Shear-induced degradation of linear polyacrylamide solutions during pre-electrophoretic loading.

Electrophoretic channels are filled with a polymer matrix prior to their use in DNA separations. This process, called gel-loading, can be accomplished manually, using syringes, or can be automated through the use of small pumps or vacuum. The injection rate is constrained by the desire to minimize shear-induced degradation of the polymer molecules. Currently, the community lacks quantitative data with which to gauge the range of flow rates that prevent polymer degradation. In this study, measurements of the zero shear rate viscosity of linear polyacrylamide (LPA) solutions are used to determine the LPA molecular weight before and after gel-loading. The results indicate molecular degradation in polymer solutions even when injected at minimal flow rates of 1 microL/min. To correlate these rheological observations of shear-induced degradation with subsequent electrophoretic performance, the degraded solutions were used as sieving matrixes for DNA sequencing analysis. The decreases in electrophoretic resolution and increases in peak widths between sheared and nonsheared LPA solutions are related to the degradation in molecular weight experienced by the polymer solutions.

Recent advances in DNA sequencing by capillary and microdevice electrophoresis.

A number of significant improvements in the electrophoretic performance and design of DNA sequencing devices have culminated in the introduction of truly industrial grade production scale instruments. These instruments have been the workhorses behind the massive increase in genomic sequencing data available in public and private databases. We highlight the recent progress in aspects of capillary electrophoresis (CE) that has enabled these achievements. In addition, we summarize recent developments in the use of microfabricated devices for DNA sequencing that promise to bring the next leap in productivity.

Optimization of high-performance DNA sequencing on short microfabricated electrophoretic devices.

We have examined the parametric performance of short microfabricated electrophoresis devices that operate with a replaceable linear poly(acrylamide) (LPA) solution for the application of DNA sequencing. A systematic study is presented of the dependence of selectivity, separation efficiency, and resolution of sequencing fragments on buffer composition, LPA concentration, LPA composition, microdevice temperature, electric field, and device length. A specific optimization is made for DNA sequencing on 11.5-cm devices. Using a separation matrix composed of 3.0% (w/w) 10 MDa plus 1.0% (w/w) 50 kDa LPA, elevated microdevice temperature (50 degrees C), and 200 V/cm, high-speed DNA sequencing of 580 bases on standard M13mp18 was obtained in only 18 min with a base-calling accuracy of 98.5%. Read lengths of 640 bases at 98.5% accuracy were achieved in approximately 30 min by reducing the electric field strength to 125 V/cm. We believe that this constitutes matrix-limited performance for microdevices of this length using LPA sieving matrix and this buffer chemistry. In addition, it was confirmed, that shorter devices are rather impractical for production sequencing applications when LPA is used as sieving matrix.

Eight hundred-base sequencing in a microfabricated electrophoretic device.

The human genome will be sequenced using capillary array electrophoresis technology. Although currently achieving only 550 base reads per run, capillary arrays have increased the efficiency and lowered the cost of sequencing by eliminating gel plate preparation, reducing sample volumes, and offering automation and speed. However, much higher throughput and greater cost reductions are needed. The next major advancement in sequencing technology is expected from the development of arrays of microfabricated channels in a plate or "chip" format. For de novo sequencing, the practical utility of the microdevice approach has been limited by device length to a read of 500-600 bases per run. We demonstrate a significant milestone for a microfabricated device by obtaining an average read length of 800 bases in 80 min (98% accuracy) for either M13 standards or DNA sequencing samples from the Whitehead Institute Center for Genomic Research (WICGR) production line. This result is achieved in 40-cm-long channels using a new class of large-scale microfabricated devices. Both microfabrication of extended structures and achievement of long reads are essential steps toward a 384-lane very-large-scale microfluidic (VLSMF) system for ultrahigh-throughput DNA sequencing analysis, currently under construction in our laboratory.

Microchip electrophoresis: a method for high-speed SNP detection.

