DNA sequencing and multiplex STR analysis on plastic microfluidic devices

The ability of plastic microfluidic devices with separation channel lengths of 6, 10 or 18 cm to perform high-quality and high-performance ssDNA analysis was evaluated. Specifically, four-color DNA sequencing separation of a terminator sequencing standard using replaceable, urea-denaturing linear polyacrylamide (LPA) solution as a sieving matrix, yielded read lengths of 410 bases in 15 min with base calling accuracy of 99.2% on a 6-cm device, and 640 bases in 35 min with accuracy of 98.0% on a 18-cm device. A two-color sizing analysis of four-locus (CSF1PO, TPOX, TH01, vWA) short tandem repeats (STRs) allelic ladder on a 10-cm device indicated a mean SD of +/- 0.08 base pairs (bp) between runs, and single bp resolution of spiked TH01 allele 9.3 (198 bp) from TH01 allele 10 (199 bp) of the CTTv ladder with R = 0.81. A four-color multiplex sizing analysis of three different AmpFlSTR allelic ladders consisting of nine loci (D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820) and gender alleles (Amelogenin) on a 10-cm device had a mean SD of +/- 0.15 bp between runs for sizing three loci, i.e., FGA, D18S51 and D3S818; alleles differing by 2 bp in size were resolved with resolutions close to baseline. This work demonstrates that plastic microfluidic devices are capable of quality sequencing and STR sizing comparable to that of glass devices of similar separation lengths.     

High-resolution micropatterned Teflon AF substrates for biocompatible nanofluidic devices

We describe a general photolithography-based process for the microfabrication of surface-supported Teflon AF structures. Teflon AF patterns primarily benefit from superior optical properties such as very low autofluorescence and a low refractive index. The process ensures that the Teflon AF patterns remain strongly hydrophobic in order to allow rapid lipid monolayer spreading and generates a characteristic edge morphology which assists directed cell growth along the structured surfaces. We provide application examples, demonstrating the well-controlled mixing of lipid films on Teflon AF structures and showing how the patterned surfaces can be used as biocompatible growth-directing substrates for cell culture. Chinese hamster ovary (CHO) cells develop in a guided fashion along the sides of the microstructures, selectively avoiding to grow over the patterned areas.     

Design and fabrication of a multilayered polymer microfluidic chip with nanofluidic interconnects via adhesive contact printing

The design and fabrication of a multilayered polymer micro-nanofluidic chip is described that consists of poly(methylmethacrylate) (PMMA) layers that contain microfluidic channels separated in the vertical direction by polycarbonate (PC) membranes that incorporate an array of nanometre diameter cylindrical pores. The materials are optically transparent to allow inspection of the fluids within the channels in the near UV and visible spectrum. The design architecture enables nanofluidic interconnections to be placed in the vertical direction between microfluidic channels. Such an architecture allows microchannel separations within the chip, as well as allowing unique operations that utilize nanocapillary interconnects: the separation of analytes based on molecular size, channel isolation, enhanced mixing, and sample concentration. Device fabrication is made possible by a transfer process of labile membranes and the development of a contact printing method for a thermally curable epoxy based adhesive. This adhesive is shown to have bond strengths that prevent leakage and delamination and channel rupture tests exceed 6 atm (0.6 MPa) under applied pressure. Channels 100 microm in width and 20 microm in depth are contact printed without the adhesive entering the microchannel. The chip is characterized in terms of resistivity measurements along the microfluidic channels, electroosmotic flow (EOF) measurements at different pH values and laser-induced-fluorescence (LIF) detection of green-fluorescent protein (GFP) plugs injected across the nanocapillary membrane and into a microfluidic channel. The results indicate that the mixed polymer micro-nanofluidic multilayer chip has electrical characteristics needed for use in microanalytical systems.     

Embossed polymer leaky waveguide devices for spectroscopic analysis

A combination of UV embossing, hot embossing and laminating techniques have been exploited during the fabrication of grating-coupled waveguiding devices in which the flow channel materials and geometry are designed for the effective support of light condenser modes through a sample solution. Used in conjunction with LED sources, these devices have been employed as optical platforms to obtain fluorescence emission and molecular absorption spectra in aqueous media for microTAS (micro total analytical system) applications.     

All-silica nanofluidic devices for DNA-analysis fabricated by imprint of sol-gel silica with silicon stamp

We present a simple and cheap method for fabrication of silica nanofluidic devices for single-molecule studies. By imprinting sol-gel materials with a multi-level stamp comprising micro- and nanofeatures, channels of different depth are produced in a single process step. Calcination of the imprinted hybrid sol-gel material produces purely inorganic silica, which has very low autofluorescence and can be fusion bonded to a glass lid. Compared to top-down processing of fused silica or silicon substrates, imprint of sol-gel silica enables fabrication of high-quality nanofluidic devices without expensive high-vacuum lithography and etching techniques. The applicability of the fabricated device for single-molecule studies is demonstrated by measuring the extension of DNA molecules of different lengths confined in the nanochannels.     

