence imaging were 480 and 535 nm, respectively. Captured images were pseudo-colored in Photoshop without further processing or manipulation. Flows of single quantum dots were imaged using a 60X oil-immersion objective (Nikon Plan Apochromat, NA = 1.40) at peak excitation and emission wavelengths of 425 and 605 nm, respectively. The whole image was adjusted uniformly for brightness and contrast in Photoshop. Figure 3: image acquisition and processing conditions for quantum dot images are the same as those for Figure 1b. Figure 4: a 60X oil-immersion objective (Nikon Plan Apochromat, NA = 1.40) was used for imaging DNA molecules and polyacrylamide nanofilaments shown in Figure 4. Peak excitation and emission wavelengths for fluorescence imaging were 480 and 535 nm, respectively. Supplementary Figure 1: the micrographs were taken using a 20X objective (Nikon Plan Fluorite, NA = 0.45). Fluorescein molecules and 1-µm green-fluorescent particles were imaged at peak excitation and emission wavelengths of 480 and 535 nm, respectively. For 20-nm quantum dots and 1-µm red-fluorescent particles, peak excitation and emission wavelengths were 535 and 590 nm, respectively. The captured images were pseudo-colored and superimposed in Photoshop without further processing. Supplementary Figure 2 & Figure 3: the light-transmitted images were obtained using a 20X objective (Nikon Plan Fluorite, NA = 0.45). Supplementary Figure 5: fluorescein in the outlet microchannel was imaged at peak excitation and emission wavelengths of 480 and 535 nm using a 20X objective (Nikon Plan Fluorite, NA = 0.45). 5

6 Supplementary Figure 6: a 60X oil-immersion objective (Nikon Plan Apochromat, NA = 1.40) was used for imaging DNA. Peak excitation and emission wavelengths for fluorescence imaging were 480 and 535 nm, respectively. 6

7 Supplementary Figure 1. Examples of simple size-selective nanofluidic transport without mechanical deformation of elastomeric nanochannels. a, A mixture of green fluorescent polystyrene microspheres (diameter = 1 µm) and carboxylate-modified red fluorescent beads (diameter = 20 nm) is filtered through nanochannels. At the outlet, there is a continuous increase in red fluorescence (red diamond), whereas green fluorescence (green circle) remains unchanged at zero, because the size of non-deformed nanochannels only supports the transport of 20-nm particles. b, Selective transport of fluorescein molecules (green diamond) initially mixed with 1-µm red fluorescent microspheres (red circle). Flows were driven by a pressure gradient. Scale bar, 100 µm. 7

8 Supplementary Figure 2. Fabrication of elastomeric nanochannels integrated with microscale inlet and outlet compartments. a, A PDMS surface with recessed microchannel features that are 100 µm in width and 50 µm in height is prepared by casting PDMS prepolymer against a photolithographically-fabricated mold. The surface is oxidized and subjected to a mechanical strain to generate nanocracks joined with inlet and outlet microchannels. The hybrid pattern is processed by the replication procedure described in the main text to form elastomeric nanochannels shown in b. 8

9 Channel arrays consist of 100 ~ 700 nanochannels over 7 mm. Scale bar, 100 µm. 9

10 Supplementary Figure 3. Effect of PDMS stiffness on irreversible collapse of nanochannels. a, Conformal contact between bare PDMS surfaces without oxidation causes the nanochannels to collapse irreversibly. This situation corresponds to E 1 E 2 = 1 in Fig. 2d of the main text. b, Plasma oxidation modifies PDMS to form a thin, silica-like layer on the surface. Contact between oxidized 10:1 PDMS surfaces results in partially collapsed nanochannels (black arrows). The ratio represents the weight ratio of a liquid PDMS base to a curing agent. A higher ratio leads to a higher stiffness of cured PDMS. c, A smaller number of partially collapsed nanochannels are observed as the stiffness of PDMS increases. d, Optimal sealing without unwanted channel collapse is achieved by using oxidized 3:1 PDMS surfaces, as predicted by the simulation results at E 1 E 2 20 µm. = 130 shown in Fig. 2d of the main text. Scale bar, 10

11 Supplementary Figure 4. Electrical resistance measurements under different compressive stress conditions. The channel system was filled with 0.1 molar potassium chloride (KCl) solution, and silver/silver chloride electrodes were inserted into the inlet and outlet compartments separated by 500 µm. A picoammeter was used to measure electrical resistance and the voltage applied to the fluidic circuit was 0.1 V DC. Two control measurements were obtained from the channel system without nanochannels (asterisk) and a Petri-dish filled with 0.1 M KCl (filled square). First, a baseline resistance level was established by taking measurements from uncompressed nanochannels (filled triangle). When the nanochannels were uniformly compressed from atop with 22 kpa of pressure (open square), electrical resistance instantaneously 11

12 increased and remained constant until the force was released, at which time the resistance returned immediately to its original value. Increasing the applied stress to 42 kpa (open circle) resulted in a larger resistance (hundred times as large as the baseline values), closely approximating the measurements taken from a channel system having no nanochannels between inlet and outlet compartments. 12

13 Supplementary Figure 5. Force-induced modulation of molecular transport. a, Transport of fluorescein molecules through water-filled nanochannels with different cross-sectional areas was characterized by measuring fluorescence signals from fluorescein accumulation in the 13

14 observation area at the outlet. A flow was driven electrokinetically by 62 V/cm. Measurements were taken at fixed detection conditions. In the relaxed nanochannels with larger cross-sections, fluorescence intensity increases over time (open square). When the nanochannels are compressed with 22 kpa, the rate of incremental fluorescence change decreases dramatically (filled triangle), due to the significantly reduced number of fluorescein molecules transported through the nanochannels per unit time. The transport of fluorescein is blocked completely at 42 kpa (open circle) because deformed nanochannels exclude fluorescein molecules. Inset shows a close-up view of intensity change at 22 and 42 kpa. b, Nanofluidic valving of fluorescein transport through reversible deformation of the channel cross-section. Increase in fluorescence intensity is arrested by channel compression with 42 kpa and resumes upon release of force owing to a restored channel cross-section. Scale bar, 100 µm. 14

15 Supplementary Figure 6. Stretching of DNA in relaxed nanochannels kbp-long λ-phage DNA stained with YOYO-1 and suspended in Tris-borate EDTA buffer was electrophoretically introduced into relaxed nanochannels and partially stretched to 5.6 ± 1.1 µm (mean ± s.d.). Scale bar, 5 µm. 15