Photopolymerized cross-linked polyacrylamide gels for on-chip protein sizing

A new method for on-chip sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) of proteins is reported. Miniaturization of SDS-PAGE has attracted significant attention because it offers rapid analysis times, excellent resolution, high throughput, and the potential for integration and automation, as compared to conventional counterparts. The presented on-chip SDS-PAGE technique employed photolithographically patterned, cross-linked gels fabricated in situ in <20 min. The effects of sieving gel composition on the migration properties of fluorescently labeled protein standards (ranging in molecular weight from 14.2 to 66 kDa) were quantified, as was the ability of the gels to function as a sieving matrix for biologically relevant species. Ferguson analysis was employed to calculate retardation coefficients and free solution mobilities. In conjunction with fluorescence imaging, the on-chip SDS-PAGE separation mechanism was evaluated in terms of separation performance indexes, as well as limiting behaviors (i.e., free solution mobility, exclusion characteristics). The photolithographically fabricated gels employed for on-chip SDS-PAGE allowed rapid (<30 s) separations of proteins in short separation lengths (4 mm) with efficiencies as high as 4.41 x 10(5) plates/m. The on-chip SDS-PAGE separations were approximately 100 times faster than conventional slab gel SDS-PAGE (60 min) and occurred in a fraction of the separation length required by slab gels. The migration behavior of protein standards correlated well with molecular weight and allowed molecular weight determination for interleukin-2, fibroblast growth factor, insulin-like growth factor, and tetanus toxin C-fragment.     

Preconcentration of proteins on microfluidic devices using porous silica membranes

Fluorescently labeled proteins were electrophoretically concentrated on microfabricated devices prior to separation and laser-induced fluorescence detection on the same device. The proteins were concentrated using a porous silica membrane between adjacent microchannels that allowed the passage of buffer ions but excluded larger migrating molecules. Concentrated analytes were then injected into the separation column for analysis. Two basic microchip designs were tested that allowed sample concentration either directly in the sample injector loop or within the microchannel leading from the sample reservoir to the injector. Signal enhancements of approximately 600-fold were achieved by on-chip preconcentration followed by SDS-CGE separation. Preconcentration for CE analysis in both coated and uncoated open channels was also demonstrated. Fluorescently labeled ovalbumin could be detected at initial concentrations as low as 100 fM by using a combination of field-amplified injection and preconcentration at a membrane prior to CE in coated channels.     

Identification of proteins in single-cell capillary electrophoresis fingerprints based on comigration with standard proteins

In the previous paper in this Journal, we reported the use of capillary sieving electrophoresis to characterize proteins expressed by single cancer cells at specific phases in the cell cycle. Analysis of the data revealed one component with cell cycle-dependent changes in expression at the 99% confidence limit. However, the amount of protein present in a single cell is far too small to allow its direct identification by mass spectrometry. In this paper, we report a method by which such proteins can be tentatively identified. We perform standard SDS-PAGE electrophoresis of the proteins contained within a homogenate prepared from an HT29 cell culture. Proteins extracted from bands in the gel are identified by mass spectrometry. The proteins also provide a set of standards that can be used to spike the sample before capillary sieving electrophoresis (CSE) separation; comigration is taken as evidence for the identity of the target protein. In a proof-of-principle experiment, a single band migrating at approximately 47 kDa was isolated from the SDS-PAGE gel generated from the HT29 cell line. Proteins extracted from this band were used to spike a CSE separation of the same extract. This band comigrated with a cell cycle-dependent component identified from single-cell analysis. In-gel digestion and LC/MS/MS were used to identify five proteins, including cytokeratin 18, which is the product of the most highly expressed gene in this cell line.     

Electrophoretic separation of proteins on a microchip with noncovalent, postcolumn labeling

Proteins were separated by microchip capillary electrophoresis and labeled on-chip by postcolumn addition of a fluorogenic dye, NanoOrange, for detection by laser-induced fluorescence. NanoOrange binds noncovalently with hydrophobic protein regions to form highly fluorescent complexes. Kinetic measurements of complex formation on the microchips suggest that the reaction rate is near the diffusion limit under the conditions used for protein separation. Little or no band broadening is caused by the postcolumn labeling step. Lower limits of detection for model proteins, alpha-lactalbumin, beta-lactoglobulin A, and beta-lactoglobulin B, were <0.5 pg (approximately 30 amol) of injected sample. The relative fluorescence and reaction rates are compared with those of a number of other fluorogenic dyes used for protein labeling.     

