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Biomedical subjects

D Jed Harrison

Publications and source records attributed to D Jed Harrison.

11 recordsLinked to original sources
PubMed2006

Confinement effects on electromigration of long DNA molecules in an ordered cavity array.

Confinement effects on the electromigration of long dsDNA molecules in an array of well-ordered, molecular sized cavities interconnected by nanopores are described. The array was prepared by replicating the structure of a colloidal crystal of microspheres in a polymer matrix. Both conformation and mobility studies show that the electrophoretic behavior of large DNA molecules is distinct from that in gels and other microfabricated sieves, showing a peak in mobility versus electric field, and an inversion in the separation order with field strength. A simple model was proposed to interpret this unexpected observation qualitatively. We conclude that the molecular behavior of DNA can be modified by the combination of entropic effect and electric trapping as a consequence of both unique geometry and conductivity of this cavity array material. This approach provides insights for design and optimization of on-chip molecular sieving structures for rapid separation of long DNA molecules. It may lead to a promising material for manipulation and size fractionation of other biological macromolecules.

DNA↗
PubMed2004

Label-free reading of microarray-based immunoassays with surface plasmon resonance imaging.

A simple method is presented for patterning of protein antigens at a gold surface for use in surface plasmon resonance (SPR) imaging experiments. Microfluidic devices fabricated from poly(dimethylsiloxane) were used to flow various fluids over a gold substrate in spatially defined channels. This technique was used to pattern the surface chemistry of the gold as well as to adsorb antigens from solution to the modified substrates. The resulting antigen arrays were probed with complementary antibodies in order to demonstrate the effectiveness of the patterning for antibody capture experiments. SPR imaging was used to aid in the optimization of array fabrication and to observe the interactions of unlabeled antibodies with these microarrays. This work presents a means of fabricating microarrays with controlled surface density of antigens. SPR imaging provides both quantitative and qualitative evaluation of antibody binding in a label free format.

Animals↗
PubMed2004

Immunomagnetic T cell capture from blood for PCR analysis using microfluidic systems.

A one-step immunomagnetic separation technique was performed on a microfluidic platform for the isolation of specific cells from blood samples. The cell isolation and purification studies targeted T cells, as a model for low abundance cells (about 1:10,000 cells), with more dilute cells as the ultimate goal. T cells were successfully separated on-chip from human blood and from reconstituted blood samples. Quantitative polymerase chain reaction analysis of the captured cells was used to characterize the efficiency of T cell capture in a variety of flow path designs. Employing many (4-8), 50 microm deep narrow channels, with the same overall cross section as a single, 3 mm wide channel, was much more effective in structuring dense enough magnetic bead beds to trap cells in a flowing stream. The use of 8-multiple bifurcated flow paths increased capture efficiencies from approximately 20 up to 37%, when compared to a straight 8-way split design, indicating the value of ensuring uniform flow distribution into each channel in a flow manifold for effective cell capture. Sample flow rates of up to 3 microL min(-1) were evaluated in these capture beds.

Blood Cell Count↗
PubMed2004

A glassy carbon microfluidic device for electrospray mass spectrometry.

Due to the broad impact of microfabrication technology on chemistry and biology, new methods to pattern and etch a variety of materials are being explored in a number of laboratories. Here, we report the design, fabrication, and operation of a glassy carbon (GC) microchip interfaced to a nanoelectrospray ionization source and a quadrupole mass spectrometer. The method involves standard photolithographic pattern transfer to a photoresist layer and anodization of the exposed GC substrate in basic electrolyte to produce a series of channels with well-defined wall structure. The performance of the microchip was evaluated with standard polymer and peptide samples.

Carbon↗
PubMed2003

Microchip-based capillary electrochromatography using packed beds.

Integration of a packed column onto a microchip for performance of capillary electrochromatography (CEC) is described. The quartz device incorporated a cross-injector, and a double weir trapping design for formation of 1, 2 and 5 mm long CEC columns. Three fluorescent dyes were baseline-resolved with plate numbers of 330,(330,000 plates/m; height equivalent to a theoretical plate, H = 3.0 microm) for BODIPY 493/503, 360 (360,000 plates/m; H = 2.8 microm) for rhodamine 123 and 244 (244,000 plates/m; H = 4.1 microm) for acridine orange (AO) with 500 V applied on a 1 mm long column. The 2 mm column yielded approximately 1.8 times more theoretical plates than did the 1 mm column, when operated at the same flow rate. Van Deemter plots were obtained for the three column lengths, showing increased plate height for the 5 mm length. A 2 mm column gave peak height and area relative standard deviation (RSD) values of 2.5 and 3.3%, respectively, as averages for the three dyes (n = 15). The RSD for the dye retention times was 1% (n = 6) over one day, and 3% (n = 30) over five days. Indirect fluorescence detection of thiourea and of amino acids was possible using a neutral indicator dye (BODIPY 493/503), with a detection limit of 10 microM for amino acids.