Direct loading of polymer matrices in plastic microchips for rapid DNA analysis: A comparative study

We report the design and performance validation of microfluidic separation technologies for human identification using a disposable plastic device suitable for integration into an automated rapid DNA analysis system. A fabrication process for a 15-cm long hot-embossed plastic microfluidic devices with a smooth semielliptical cross section out of cyclic olefin copolymer is presented. We propose a mixed polymer solution of 95% w/v hydroxyethylcellulose and 5% w/v polyvinylpyrrolidone for a final polymer concentration of 2.5 or 3.0% to be used as coating and sieving matrix for DNA separation. This formulation allows preparing the microchip without pretreatment in a single-loading step and provides high-resolution separation (≈1.2 bp for fragments <200 bp), which is superior to existing commercial matrices under the same conditions. The hot-embossed device performance is characterized and compared to injection-molded devices made out of cyclic olefin copolymer based on their respective injector geometry, channel shape, and surface charges. Each device design is assessed by fluorescence videomicroscopy to evaluate the formation of injection plugs, then by comparing electropherograms for the separation of a DNA size standard relevant to human identification.     

Novel polymer system for molecular imprinting polymer against amino acid derivatives

Molecular imprinting polymers (MIPs) against N-Cbz-L-Tyr were prepared utilizing different polymer systems and evaluated in HPLC mode. It was found that MEP utilizing cocktail functional monomers, acrylamide 2-vinylpyridine showed better molecular recognition and better separation ability for the template molecule than those utilizing other functional monomers. MIP utilizing trimethylolpropane trimethacrylate as cross-linker showed higher load capacity and separation factor than those utilizing ethylene glycol dimethacrylate as cross-linker. Increasing the concentration of competing solvent, acetic acid weakened the ionic interaction and hydrogen bonding between the analyte and the functional monomers, 2-vinylpyridine and acrylamide, when the template enantiomer was separated by HPLC. Therefore increasing of the concentration of acetic acid leads to decreasing of capacity factor, separation factor and resolution.     

Efficiently accounting for ion correlations in electrokinetic nanofluidic devices using density functional theory

The electrokinetic behavior of nanofluidic devices is dominated by the electrical double layers at the device walls. Therefore, accurate, predictive models of double layers are essential for device design and optimization. In this paper, we demonstrate that density functional theory (DFT) of electrolytes is an accurate and computationally efficient method for computing finite ion size effects and the resulting ion-ion correlations that are neglected in classical double layer theories such as Poisson-Boltzmann. Because DFT is derived from liquid-theory thermodynamic principles, it is ideal for nanofluidic systems with small spatial dimensions, high surface charge densities, high ion concentrations, and/or large ions. Ion-ion correlations are expected to be important in these regimes, leading to nonlinear phenomena such as charge inversion, wherein more counterions adsorb at the wall than is necessary to neutralize its surface charge, leading to a second layer of co-ions. We show that DFT, unlike other theories that do not include ion-ion correlations, can predict charge inversion and other nonlinear phenomena that lead to qualitatively different current densities and ion velocities for both pressure-driven and electro-osmotic flows. We therefore propose that DFT can be a valuable modeling and design tool for nanofluidic devices as they become smaller and more highly charged.     

DNA analysis on microfabricated electrophoretic devices with bubble cells

Microfluidic devices with bubble cells have been fabricated on poly(methyl methacrylate) (PMMA) plates and have been employed for the analysis of DNA using polyethylene oxide (PEO) solutions. First, the separation channel was fabricated using a wire-imprinting method. Then, wires with greater sizes or a razor blade glued in a polycarbonate plate was used to fabricate bubble cells, with sizes of 190-650 microm. The improvements in resolution and sensitivity have been achieved for large DNA (> 603 base pair, bp) using such devices, which depend on the geometry of the bubble cell. The main contributor for optimal resolution is mainly due to DNA migration at lower electric field strengths inside the bubble cell. On the other hand, slight losses of resolution for small DNA fragments have been found mainly due to diffusion, supported by the loss of resolution when separating two small solutes. With a bubble cell of 75 microm (width) x 500 microm (depth), the sensitivity improvement up to 17-fold has been achieved for the 271 bp fragment in the separation of PhiX-174/HaeIII DNA restriction fragments. We have also found that a microfluidic device with a bubble cell of 360 microm x 360 microm is appropriate for DNA analysis. Such a device has been used for separating DNA ranging from 8 to 2176 bp and polymerase chain reaction (PCR) products amplified after 30 cycles, with rapidity and improvements in the sensitivity as well as resolution.     