As a trial practical application, we have applied optimized microfabricated electrophoresis devices, combined with enzymatic mutation detection methods, to the determination of single nucleotide polymorphism (SNP) sites in the p53 suppressor gene. Using clinical samples, we have achieved robust assays with quality factors as good as conventional electrophoresis in approximately 100 s. This is 10 and 50 times faster than capillary and slab gel electro-phoresis, respectively. The method was highly accurate with an average error of mutation site measurement of only +/-5 bp. No clean-up of the digestion mixtures was needed prior to injection. This greatly simplifies sample handling relative to capillary instruments, which is important for high-throughput screening applications. Following identification, absolute mutation determination of the screened samples was achieved in a second microdevice optimized for four-color DNA sequencing. Total run time was 25 min in this second device and sequencing data were in full agreement with ABI Prism 377 sequencing runs which required 3.5 h. The tandem application of microdevices for location then full characterization of SNPs appears to confirm many of the improvements claimed for future application of microdevices in practical scaled screening for mutational analysis.

Capillary electrophoresis-based immunoassays.

This review covers the progress and developments in the field of capillary electrophoresis immunoassay (CEIA) over the past three years. Because many excellent descriptions of the principles of these methods are available (e.g., in the reviews listed in this article), no elementary introduction is given to the field of immunoassays (IAs) or CEIAs. This report focuses exclusively on experimental results, dividing the CEIA papers into the categories of direct, indirect, and microchip electrophoretic immunoassays. In the last section, a brief summary of the current status of the CEIA field is presented.

Recent developments in DNA sequencing by capillary and microdevice electrophoresis.

The present review covers papers published in the years 1997 and 1998 on DNA sequencing by capillary and microdevice electrophoresis. The article does not include other electrophoretic DNA applications such as analysis of oligonucleotides, genotyping, and mutational analysis. Capillary gel electrophoresis (CGE) is starting to become a viable competitor to slab gel electrophoresis for DNA sequencing. Commercially available multicapillary array sequencers are now entering sequencing facilities which to date have totally relied on traditional slab gel technology. CGE research on DNA sequencing therefore becomes increasingly concerned with the critical task of fine-tuning the operational parameters to create robust sequencing systems. Electrophoretic microdevices are being considered the next technological step in DNA sequencing by electrophoresis.

Toward real-world sequencing by microdevice electrophoresis.

We report results using a microdevice for DNA sequencing using samples from chromosome 17, obtained from the Whitehead Institute Center for Genome Research (WICGR) production line. The device had an effective separation distance of 11.5 cm and a lithographically defined injection width of 150 microm. The four-color raw data were processed, base-called by the sequencing software Trout, and compared to the corresponding ABI 377 sequence from WICGR. With a criteria of 99% accuracy, we achieved average continuous reads of 505 bases in 27 min with 3% linear polyacrylamide (LPA) at 150 V/cm, and 460 bases in 22 min with 4% LPA at 200 V/cm at a temperature of 45 degrees C. In the best case, up to 565 bases could be base-called with the same accuracy in <25 min. In some instances, Trout allowed for accurate base-calling down to a resolution R as low as R = 0.35. This may be due in part to the high signal-to-noise ratio of the microdevice. Unlike many results reported on capillary machines, no additional sample cleanup other than ethanol precipitation was required. In addition, DNA fragment biasing (i.e., discrimination against larger fragments) was reduced significantly through the unique sample injection mechanism of the microfabricated device. This led to increased signal strength for long fragments, which is of great importance for the high performance of the microdevice.

Two-color multiplexed analysis of eight short tandem repeat loci with an electrophoretic microdevice.

Single-channel microfabricated electrophoretic devices equipped with a dual-wavelength laser-induced fluorescence detection system were used for the fast analysis of an eight-loci, two-color multiplex short tandem repeat (STR) system for human identification. Routine analyses of the eight loci (CSF1PO, TPOX, TH01, vWA and D16S539, D7S820, D13S317, D5S818), requiring four-base resolution, were performed in only 2 min. Specific analyses for a microvariant allele (allele 9.3 of the TH01 locus) demanded single-base resolution and was performed in less than 10 min. The high accuracy of the microdevice for real-world STR sample analyses was demonstrated by comparison with conventional slab-gel electrophoresis. Our results show that a fast multiwavelength multichannel electrophoretic microsystem will be capable of routinely processing thousands of complex STR samples per day.