Microchip HPLC of peptides and proteins

Rapid microchip reversed-phase HPLC of peptides and proteins at pressure gradients of 12 bar/cm (180 psi/cm) has been performed using a microdevice that integrates subnanoliter on-chip injection and separation with a miniaturized fluorescence detector. Proteins and peptides were separated on a C18 side-chain porous polymer monolith defined by contact lithography, and injection was achieved via a pressure-switchable fluoropolymer valve defined using projection lithography. Preliminary separations of peptide standards and protein mixtures were performed in 40-200 s, and switching between samples with no detectible sample carryover has been performed. The injections and separations were reproducible; the relative standard deviation (RSD) for retention time was 0.03%, and peak area RSD was 3.8%. Sample volumes ranging from 220 to 800 pL could be linearly metered by controlling the pressure injection pulse duration with conventional timing and valving. The current prototype system shows the potential for rapid and autonomous HPLC separations with varying modalities and the potential for direct connection to mass spectrometers at nanospray flow rates.     

Protein sizing on a microchip

We have developed a microfabricated analytical device on a glass chip that performs a protein sizing assay, by integrating the required separation, staining, virtual destaining, and detection steps. To obtain a universal noncovalent fluorescent labeling method, we have combined on-chip dye staining with a novel electrophoretic dilution step. Denatured protein-sodium dodecyl sulfate (SDS) complexes are loaded on a chip and bind a fluorescent dye as the separation begins. At the end of the separation channel, an intersection is used to dilute the SDS below its critical micelle concentration before the detection point. This strongly reduces the background due to dye molecules bound to SDS micelles and also increases the peak amplitude by 1 order of magnitude. Both the on-chip staining and SDS dilution steps occur in the 100-ms time scale and are approximately 10(4) times faster than their conventional counterparts in SDS-PAGE. This represents a much greater speed increase due to microfabrication than has been obtained in other assay steps such as electrophoretic separations. We have designed and tested a microchip capable of sequentially analyzing 11 different samples, with sizing accuracy better than 5% and high sensitivity (30 nM for carbonic anhydrase).     

Templated pores in hydrogels for improved size selectivity in gel permeation chromatography

The pore structures of cross-linked polyacrylamide gels can be altered by polymerizing in the presence of high concentrations of unreactive, micellar surfactant cosolutes which act as "templates". Removal of surfactant after polymerization is expected to leave pores with the approximate shape and dimensions of the surfactant micelles. A simple model was developed to simulate gel permeation chromatography (GPC) separations of globular proteins on templated gels. The model assumes that the partition coefficient for sieving of a protein is equal to the fraction of gel volume accessible to a sphere with a radius equal to the protein Stokes radius. The total gel volume is considered to include a fraction that is a conventional, random gel matrix and a remaining fraction contributed by templated pores. The pore size distribution of the conventional gel was estimated using the Ogston equation, which approximates the matrix as a random collection of long, thin, rigid fibers. Templated pores were assumed to have a Gaussian distribution of radii centered about some mean determined by the micelle radius. In comparison to conventional media, gels with templated pores are predicted to exhibit more sharply defined exclusion limits and improved resolution over a narrow size range centered on the mean templated pore size. Selectivity and resolution are expected to increase as the volume fraction of templated pores is increased and as the dispersion of templated pore radius is decreased. Small changes in template radius lead to large changes in the molecular weight range of optimal separation of globular proteins. It should be possible to create a series of GPC media that collectively offer high resolution over the molecular weight range of most globular proteins of interest.     

Online preconcentration by transient isotachophoresis in linear polymer on a poly(methyl methacrylate) microchip for separation of human serum albumin immunoassay mixtures

Online preconcentration of human serum albumin (HSA) and its immunocomplex with a monoclonal antibody by on-chip transient isotachophoresis is reported. An 800-fold signal enhancement was achieved following the preconcentration on standard cross-channel microchips made of poly (methyl methacrylate). Sample injection, preconcentration, and separation were done continuously and controlled solely by a sequential voltage switching program. The preconcentration was followed by on-chip nondenaturing gel electrophoresis in methylcellulose solution. The method was applied to microchip electrophoresis immunoassay of HSA. Baseline separation of HSA and its immunocomplex was achieved in 25 s in the first 1 cm of the microchannel. In a direct immunoassay, the minimum detectable concentration of fluorescent labeled HSA by laser-induced fluorescence detection was 7.5 pM.     