Dynamic analyte introduction and focusing in plastic microfluidic devices for proteomic analysis

Isoelectric focusing (IEF) separations, in general, involve the use of the entire channel filled with a solution mixture containing protein/peptide analytes and carrier ampholytes for the creation of a pH gradient. Thus, the preparative capabilities of IEF are inherently greater than most microfluidics-based electrokinetic separation techniques. To further increase sample loading and therefore the concentrations of focused analytes, a dynamic approach, which is based on electrokinetic injection of proteins/peptides from solution reservoirs, is demonstrated in this study. The proteins/peptides continuously migrate into the plastic microchannel and encounter a pH gradient established by carrier ampholytes originally present in the channel for focusing and separation. Dynamic sample introduction and analyte focusing in plastic microfluidic devices can be directly controlled by various electrokinetic conditions, including the injection time and the applied electric field strength. Differences in the sample loading are contributed by electrokinetic injection bias and are affected by the individual analyte's electrophoretic mobility. Under the influence of 30 min electrokinetic injection at constant electric field strength of 500 V/cm, the sample loading is enhanced by approximately 10-100 fold in comparison with conventional IEF.     

Rapid direct nanowriting of conductive polymer via electrochemical oxidative nanolithography

Conductive polymer nanolines having widths as small as 45 nm were obtained on glass using a novel scanning probe lithographic (SPL) technique at writing speeds of >5 mum/s. Herein we demonstrate that our nanowriting is >1500 times faster than current SPL nanoscale writing of conductive polymers. The lack of a specific restriction on the choice of substrates and the ability to write within a polymer matrix to provide a continuous film that is either 2-D or 2.5-D provide tremendous potential for our SPL technique in nanotechnology and plastic electronics applications.     

Atrazine transforming polymer prepared by molecular imprinting with post-imprinting process

Molecularly imprinted polymers bearing atrazine transforming activity were prepared by using newly designed templates that are atrazine analogues attached with an allyl or a styryl group via a disulfide bond at the 6-position, methacrylic acid as a functional monomer and styrene/divinylbenzene as crosslinkers. After polymerization, the disulfide bond was reduced to remove the atrazine moiety from the polymer matrix, followed by oxidation of the remaining thiol group to generate sulfonic acid (post-imprinting treatment), so that both a methacrylic acid residue and a sulfonic acid residue existed in an atrazine-imprinted cavity. The polymers indicated the selective binding of triazine herbicides and catalytic activity for methanolysis at the 6-position of atrazine, yielding a low toxic atraton.     

Anisotropic friction model of DNA electrophoresis in polymer solutions: Comparison with direct observations

The electrophoresis of DNA chains in uncrosslinked polymer solutions with a Brownian dynamics simulation with an anisotropic friction tensor was analyzed. According to the degree of anisotropy, three types of migration behavior are obtained: fluctuation without or with periodicity between U‐shaped and compact conformations, or migration with linear conformation. We found good agreement between our simulation results and the direct observations of DNA by fluorescence microscopy. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 1316–1322, 2003     

DNA micropatterning on polycrystalline diamond via one-step direct amination

We report a novel method of one-step direct amination on polycrystalline diamond to produce functionalized surfaces for DNA micropatterning by photolithography. Polycrystalline diamond was exposed to UV irradiation in ammonia gas to generate amine groups directly. After patterning, optical microscopy confirmed that micropatterns covered with an Au mask were regular in size and shape. The regions outside the micropatterns were passivated with fluorine termination by C3F8 plasma, and the chemical changes on the two different surfaces--the amine groups inside the patterned regions by one-step direct amination and fluorine termination outside the patterned regions--were characterized by spatially resolved X-ray photoelectron spectroscopy (XPS). The patterned areas terminated with active amine groups were then immobilized with probe DNA via a bifunctional molecule. The sequence specificity was conducted by hybridizing fluorescently labeled target DNA to both complementary and noncomplementary probe DNA attached inside the micropatterns. The fluorescence micropatterns observed by epifluorescence microscopy corresponded to those imaged by optical microscopy. DNA hybridization and denaturation experiments on a DNA-modified diamond show that the diamond surfaces reveal superior stability. The influence of a different amination time on fluorescence intensity was compared. Different terminations as passivated layers were investigated, and as a result, fluorine termination points to the greatest signal-to-noise ratio.     

Preconcentration and separation of double-stranded DNA fragments by electrophoresis in plastic microfluidic devices

We have evaluated double-stranded DNA separations in microfluidic devices which were designed to couple a sample preconcentration step based on isotachophoresis (ITP) with a zone electrophoretic (ZE) separation step as a method to increase the concentration limit of detection in microfluidic devices. Developed at ACLARA BioSciences, these LabCard trade mark devices are plastic 32 channel chips, designed with a long sample injection channel segment to increase the sample loading. These chips were designed to allow stacking of the sample into a narrow band using discontinuous ITP buffers, and subsequent separation in the ZE mode in sieving polymer solutions. Compared to chip ZE, the sensitivity was increased by 40-fold and we showed baseline resolution of all fragments in the PhiX174/HaeIII DNA digest. The total analysis time was 3 min/sample, or less than 100 min per LabCard device. The resolution for multiplexed PCR samples was the same as obtained in chip ZE. The limit of detection was 9 fg/microL of DNA in 0.1xpolymerase chain reaction (PCR) buffers using confocal fluorescence detection following 488 nm laser excitation with thiazole orange as the fluorescent intercalating dye.     