DNA sequencing on microfabricated electrophoretic devices.

We present a model that quantitatively describes the performance of microfabricated electrophoretic devices filled with linear polyacrylamide as replaceable sieving material for single-stranded DNA analyses. The dependence of resolution on various separation parameters such as selectivity, diffusion, injector size, device length, and channel folding was investigated. A previously predicted dependence of longitudinal diffusion coefficient on electric field strength has been verified. We have used this model to develop and optimize microfabricated electrophoretic devices for DNA analyses. For single-color DNA sequencing mixtures, we routinely achieve separations of 400 bases in under 14 min at 200 V/cm, and separation of 350 bases in only 7 min at 400 V/cm, with a minimum resolution of R = 0.5. Our results also indicate reduced fragment biasing and efficient sample stacking for DNA sample loading on microfabricated devices.

Immunoassay for thyroxine (T4) in serum using capillary electrophoresis and micromachined devices.

As part of our ongoing effort to develop electrophoretic assay technology for clinical diagnostics, we describe a competitive immunoassay for the determination of serum thyroxine (T4) based on electrophoresis and laser induced fluorescence (LIF). Measurements of total T4 are useful for the clinical evaluation of thyroid function. A fluorescein thyroxine conjugate was utilized in conjunction with a polyclonal antibody preparation as assay reagents. Capillary electrophoresis (CE) conditions tolerant of the direct injection of serum without extraction or other sample preparation steps were developed and used for quantitation of total T4 in serum. We have been exploring the use of micromachined devices with arrays of channels for high assay throughput. Our assay protocol was carried in a microchip format. The results illustrate that gains in speed can be additionally achieved, with the electrophoretic separation of free from bound labelled T4 being performed in about 15 s for serum samples.

DNA typing in thirty seconds with a microfabricated device.

We report the development of a practical ultrafast allelic profiling assay for the analysis of short tandem repeats (STRs) by using a highly optimized microfluidic electrophoresis device. We have achieved baseline-resolved electrophoretic separations of single-locus STR samples in 30 sec. Analyses of PCR samples containing the four loci CSF1PO, TPOX, THO1, and vWA (abbreviated as CTTv) were performed in less than 2 min. This constitutes a 10- to 100-fold improvement in speed relative to capillary or slab gel systems. The separation device consists of a microfabricated channel 45 micron x 100 micron in cross section and 26 mm in length, filled with a replaceable polyacrylamide matrix operated under denaturing conditions at 50 degrees C. A fluorescently labeled STR ladder was used as an internal standard for allele identification. Samples were prepared by standard procedures and only 4 microl was required for each analysis. The device is capable of repetitive operation and is suitable for automated high-speed and high-throughput applications.

Capillary electrophoresis based immunoassays: a critical review.

The purpose of this article is to review and evaluate the uses and potentials of capillary electrophoresis (CE) in immunoassay analysis (IA). This review will be divided into four sections. First, a brief summary of the fundamentals, applications and requirements of immunoassays in both research and clinical diagnostics will be given. This section will also cover the rationale behind the current research to combine CE and IA. Also, the specific needs to CE in this field will be addressed. Second, the modes of use of CE in IA will be discussed and typical applications for each will be given. Third, a separate section will be devoted to the investigation of performing immunoassays on micro fabricated devices, an interesting alternative to the conventional capillary-based approach. Finally, a critical assessment of the current status and merits of this technology will be presented.

Microchip electrophoretic immunoassay for serum cortisol.

An immunoassay performed using a microchip electrophoretic system is described. Separation and quantitation of free and bound labeled antigen in a competitive assay are carried out in channels micromachined into fused silica substrates. Such microchips are attractive because of their small size, ruggedness, and amenability to automated handling. The assay achieves the determination of cortisol in blood serum over the range of clinical interest (1-60 micrograms/dL) without the need for extraction or other sample preparation steps. The separation is performed in less than 30 s. Very high throughput is possible by operating the assay in multiple channels in parallel. These characteristics make microchip electrophoretic systems a promising technology for the rapid analysis of clinical samples.