Electrokinetic protein preconcentration using a simple glass/poly(dimethylsiloxane) microfluidic chip

We discovered that a protein concentration device can be constructed using a simple one-layer fabrication process. Microfluidic half-channels are molded using standard procedures in PDMS; the PDMS layer is reversibly bonded to a glass base such as a microscope slide. The microfluidic channels are chevron-shaped, in mirror image orientation, with their apexes designed to pass within approximately 20 microm of each other, forming a thin-walled section between the channels. When an electric field is applied across this thin-walled section, negatively charged proteins are observed to concentrate on the anode side of it. About 10(3)-10(6)-fold protein concentration was achieved in 30 min. Subsequent separation of two different concentrated proteins is easily achieved by switching the direction of the electric field in the direction parallel to the thin-walled section. We hypothesize that a nanoscale channel forms between the PDMS and the glass due to the weak, reversible bonding method. This hypothesis is supported by the observation that, when the PDMS and glass are irreversibly bonded, this phenomenon is not observed until a very high E-field was applied and dielectric breakdown of the PDMS is observed. We therefore suspect that the ion exclusion-enrichment effect caused by electrical double layer overlapping induces cationic selectivity of this nanochannel. This simple on-chip protein preconcentration and separation device could be a useful component in practically any PDMS-on-glass microfluidic device used for protein assays.     

Separation of plasma from whole human blood in a continuous cross-flow in a molded microfluidic device

We designed, fabricated, and tested a microfluidic device for separation of plasma from whole human blood by size exclusion in a cross-flow. The device is made of a single mold of a silicone elastomer poly(dimethylsiloxane) (PDMS) sealed with a cover glass and is essentially disposable. When loaded with blood diluted to 20% hematocrit and driven with pulsatile pressure to prevent clogging of the channels with blood cells, the device can operate for at least 1 h, extracting approximately 8% of blood volume as plasma at an average rate of 0.65 microL/min. The flow in the device causes very little hemolysis; the extracted plasma meets the standards for common assays and is delivered to the device outlet approximately 30 s after injection of blood to the inlet. Integration of the cross-flow microchannel array with on-chip assay elements would create a microanalysis system for point-of-care diagnostics, reducing costs, turn-around times, and volumes of blood sample and reagents required for the assays.     

Aptamer-modified monolithic capillary chromatography for protein separation and detection

A capillary chromatography technique was developed for the separation and detection of proteins, taking advantage of the specific affinity of aptamers and the porous property of the monolith. A biotinylated DNA aptamer targeting cytochrome c was successfully immobilized on a streptavidin-modified polymer monolithic capillary column. The aptamer, having a G-quartet structure, could bind to both cytochrome c and thrombin, enabling the separation of these proteins from each other and from the unretained proteins. Elution of strongly bound proteins was achieved by increasing the ionic strength of the mobile phase. The following proteins were tested using the aptamer affinity monolithic columns: human immunoglobulin G (IgG), hemoglobin, transferrin, human serum albumin, cytochrome c, and thrombin. Determination of cytochrome c and thrombin spiked into dilute serum samples showed no interference from the serum matrix. The benefit of porous properties of the affinity monolithic column was demonstrated by selective capture and preconcentration of thrombin at low ionic strength and subsequent rapid elution at high ionic strength. The combination of the polymer monolithic column and the aptamer affinities makes the aptamer-modified monolithic columns useful for protein detection and separation.     

Size exclusion chromatography of microliter volumes for on-line use in low-pressure microfluidic systems

We have developed a new cartridge format for on-line size exclusion processing in low-pressure, portable microfluidic devices. The described system allows size exclusion chromatography of microliter volumes (termed muL-SEC) to be performed with ready integration in complex protocols for continuous-flow sample processing and analysis. The refillable cartridge format was employed for the preparation of Bacillus subtilus spores lysed in the presence of a strong reducing agent. While the reducing agent is known to interfere with subsequent fluorescent labeling of the solubilized proteins, the described continuous-flow size exclusion processing allowed complete isolation of interferences from a 10-muL sample in 70 s. Following efficient labeling, the protein sample was injected and separated on-chip using gel electrophoresis. To increase the resolution, speed, and sample capacity of buffer exchange under low-pressure operation (40 psi), parameters such as the size exclusion resin, load volumes, flow rates, buffer composition, and cartridge geometry were optimized and are presented here. The muL-SEC analysis is compatible with automated sample preparation for microfluidic systems and has resulted in significantly increased analysis speed and throughput over benchtop methods. The presented technique has the potential to improve capabilities such as buffer exchange, size fractionation, and high-abundance protein removal-steps that are frequently required prior to on-chip, point-of-care, and mass spectrometric analyses.     