Scale-up development of high-performance polymer matrix for DNA sequencing analysis

Linear polyacrylamide (LPA) has been widely used as a replaceable separation matrix in CE. An increase in the molecular weight of the separation medium favors the separation of larger DNA fragments. In order to obtain ultrahigh-molecular-weight (UHMW) LPA, a "frozen" method was developed to synthesize the LPA homopolymer. This approach has three major advantages when compared with other existing routes of LPA synthesis: (i) long LPA chains could be obtained easily, with their average molecular weight (MW) being in the high 10 MDa range; (ii) the desired MW could be adjusted over a broad range by controlling the temperature and the concentration of initiators during synthesis; (iii) the product solution contains only a tiny amount of impurity besides the solvent and LPA. Both static and dynamic laser light scattering measurements were carried out to characterize the synthesized LPA in the buffer solution. The DNA sequencing matrix prepared from LPA using this method was studied and the results were compared with the newly developed commercial product POP7 from Applied Biosystems. It should be noted that this approach can be applied to synthesize other water-soluble polymers, resulting in UHMW products because the chain transfer constant is smaller at lower temperatures.     

Chiral polymer hosts for circularly polarized electroluminescence devices

Polymer electroluminescence devices producing circularly polarized luminescence (CP PLEDs) have valuable photonic applications. The fabrication of a CP PLED requires a polymer host that provides the appropriate chiral environment around the emitting dopant. However, chemical strategies for the design of chiral polymer hosts remain underdeveloped. We have developed new polymer hosts for CP PLED applications. These polymers were prepared through a free-radical polymerization of 3-vinylcarbazole with a chiral N-alkyl unit. This chiral unit forces the carbazole repeat units to form mutually helical half-sandwich conformers with preferred (P)-helical sense along the polymer main chain. Electronic circular dichroism measurements demonstrate the occurrence of chirality transfer from chiral monomers to achiral monomers during chain growth. The (P)-helical-sense-enriched polymer interacts diastereoselectively with an enantiomeric pair of new phosphorescent (R)- and (S)-dopants. The magnitude of the Kuhn dissymmetry factor (g_abs) for the (P)-helically-enriched polymer film doped with the (R)-dopant was found to be one order of magnitude higher than that of the film doped with the (S)-dopant. Photoluminescence dissymmetry factors (g_PL) of the order of 10⁻³ were recorded for the doped films, but the magnitude of diastereomeric enhancement decreased to that of g_abs. The chiral polymer host permits faster energy transfer to the phosphorescent dopants than the achiral polymer host. Our photophysical and morphological investigations indicate that the acceleration in the chiral polymer host is due to its longer Förster radius and improved compatibility with the dopants. Finally, multilayer CP PLEDs were fabricated and evaluated. Devices based on the chiral polymer host with the (R)- and (S)-dopants exhibit electroluminescence dissymmetry factors (g_EL) of 1.09 × 10⁻⁴ and −1.02 × 10⁻⁴ at a wavelength of 540 nm, respectively. Although challenges remain in the development of polymer hosts for CP PLEDs, our research demonstrates that chiroptical performances can be amplified by using chiral polymer hosts.

Polymer electroluminescence devices producing circularly polarized luminescence (CP PLEDs) have valuable photonic applications.     

Photochemical functionalization of polymer surfaces for microfabricated devices

Herein we report the topochemical modification of polymer surfaces with perfluorinated aromatic azides. The aryl azides, which have quaternary amine or aldehyde functional groups, were linked to the surface of the polymer by UV irradiation. The polymer substrates used in this study were cyclic olefin copolymer and poly(methyl methacrylate). These substrates were characterized before and after modification using reflection-absorption infrared spectroscopy, sessile water contact angle measurements, and X-ray photoelectron spectroscopy. Analysis of the surface confirmed the presence of aromatic groups with aldehyde or quaternary amine functionality. Enzyme immobilization and patterning onto polymer surfaces were studied using confocal microscopy. Enzymatic digests of protein were carried out on modified probes manufactured from thermoplastic substrates, and the resulting peptide analysis was completed using matrix-assisted laser desorption/ionization mass spectrometry. The use of functionalized perfluorinated aromatic azides allows the surface chemistry of thermoplastics to be tailored for specific lab-on-a-chip applications.