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A short focused pulse of light was used to selectively cut lambda-phage DNA molecules at specific restriction sites. Lambda DNA (48.5 kbp) was stretched and placed in a solution containing a restriction enzyme (Sma 1), caged magnesium ions (using a DM-Nitrophen complex), and a chelating agent (EDTA). When a pulse of UV light was directed at a particular location on the stretched DNA molecule, magnesium ions were released into solution. A series of binding reactions then occur in which the enzyme and the chelating agent compete for free Mg2+ ions. Since Sma 1 functions only in the presence of Mg2+, as is true of most endonucleases, the site(s) in the vicinity of the pulse (typically approximately 6 microm) were cut while other sites (three total for this DNA/enzyme pair) were not. The ratio of the concentration of the chelating agent to that of the magnesium ions was used to control the radius of this reaction zone with higher ratios leading to smaller, localized reaction areas. This optically based reaction mechanism could be useful to understand single molecule enzymatic kinetics, and when coupled with other DNA analysis techniques, this could be used to construct complex genotyping and sequencing devices that would analyze parts of single DNA molecules.

A class of "lab-on-a-chip" devices use external air pressure for pumping discrete drops in a microchannel network. External air connectors can be cumbersome and are real-estate intensive. We have developed an on-chip technique to generate pressures required for metering and pumping of nanoliter-volume discrete drops. This is achieved by heating of trapped air in a pressure-generating chamber. The pressure-generating chamber is connected to the point of pressure application in the liquid-conveying microchannel through an air-delivery channel. The trapped air volume on the order of 100 nL is heated by resistive metal heaters by tens of degrees celcius to generate air pressures on the order of 7.5 kN/m2. The rate of discrete drop pumping is electronically controlled in the microchannel device by controlling the rate of air heating. Flow rates on the order of 20 nL/s are obtained in the microchannel (300 microns x 30 microns) by heating the air chamber at the rate of approximately 6 degrees C/s. In this paper, we describe the design, fabrication, and operation of this new technique of generating on-chip air pressure, used for metering and pumping nanoliter discrete drops in microchannels.

A monolithic capillary electrophoresis system with integrated on-chip fluorescence detector has been microfabricated on a silicon substrate. Photodiodes in the silicon substrate measure fluorescence emitted from eluting molecules. The device incorporates an on-chip thin-film interference filter that prevents excitation light from inhibiting the fluorescence detection. A transparent AZO conducting ground plane is also used to prevent the high electric fields used for the separation from interfering with the photodiode response. Separations of DNA restriction fragments have been performed in these devices with femtogram detection limits using SYBR Green I intercalating dye.

Nanoliter-sized liquid drops can be accurately metered inside hydrophilic microchannels using a combination of hydrophobic surface treatment and air pressure. The technique involves spontaneously filling the microchannels up to a hydrophobic region and splitting a liquid drop by injecting air through a hydrophobic side channel. The hydrophobic regions are fabricated by using a patterned metal mask on a substrate. The patterned substrate is immersed in an isooctane solution containing 1H,1H,2H,2H-per-fluorodecyltrichlorosilane to form hydrophobic patches on the exposed surface. Stripping the metal mask leaves the hydrophobic patches and restores the hydrophilic substrate surface. Precise and accurate liquid volumes, ranging from 0.5 to 125 nanoliters, have been metered using this technique. Theoretical predictions of the pressure needed to meter drops compare well with the experimental values.

Fraction collection following electrophoresis is of major importance for a variety of biological analyses. These assays typically need to identify specific fractions in the separated sample for further processing and require extraction of one or a group of fragments. In this paper, we have developed and characterized a technique to generate addressable electric fields for improved extraction during electrophoresis in microfluidic devices. The addressable electric field is achieved by applying a low bias voltage (1-2 V) to microelectrode pairs within the electrophoresis microchannel. Theoretical analysis shows the purity of the extracted sample can be improved as much as 30% over extraction without the shaped electric fields, and nearly 100% predicted yield can be achieved. We also describe the theoretical design of shaped electric fields by characterizing the optimal electrode geometry, field strength, channel configuration, and electrophoretic migration behavior needed for efficient band extraction.

We have performed the Taqman beta-actin PCR system in high-surface-to-volume ratio (0.02-0.13 microm(-1)) SiO2 microchannels and observed the reaction yield and uniformity. The concentrations of the enzyme, magnesium chloride, and reaction template were varied in the reaction mix, and PCR amplification was performed in devices of various surface-to-volume ratios. We found that microchannels with higher surface-to-volume ratios required higher enzyme concentrations to achieve the same amplification efficiency. We investigated the possibility that the observed reaction nonuniformity was related to the specific adsorption of magnesium ions to the negatively charged SiO2 surface. The effect of several modifications to the reaction chemistry, the addition of the caged-magnesium dye DM-Nitrophen, the replacement of human DNA template with PCR product, and the coating of the microchannel surface with Teflon were all studied. These modifications resulted in improved reaction uniformity in the microchannels and present opportunities for further studies on enhancing the efficiency and uniformity of PCR in high surface-to-volume ratio SiO2 microchannels.

An active microvalve that uses a meltable piston in place of a conventional solid material to obstruct fluid flow in a microfluidic channel has been developed. This phase change valve is simple to operate and requires no additional fabrication steps. The valve is inherently latched, reusable, and leak-proof (to at least 250 psi) and can be electronically addressed using resistive heaters. The valve has been characterized for a range of operational parameters that will serve as a design guide. For the designs tested, piston displacements of 5 mm or more in 1 s have been achieved. Valves 1.4 mm in length in a 50 microm x 200 microm channel have been integrated on a biochemical reaction device, and successful DNA amplification using PCR has been achieved. The phase change valve can be easily implemented in an array format that can be used to realize complex microfluidic circuits.

In this paper, we demonstrate immobilization and stretching of single lambda-phage DNA molecules within microfluidic systems using ac fields. We present a novel "thiol-on-gold"-based immobilization technique for fixing one specific end (3' end) of a DNA molecule onto a gold electrode. A polymer-enhanced medium (approximately 3.75 wt % linear polyacrylamide in Tris-HCl) is used to obtain fully stretched configurations (21 microm) of fluorescently stained lambda-DNA molecules. We also present an optimized microelectrode design with pointed electrodes and an electrode spacing of 20 microm for stretching DNA molecules with an ac field (1 MHz, 3 x 10(5) V/m). Finally, using these techniques, we immobilize a single DNA molecule at one electrode edge, stretch the molecule, and fix the other end at an adjacent electrode edge, forming a bridge between two electrodes within a microfabricated device.