Unlimited-volume electrokinetic stacking injection in sweeping capillary electrophoresis using a cationic surfactant

Sweeping is an effective and convenient way for online sample preconcentration in micellar electrokinetic chromatography. The usual procedure includes a hydrodynamic injection step carried out by applying pressure to the sample vial followed by the subsequent sweeping and separation processes. The injected sample volume is limited by the dimensions of the capillary because a part of the capillary has to be left free of sample solution for the subsequent sweeping and separation steps. In addition, when a short capillary, such as 4-10 cm, is used for sweeping, the injected sample volume is small even if the entire capillary is filled with sample solution. To solve this problem, an electrokinetic stacking injection (EKSI) scheme was developed by using a cationic surfactant, dodecyltrimethylammonium bromide, for sweeping in capillary electrophoresis. An experimental model was proposed, and the entire process was theoretically analyzed. According to the theoretical discussion, the optimal conditions for two model analytes, 5-carboxyfluorescein (5-FAM) and sodium fluorescein (FL), were experimentally determined. The injected sample plug lengths for 5-FAM and FL under 20.1 kV for 60 min were experimentally estimated as 836 and 729 cm, corresponding to 28- and 24-fold the effective capillary length, respectively. The EKSI scheme resulted in increased detection factors for 5-FAM and FL of 4.5 x 10(3) and 4.0 x 10(3) using 60-min injection relative to a traditional pressure injection.     

定向聚合制备硅分子筛复合膜

研制出一种高强度、高选择透过性的硅分子筛复合膜 .这种膜的最大特点 ,是其表面分离层是由定向聚合制得的硅树脂膜裂解制成 .由于这种硅树脂的大分子呈规则排列 ,因而导致最终裂解膜的孔径分布极窄 ,膜选择透过性能较大幅度提高 .这种膜对气体的渗透系数约为1 0 3Barrer(1Barrer =7.6× 1 0 - 8cm3·cm/cm2 ·s·MPa) ,H2 /N2 分离因子可达 90 ,其选择透过性能远优于常规的有机膜和无机膜 ,也优于常规碳分子筛膜和硅分子筛膜 .这种膜以多孔陶瓷为支撑体制成复合膜 ,因而具有较高的强度 .     

Phase-changing sacrificial materials for interfacing microfluidics with ion-permeable membranes to create on-chip preconcentrators and electric field gradient focusing microchips

We have developed a novel approach for interfacing ionically conductive membranes with microfluidic systems using phase-changing sacrificial layers. Imprinted microchannels in a polymer substrate are filled with a heated liquid that solidifies at room temperature, a monomer solution is placed over the protected channels and polymerized to form a rigid semipermeable copolymer, and then the protective layer is melted and removed, leaving an open microchannel interfaced with a polymer membrane. We have applied this method in miniaturizing electric field gradient focusing (EFGF) and carrying out on-chip protein preconcentration. A semipermeable copolymer in the EFGF microchips fills a region of changing cross-sectional area, which allows a gradient in electric field to be established when an electrical potential is applied. Our technique provides microchip EFGF devices that offer 3-fold improved resolution in protein focusing compared with capillary-based systems. In addition, these EFGF microchips can separate peptide samples with resolution similar to what is obtained in capillary electrophoresis microdevices, and the micro-EFGF systems enrich analytes by a factor of >150. Finally, we have fabricated membrane-integrated microfluidic devices that can concentrate protein samples (R-phycoerythrin) over 10 000-fold to facilitate microchip capillary electrophoresis. Interfacing microchannels with ion-permeable membranes has great potential to enhance microchip analysis of biomolecules.     

Simultaneous on-chip DC dielectrophoretic cell separation and quantitative separation performance characterization

Through integration of a MOSFET-based microfluidic Coulter counter with a dc-dielectrophoretic cell sorter, we demonstrate simultaneous on-chip cell separation and sizing with three different samples including 1) binary mixtures of polystyrene beads, 2) yeast cells of continuous size distribution, and 3) mixtures of 4T1 tumor cells and murine bone marrow cells. For cells with continuous size distribution, it is found that the receiver operator characteristic analysis is an ideal method to characterize the separation performance. The characterization results indicate that dc-DEP separation performance degrades as the sorting throughput (cell sorting rate) increases, which provides insights into the design and operation of size-based microfluidic cell separation.     

