Conductivity detection of polymerase chain reaction products separated by micro-reversed-phase liquid chromatography.

In this paper, we describe the application of micro-reversed-phase high-performance liquid chromatography (mu-RP-HPLC) for the separation and/or purification of polymerase chain reaction (PCR) products with detection accomplished using a miniaturized conductivity detector. The conductivity detector used two Pt wires and a bipolar waveform applied to the electrode pair from which the conductivity of the bulk solution could be measured. In the mobile phase used for the mu-RP-HPLC separation of the PCR product, the mass detection limit for herring sperm DNA using conductivity was found to be 11 ng. Efficient separation of the PCR amplicon from the other reagents present in the PCR cocktail was achieved in less than 4 min with a capacity factor of 2.5 and separation efficiency of 9.1 x 10(3) plates. The separation was carried out using reversed-phase ion-pair chromatography with a triethylammonium acetate ion-pairing agent.

Nanoliter-scale sample preparation methods directly coupled to polymethylmethacrylate-based microchips and gel-filled capillaries for the analysis of oligonucleotides.

We are currently developing miniaturized, chip-based electrophoresis devices fabricated in plastics for the high-speed separation of oligonucleotides. One of the principal advantages associated with these devices is their small sample requirements, typically in the nanoliter to sub-nanoliter range. Unfortunately, most standard sample preparation protocols, especially for oligonucleotides, are done off-chip on a microliter-scale. Our work has focused on the development of capillary nanoreactors coupled to micro-separation platforms, such as micro-electrophoresis chips, for the preparation of sequencing ladders and also polymerase chain reactions (PCRs). These nanoreactors consist of fused-silica capillary tubes (10-20 cm x 20-50 microns I.D.) with fluid pumping accomplished using the electroosmotic flow generated by the tubes. These reactors were situated in fast thermal cyclers to perform cycle sequencing or PCR amplification of the DNAs. The reactors could be interfaced to either a micro-electrophoresis chips via capillary connectors micromachined in polymethylmethacrylate (PMMA) using deep X-ray etching (width 50 microns; depth 50 microns) or conventional capillary gel tubes using zero-dead volume glass unions. For our chips, they also contained an injector, separation channel (length 6 cm; width 30 microns; depth 50 microns) and a dual fiber optic, near-infrared fluorescence detector. The sequencing nanoreactor used surface immobilized templates attached to the wall via a biotin-streptavidin-biotin linkage. Sequencing tracks could be directly injected into gel-filled capillary tubes with minimal degradation in the efficiency of the separation process. The nanoreactor could also be configured to perform PCR reactions by filling the capillary tube with the PCR reagents and template. After thermal cycling, the PCR cocktail could be pooled from multiple reactors and loaded onto a slab gel or injected into a capillary tube or microchip device for fractionation.

Near-infrared laser-induced fluorescence detection in capillary electrophoresis.

As capillary electrophoresis continues to focus on miniaturization, either through reducing column dimensions or situating entire electrophoresis systems on planar chips, advances in detection become necessary to meet the challenges posed by these electrophoresis platforms. The challenges result from the fact that miniaturization requires smaller load volumes, demanding highly sensitive detection. In addition, many times multiple targets must be analyzed simultaneously (multiplexed applications), further complicating detection. Near-infrared (NIR) fluorescence offers an attractive alternative to visible fluorescence for critical applications in capillary electrophoresis due to the impressive limits of detection that can be generated, in part resulting from the low background levels that are observed in the NIR. Advances in instrumentation and fluorogenic labels appropriate for NIR monitoring have led to a growing number of examples of the use of NIR fluorescence in capillary electrophoresis. In this review, we will cover instrumental components used to construct ultrasensitive NIR fluorescence detectors, including light sources and photon transducers. In addition, we will discuss various types of labeling dyes appropriate for NIR fluorescence and finally, we will present several applications that have used NIR fluorescence in capillary electrophoresis, especially for DNA sequencing and fragment analysis.

Micromachining in plastics using X-ray lithography for the fabrication of microelectrophoresis devices.

Micromachining was performed in polymethylmethacrylate (PMMA) using X-ray lithography for the fabrication of miniaturized devices (microchips) for potential applications in chemical and genetic analyses. The devices were fabricated using two different techniques: transfer mask technology and a Kapton mask. For both processes, the channel topography was transferred (1:1) to the appropriate substrate via the use of an optical mask. In the case of the transfer mask technique, the PMMA substrate was coated with a positive photoresist and a thin Au/Cr plating base. Following UV exposure, the resist was developed and a thick overlayer (approximately 3 microns) of Au electroplated onto the PMMA substrate only where the resist was removed, which acted as an absorber of the X-rays. In the other technique, a Kapton film was used as the X-ray mask. In this case, the Kapton film was UV exposed using the optical mask to define the channel topography and following development of the resist, a thick Au overlayer (8 microns) was electrodeposited onto the Kapton sheet. The PMMA wafer during X-ray exposure was situated directly underneath the Kapton mask. In both cases, the PMMA wafer was exposed to soft X-rays and developed to remove the exposed PMMA. The resulting channels were found to be 20 microns in width (determined by optical mask) with channel depths of approximately 50 microns (determined by x-ray exposure time). In order to demonstrate the utility of this micromachining process, several components were fabricated in PMMA including capillary/chip connectors, injectors for fixed-volume sample introduction, separation channels for electrophoresis and integrated fiber optic fluorescence detectors. These components could be integrated into a single device to assemble a system appropriate for the rapid analysis of various targets.

High-resolution near-infrared imaging of DNA microarrays with time-resolved acquisition of fluorescence lifetimes.

Ultrasensitive, near-infrared (NIR), time-resolved fluorescence is evaluated as a detection method for reading DNA hybridization events on solid surfaces for microarray applications. In addition, the potential of mulitiplexed analyses using time-resolved identification protocols is described. To carry out this work, a NIR time-resolved confocal imager was constructed to read fluorescence signatures from the arrays. The device utilized a 780-nm pulsed diode laser, a single-photon avalanche diode (SPAD), and a high-numerical-aperture microscope objective mounted in an epi-illumination format. Due to the small size of the components that are required to construct this imager, the entire detector could easily be mounted on high-resolution translational stages and scanned over the stationary arrays. The instrument response function of the device was determined to be 275 ps (fwhm), which is adequate for measuring fluorophores with subnanosecond lifetimes. To characterize the system, NIR dyes were deposited directly on different substrate materials typically used for DNA microarrays, and the fluorescence lifetimes of two representative dyes were measured. The fluorescence lifetime for aluminum tetrasulfonated naphthalocyanine was found to be 1.92 ns, and a value of 1.21 ns was determined for the tricarbocyanine dye, IRD800, when it was deposited onto poly(methyl methacrylate) (PMMA) and measured in the dry state. Finally, the imager was used to monitor hybridization events using probe oligonucleotides chemically tethered to a PMMA substrate via a glutardialdehyde linkage to an aminated-PMMA surface. The limit of detection for oligonucleotides containing a NIR fluorescent reporter was determined to be 0.38 molecules/microm2, with this detection limit improving by a factor of 10 when a time-gate was implemented. Fluorescence lifetime analysis of the hybridization events on PMMA indicated a lifetime value of 1.23 ns for the NIR-labeled oligonucleotides when using maximum-likelihood estimators.