Arginine↗
PubMed2002

Protein separation and surfactant control of electroosmotic flow in poly(dimethylsiloxane)-coated capillaries and microchips.

A thermally pyrolyzed poly(dimethylsiloxane) (PDMS) coating intended to prevent surface adsorption during capillary electrophoretic (CE) [Science 222 (1983) 266] separation of proteins, and to provide a substrate for surfactant adsorption for electroosmotic mobility control was prepared and evaluated. Coating fused-silica capillaries or glass microchip CE devices with a 1% solution of 100 cSt silicone oil in CH2Cl2, followed by forced N2 drying and thermal curing at 400 degrees C for 30 min produced a cross-linked PDMS layer. Addition of 0.01 to 0.02% Brij 35 to a 0.020 M phosphate buffer gave separations of lysozyme, cytochrome c, RNase, and fluorescein-labeled goat anti-human IgG Fab fragment. Respective plates/m typically obtained at 20 kV (740 V cm(-1)) were 2, 1.5, 1.25, and 9.4-10(5). In 50 mM ionic strength phosphate, 0.01% Brij 35 running buffer, the electroosmotic flow observed was about 25% of that in a bare capillary, and showed no pH dependence between pH 6.3-8.2. Addition of sodium dodecylsulfate (SDS) or cetyltrimethylammonium bromide (CTAB) to this running buffer allowed ready control of electroosmotic mobility, mu(eo). Concentrations of SDS between 0.005 to 0.1% resulted in mu(eo) ranging from 3 to 5 x 10(-4) cm2 V(-1) s(-1). Addition of 1 to 2.3 x 10(-4)% (2.7-6.3 microM) CTAB caused flow reversal. CTAB concentrations between 3.5 x 10(-4) and 0.05% (0.0014-1.37 mM) allowed control of mu(eo) between -1 x 10(-4) and -5.0 x 10(-4) cm2 V(-1) s(-1). For both surfactants the added presence of 0.01% Brij 35 provided slowly varying changes in mu(eo) with charged surfactant concentration.

Cations↗
PubMed2002

Integrated microfluidic electrophoresis system for analysis of genetic materials using signal amplification methods.

An isothermal signal amplification technique for specific DNA sequences, known as cycling probe technology (CPT), was performed within a microfluidic chip. The presence of DNA from methicillin-resistant Staphylococcus aureus was determined by signal amplification of a specific DNA sequence. The microfluidic device consisted of four channels intersecting to mix the sample and reagents within 55 s, as they were directed toward the reactor coil by electrokinetic pumping. The 160-nL CPT reactor occupied approximately 220 mm2. Gel-free capillary electrophoresis separation of the biotin- and fluorescein-labeled probe from the probe fragments was performed on-chip following the on-chip reaction. An off-chip CPT reaction, with on-chip separation gave a detection limit of 2 fM (0.03 amol) target DNA and an amplification factor of 85,000. Calibration curves, linear at <5% probe fragmentation, obeyed a power law relationship with an argument of 0.5 [target] at higher target DNA concentrations for both on-chip and off-chip CPT reaction and analysis. An amplification factor of 42,000 at 250 fM target (25,000 target molecules) was observed on-chip, but the reaction was approximately 4 times less sensitive than off-chip under the conditions used. Relative SD values for on-chip CPT were 0.8% for the peak migration times, 9% for the area of intact probe peak, and 8% for the fragment/probe peak area ratio.

DNA↗
PubMed2002

Affinity protection chromatography for efficient labeling of antibodies for use in affinity capillary electrophoresis.