Si Nanowires Forest-Based On-Chip Biomolecular Filtering, Separation and Preconcentration Devices: Nanowires Do it All

The development of efficient biomolecular separation and purification techniques is of critical importance in modern genomics, proteomics, and biosensing areas, primarily due to the fact that most biosamples are mixtures of high diversity and complexity. Most of existent techniques lack the capability to rapidly and selectively separate and concentrate specific target proteins from a complex biosample, and are difficult to integrate with lab-on-a-chip sensing devices. Here, we demonstrate the development of an on-chip all-SiNW filtering, selective separation, desalting, and preconcentration platform for the direct analysis of whole blood and other complex biosamples. The separation of required protein analytes from raw biosamples is first performed using a antibody-modified roughness-controlled SiNWs (silicon nanowires) forest of ultralarge binding surface area, followed by the release of target proteins in a controlled liquid media, and their subsequent detection by supersensitive SiNW-based FETs arrays fabricated on the same chip platform. Importantly, this is the first demonstration of an all-NWs device for the whole direct analysis of blood samples on a single chip, able to selectively collect and separate specific low abundant proteins, while easily removing unwanted blood components (proteins, cells) and achieving desalting effects, without the requirement of time-consuming centrifugation steps, the use of desalting or affinity columns. Futhermore, we have demonstrated the use of our nanowire forest-based separation device, integrated in a single platform with downstream SiNW-based sensors arrays, for the real-time ultrasensitive detection of protein biomarkers directly from blood samples. The whole ultrasensitive protein label-free analysis process can be practically performed in less than 10 min.     

Integrated system for rapid PCR-based DNA analysis in microfluidic devices

An integrated system for rapid PCR-based analysis on a microchip has been demonstrated. The system couples a compact thermal cycling assembly based on dual Peltier thermoelectric elements with a microchip gel electrophoresis platform. This configuration allows fast (approximately 1 min/ cycle) and efficient DNA amplification on-chip followed by electrophoretic sizing and detection on the same chip. An on-chip DNA concentration technique has been incorporated into the system to further reduce analysis time by decreasing the number of thermal cycles required. The concentration injection scheme enables detection of PCR products after performing as few as 10 thermal cycles, with a total analysis time of less than 20 min. The starting template copy number was less than 15 per injection volume.     

Construction of large-volume monolithic columns

Monolithic supports have become the subject of extensive study in the past years. Despite their advantageous features and many successful chromatographic applications in the analytical scale, only a very few examples of larger volume monoliths were described. In the case of GMA-EDMA monoliths, this can be attributed to the fact that due to the exothermic polymerization a pronounced temperature increase inside the monolith significantly affects the structure. The temperature increase depends on the thickness of the monolith, and consequently, there is an upper limit that allows the preparation of a unit with a uniform structure. In the present work, we have analyzed a heat release during the polymerization and have derived a mathematical model for the prediction of the maximal thickness of the monolithic annulus having a uniform structure. On the basis of the calculations, two annuluses of different diameters were polymerized and merged into a single monolithic unit with a volume of 80 mL. In addition, a special housing was designed to provide a uniform flow distribution in the radial direction over the entire monolith bed. It was shown that such a monolithic column exhibits flow-independent separation efficiency and dynamic binding capacity up to flow rates higher than 100 mL/min. The separation and loading times are in the range of a few minutes. The pressure drop on the column is linearly dependent on the flow rate and does not exceed 2.5 MPa at a flow rate of 250 ml/min.     

Microfabricated two-dimensional electrophoresis device for differential protein expression profiling

A microfluidic separation system is developed to perform two-dimensional differential gel electrophoretic (DIGE) separations of complex, cellular protein mixtures produced by induced protein expression in E. coli. The micro-DIGE analyzer is a two-layer borosilicate glass microdevice consisting of a single 3.75 cm long channel for isoelectric focusing, which is sampled in parallel by 20 channels effecting a second-dimension separation by native electrophoresis. The connection between the orthogonal separation systems is accomplished by smaller channels comprising a microfluidic interface (MFI) that prevents media leakage between the two dimensions and enables facile loading of discontinuous gel systems in each dimension. Proteins are covalently labeled with Cy2 and Cy3 DIGE and detected simultaneously with a rotary confocal fluorescence scanner. Reproducible two-dimensional separations of both purified proteins and complex protein mixtures are performed with minimal run-to-run variation by including 7 M urea in the second-dimension separation matrix. The capabilities of the micro-DIGE analyzer are demonstrated by following the induced expression of maltose binding protein in E. coli. Although the absence of sodium dodecyl sulfate (SDS) in the second-dimension sizing separation limits the orthogonality and peak capacity of the separation, this analyzer is a significant first step toward the reproducible two-dimensional analysis of complex protein samples in microfabricated devices. Furthermore, the microchannel interface structures developed here will facilitate other multidimensional separations in microdevices.