Solution-phase immunoassay for determination of cortisol in serum by capillary electrophoresis.

We describe a competitive solution-phase immunoassay for serum cortisol determination that involves capillary electrophoresis (CE) combined with laser-induced fluorescence for separation and quantification. A polyclonal antibody preparation and fluorescein-labeled cortisol are used as assay reagents. 8-Anilino-1-naphthalenesulfonic acid was added to the serum sample during the assay to promote the release of cortisol from endogenous binding proteins. Conditions for the rapid separation of free and bound labeled antigen by CE were developed. Aspects of assay performance are evaluated in this report. The resulting assay protocol allows for the analysis of serum samples without extraction or other sample preparation steps.

Capillary electrophoresis-based immunoassay for cortisol in serum.

A competitive immunoassay for cortisol based on capillary electrophoresis (CE) and laser-induced fluorescence is described. The work involved the production of assay reagents and the development of separation conditions allowing for routine analysis of serum samples. Fluorescein-labeled cortisol was synthesized and purified. Fab fragments were produced from mouse monoclonal anticortisol antibody and purified using a POROS cation exchange chromatography column. After incubation of these reagents with serum, free and bound labeled antigen were separated by CE with high reproducibility. No prior sample cleanup of the serum samples was necessary. Serum calibration curves were established and used for the quantitation of cortisol in serum. The results demonstrate feasibility for a cortisol assay based on CE operating directly on serum samples.

Characterization and performance of a neutral hydrophilic coating for the capillary electrophoretic separation of biopolymers.

Polyvinylmethylsiloxanediol (50% vinyl) was synthesized and combined with a cross-linker for static coating onto fused-silica columns. After cross-linking and binding to the surface, linear polyacrylamide was grafted to the double bonds of the siloxanediol; subsequently, this linear polymer matrix was cross-linked with formaldehyde. The grafted neutral polymeric layer provided suppression of electroosmotic flow and minimized adsorption. This combination yielded successful open tube and polymer network separations of proteins, peptides and DNA molecules. Very high efficiencies (ca. 1 x 10(6) plates/m) were achieved for open tube protein separations, and hundreds of consecutive runs were performed with minimal change in migration times.

A mixed-bed, multi-derivatization approach using polymeric reagents for derivatizations of amines in high performance liquid chromatographic detection.

Immobilized, polymeric reagents containing covalently attached tagging groups have been synthesized and reacted individually, off-line or on-line, pre-column in high performance liquid chromatographic (HPLC) detection. These reagents have also been combined into a single, mixed-bed reactor, useful for simultaneously preparing several derivatives from a single analyte, all at the same time. Each derivative possesses different chromatographic and detection properties, dependent on the nature of the original polymeric reagent containing the immobilized, tagging species. These particular reagents were designed to impart Ultraviolet/fluorescence, Ultraviolet/electrochemistry (oxidative/reductive or oxidative-hv-electrochemistry) to the final derivatives. Variations in the amounts/ratios of polymeric reagents contained in a single mixed-bed reactor will lead to varying ratios of the final derivatives. These can be predicted knowing the approximate reactivity of each polymeric reagent, percent derivatizations, and overall rates for each reagent towards a given substrate. In this first example of mixed-bed, polymeric reagents for improved derivatization approaches in chromatography, emphasis has been placed on simple amines or amine-like analytes. Multiple derivatives can be effectively used to improve the identification of an unknown analyte in a complex sample matrix, as well as to improve the detectability of that analyte. As one real world application, amphetamine in human urine was quantitated via on-line derivatizations with a mixed-bed reactor. With the least sampling work-up, the resulting sample solutions were directly injected into the on-line derivatization HPLC system for quantitation. The method was validated by single blind spiking experiments. The precision and accuracy were acceptable.