Capillary electrophoresis immunoassay (CEIA) is shown to be substantially more sensitive to the antibody (Ab) reagent quality than are immunosorbent methods such as enzyme-linked immunosorbent assays (ELISA). Cyanine 5 (Cy5)-labeled monoclonal anti-ovalbumin (mAb*) was inactive for CEIA of ovalbumin (Ov), yet was functional in ELISA for Ov. ELISA showed the mAb* was at least ten times less active, accounting for the poor CEIA performance. Labeled polyclonal Ab was inactive for a dye to protein ratio greater than 1.6. An affinity protection chromatography procedure (APC) was developed for Ab labeling, which avoided degradation of the Ab binding site. Ov was covalently bound to cyanogen bromide activated cellulose gel in a column, and used to capture the Ab. The coupling efficiency for Ov to the gel was 74-97%, Ab could then be bound with 95-100% efficiency, and Ab* was recovered in 50% yield following labeling on the column. This procedure was performed successfully in three different laboratories, indicating the robustness of the optimized APC synthetic method. No inactive Ab* could be detected in the APC product. The CEIA detection limit for ovalbumin using APC labeled mAb was 173 nM, when [Ab*] was fixed at 163 nM. The association constants of mAb and mAb* were determined by CEIA.

Affinity Labels↗
PubMed2002

An integrated solid-phase extraction system for sub-picomolar detection.

A microchip structure etched on a glass substrate for packed column solid-phase extraction (SPE) and capillary electrochromatography (CEC) is described. A 200 microm long, octadecylsilane (ODS) packed column was secured using two different approaches: solvent lock or polymer entrapment. The former method was utilized for SPE while the latter approach was applied for CEC. In SPE, the ODS packed chamber gave a detection limit of 70 fM for a nonpolar BODIPY (493/503) dye when concentrated for 3 min at an electroosmotic flow rate of 4.14 nL/min, compared to 30 pM for this detector without the SPE step. SPE beds showed reproducible, linear calibration curves (R(2) = 0.9989) between 1 and 100 pM BODIPY at fixed preconcentration times. Breakthrough curves for the 330 pL (ODS-packed) bed indicated a capacity for BODIPY dye of 8.1 x 10(-14) mmol, or 0.25 mmol dye per liter of bed. The ODS-chamber could also be used to analyze dilute amino acid and peptide solutions. In the CEC format, two neutral dyes (BODIPY and acridine orange) were baseline-separated in an isocratic run with a theoretical plate count of 84 (420 000 plates/m) and a reduced plate height of about 1. A labeled peptide was also analyzed by CEC, using the acidic eluent (84% acetonitrile, and 26% aqueous trifluoroacetic acid (0.05%)) preferred for peptide separations on ODS-coated silica particles.

Acridine Orange↗
PubMed2002

Application of microfluidic devices to proteomics research: identification of trace-level protein digests and affinity capture of target peptides.

This report describes an integrated and modular microsystem providing rapid analyses of trace-level tryptic digests for proteomics applications. This microsystem includes an autosampler, a microfabricated device comprising a large channel (2.4 microl total volume), an array of separation channels, together with a low dead volume enabling the interface to nanoelectrospray mass spectrometry. The large channel of this microfluidic device provides a convenient platform to integrate C(18) reverse phase packing or other type of affinity media such as immobilized antibodies or immobilized metal affinity chromatography beads thus enabling affinity selection of target peptides prior to electrophoretic separation and mass spectrometry analyses on a quadrupole/time-of-flight instrument. Sequential injection, preconcentration, and separation of peptide standards and tryptic digests are achieved with a throughput of up to 12 samples/per h and a concentration detection limit of approximately 5 nM (25 fmol on chip). Replicate injections of peptide mixtures indicated that reproducibility of migration time was 1.2-1.8%, whereas relative standard deviation ranging from 9.2 to 11.8% are observed on peak heights. The application of this device for trace-level protein identification is demonstrated for two-dimensional gel spots obtained from extracts of human prostatic cancer cells (LNCap) using both peptide mass-fingerprint data base searching and on-line tandem mass spectrometry. Enrichment of target peptides prior to mass spectral analyses is achieved using c-myc-specific antibodies immobilized on protein G-Sepharose beads and facilitates the identification of antigenic peptides spiked at a level of 20 ng/ml in human plasma. Affinity selection is also demonstrated for gel-isolated protein bands where tryptic phosphopeptides are captured on immobilized metal affinity chromatography beads and subsequently separated and characterized on this microfluidic system.

Amino Acid Sequence↗