1. Structure of one-dimensional periodic nanofilter array

The patterned one-dimensional periodic array of nanofilter, which serves as the model pore-constriction system, consists of alternating deep regions and confining shallow regions (Fig. 1). The depth of the shallow region (ds) is of the same order of magnitude as the size of probing molecules for optimized sieving effect. Other geometric parameters of the nanofilter array, such as the lengths of shallow and deep regions and the pitch number of the nanofilter (L), are determined and controlled during the fabrication process. The regularity of the nanofilter geometry is ideal for theoretical study of molecular sieving process in constrained spaces.

Figure 1 (a) Partitioning of rigid, rod-like DNA across a nanofilter that consists of a deep region (dd) and a shallow region (ds) of equal length. The period and width of one nanofilter is p and w, respectively. (b) Free energy landscapes experienced by DNA while crossing a nanofilter (black curve: E = 0, grey curve: Eav > 0). Es, Ed: electric fields in shallow and deep regions, respectively. Eav: average electric field over the nanofilter. DNA preserve the free draining property in the shallow and deep region, resulting in the slopes for both regions proportional solely to the local electric field. (c) SEM images of alternating deep (300 nm) and shallow (55 nm) regions. p = 2 µm.   

2. Fast biomolecular separation in one-dimensional periodic nanofilter array

The layout of the 1-D nanofilter array device is presented in Fig. 2. Nanofilters with shallow region deepness (ds) of 40 - 180 nm have been successfully fabricated. At the very beginning of the nanofilter array, a T-shaped injector for electrokinetic sample injection was fabricated to define and launch an initial sample mixture plug.

Figure 3 summarizes the separation results of SDS-protein complexes and dsDNA molecules in a 1-D nanofilter array device (ds = 60 nm, dd = 250 nm, L = 1 µm). Figure 3(a) shows a sequence of fluorescence images taken near the T-shaped injector region, shortly after the launching of the SDS-protein mixture. The three SDS-protein fragments were quickly separated within 30 sec and a 570 µm separation length. The base-line separation of the SDS-protein complexes was achieved in 4 min with a separation length of 5 mm under an electric field of 90 V/cm [Fig. 3(b)]. The theoretical plate number for cholera toxin subunit B was about 1523 and the plate number per column length was about 3×10^5 plates/m. Separation results of small dsDNA molecules are shown in Fig. 3(c). A complete separation of the dsDNA molecules was achieved in about 10 min with a separation length of 5 mm under an electric field of 70 V/cm.

Figure 2 (a) Layout of the nanofilter array chip. The device includes four buffer access holes (anode, cathode, sample and waste), a 1 cm separation column (a periodic array of nanofilter) and a T-Shaped injector. (b) Cross-sectional schematic diagram of the nanofilter array along the separation channel. The nanofilter consists of a shallow region (ds) and a deep region (dd) of equal lengths. The period of one nanofilter is L. (c) SEM images of the cross-section of shallow regions with different depths (40 nm, 60 nm, 80 nm and 180 nm).

Figure 3 Separation of SDS-protein complexes and dsDNA molecules in a nanofilter array device (ds: 60 nm, dd: 300 nm, L: 1 µm). Band assignment for SDS-protein complexes: (1) cholera toxin subunit B (MW: 11.4 kDa); (2) lectin phytohemagglutinin-L (MW: 120 kDa); (3) low density human lipoprotein (MW: 179 kDa). Band assignment for DNA (PCR marker sample): (1) 50 bp; (2) 150 bp; (3) 300 bp; (4) 500 bp; (5) 766 bp. (a) Sequence of fluorescence images showing separation of the SDS-protein complexes under the electric field of 100 V/cm. The solid lines indicate the T-shaped injector and the dashed lines indicate the nanofilter array. The values listed under the images indicate the distance from the injection point. (b&c) Separation of SDS-protein complexes and dsDNA molecules under different applied fields. Separation length: 5mm. RS,ij: separation resolution between peak i and j; Ni, Hi: theoretical plate number and plate height (in µm) for peak i ; Ni/L: theoretical plate number per column length (in plates/m). µi: electrophoretic mobility of peak i (10^-5 cm^2/(V sec)).

References

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† Copyright by American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics.