Multiple sample PCR amplification and electrophoretic analysis on a microchip

Rapid Diagnosis of Herpes Simplex Encephalitis Using Microchip Electrophoresis of PCR Products

Background: Herpes simplex virus (HSV) is the most common cause of acute sporadic encephalitis in the United States. PCR of DNA extracted from cerebrospinal fluid (CSF) allows for reliable diagnosis of herpes simplex encephalitis (HSE). A faster turnaround time for HSE testing would improve patient management and lead to better outcomes. The aims of this study, therefore, were to develop a microchip-based electrophoretic method for rapid detection of HSV PCR products, and to compare the performance characteristics of liquid hybridization/gel retardation as an established clinical PCR product detection method with the new microchip-based method.

Methods: The study examined archival DNA from 33 selected CSF specimens submitted for HSV PCR testing to the clinical laboratory. One aliquot of the HSV PCR product was analyzed by liquid hybridization/gel retardation analysis, and a second PCR aliquot was analyzed directly with a microchip capillary electrophoresis system using an instrument built in-house. PCR samples were introduced directly into the microchip without a desalting step by use of a novel fluidic interface. Channel surfaces on the glass microchip were silanized, followed by derivatization with polyvinylpyrrolidone.

Results: Of the 33 CSF specimens tested by liquid hybridization analysis of HSV PCR products, 10 tested positive for HSV DNA, 2 gave a weakly positive result, and 21 tested negative. Total analysis time for detection of HSV DNA by gel retardation assay was 18 h. Microchip electrophoresis provided identical results in <110 s/sample, achieving 100% sensitivity and specificity compared with the established method.

Conclusions: Microchip-based electrophoresis can rapidly and accurately separate HSV PCR products, giving results identical to those obtained by liquid hybridization but with substantially decreased turnaround time. Clinical implementation of the new method will help to improve patient management and outcomes.

Overview of capillary electrophoresis and capillary electrochromatography

This paper provides an overview on the current status of capillary electrophoresis (CE) and capillary electrochromatography (CEC). The focus is largely on the current application areas of CE where routine methods are now in place. These application areas include the analysis of DNA, clinical and forensic samples, carbohydrates, inorganic anions and metal ions, pharmaceuticals, enantiomeric species and proteins and peptides. More specific areas such the determination of physical properties, microchip CE and instrumentation developments are also covered. The application, advantages and limitations of CEC are covered. Recent review articles and textbooks are frequently cited to provide readers with a source of information regarding pioneering work and theoretical treatments.

Separation of double-stranded and single-stranded DNA in polymer solutions: I. Mobility and separation mechanism

We have studied the separation of single-stranded and double-stranded DNA in a matrix of entangled, linear poly-N,N-dimethylacrylamide. Our results give better insight into the mechanisms involved during separations in polymer solutions. The dependence of different parameters on DNA size, electric field, pore size and the polymer chain length are evaluated and compared to theoretical predictions. Striking differences between experimental data and predicted scaling laws are found. Our data should help to optimize DNA separation in capillary electrophoresis and to improve existing models for DNA separation in porous matrices.