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Mark A Burns

Publications and source records attributed to Mark A Burns.

25 records · Page 2Linked to original sources
PubMed2003

A versatile microfabricated platform for electrophoresis of double- and single-stranded DNA.

We demonstrate a versatile microfabricated electrophoresis platform, incorporating arrays of integrated on-chip electrodes, heaters, and temperature sensors. This design allows a range of different sieving gels to be used within the same device to perform separations involving both single- and double-stranded DNA over distances on the order of 1 cm. We use this device to compare linear and cross-linked polyacrylamide, agarose, and thermo-reversible Pluronic-F127 gels on the basis of gel casting ease, reusability, and overall separation performance using a 100 base pair double-stranded DNA ladder as a standard sample. While cross-linked polyacrylamide matrices provide consistently high-quality separations in our system over a wide range of DNA fragment sizes, Pluronic gels also offer compelling advantages in terms of the ability to remove and reload the gel. Agarose gels offer good separation performance, however, additional care must be exercised to ensure consistent gel properties as a consequence of the need for elevated gel loading temperatures. We also demonstrate the use of denaturing cross-linked polyacrylamide gels at concentrations up to 19% to separate single-stranded DNA fragments ranging in size from 18 to 400 bases in length. Primers differing by 4 bases at a read length of 30 bases can be separated with a resolution of 0.9-1.0 in under 20 min. This level of performance is sufficient to conduct a variety of genotyping assays including the rapid detection of single nucleotide polymorphisms (SNPs) in a microfabricated platform. The ability to use a single microelectrophoresis system to satisfy a wide range of separation applications offers molecular biologists an unprecedented level of flexibility in a portable and inexpensive format.

Acrylic Resins↗
PubMed2002

Electrostretching DNA molecules using polymer-enhanced media within microfabricated devices.

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.

Acrylic Resins↗
PubMed2002

Analytic chemistry. Everyone's a (future) chemist.

The development of small, portable "lab-on-a-chip" devices has the potential to provide individuals with the tools for complex chemical and biochemical analysis. In his Perspective, Burns charts recent progress toward fabricating such devices. He highlights the report by Terray et al., who use latex spheres manipulated by optical traps to pump fluids. The integration of such components into larger, more complex devices will open up applications from airborne contaminant detection to genetic testing and screening.

Air Pollutants↗
PubMed2002

Cross-linked polyacrylamide gel electrophoresis of single-stranded DNA for microfabricated genomic analysis systems.

Microfabricated devices are poised to offer inexpensive self-contained alternatives to conventional benchtop-scale laboratory equipment for performing a variety of important DNA analysis assays. In order to realize the dramatic cost savings possible through photolithographic fabrication techniques, these devices must occupy an extremely compact footprint on the silicon wafer. This requirement implies that electrophoretic separations must be performed over ultrashort distances. Employing cross-linked polyacrylamide gels in place of conventional uncross-linked sieving media offers a convenient strategy to achieve this goal. In this paper, we show how the increased resolving power offered by cross-linked polyacrylamide gels, along with improved sample injection techniques, can be exploited to enhance separation performance in microscale systems. We use these techniques to perform high-resolution gel electrophoresis of single-stranded DNA fragments in microfabricated devices over separation distances of 1.5 cm or less. The results presented here are in agreement with theoretical predictions and suggest that it is possible to perform DNA sequencing on compact microchips. More importantly, the separation performance demonstrated in this work is already more than adequate to perform a number of important genomic assays imposing less stringent resolution requirements than sequencing. Successfully adapting even a few of these assays to the microdevice format has the potential to provide a new generation of inexpensive and portable devices suitable for direct end-user applications.

Acrylic Resins↗
PubMed2002

Microdevice-based measurements of diffusion and dispersion in cross-linked and linear polyacrylamide DNA sequencing gels.

We use microfabricated gel electrophoresis devices incorporating integrated on-chip electrodes, heaters, and temperature sensors to measure diffusion and dispersion of single-stranded DNA fragments in cross-linked and uncross-linked polyacrylamide gels. The microdevice format allows a complete set of diffusion and dispersion data to be collected in approximately one hour. These results are compared with corresponding data obtained in a macroscale DNA sequencer, and the effects of gel composition and initiation chemistry are explored. Although the diffusion and dispersion data exhibit similar qualitative trends both on chip and on the macroscale, the magnitudes of the coefficients measured in the microdevice are somewhat higher. This discrepancy is likely due to altered polymerization kinetics arising as a consequence of using a UV-initiated polymerization chemistry to cast the on-chip gels as opposed to the standard chemical polymerization employed on the macroscale. We also find that reductions in the magnitudes of diffusion and dispersion coefficients are achieved at higher polymer concentrations and at operating temperatures in the vicinity of 50 degrees C. Finally, we find that cross-linked polyacrylamide gels yield significantly lower diffusion and dispersion coefficients than linear polyacrylamide. These findings can be used to identify rational strategies to improve separation performance in both micro- and macroscale gel electrophoresis systems.

Cross-Linking Reagents↗
PubMed2002

QT dispersion in 120 electrocardiographic leads in patients with structural heart disease.

The clinical significance of QT dispersion (QTd) measured in 12-lead ECGs is controversial. The aim of this study was to clarify factors that determine the QTd and its measurement errors in different lead arrays in patients with structural heart disease. Two blinded observers measured QT intervals on a computer screen from 120-channel ECG recordings in a retrospective set of 257 patients, comprising a group of 121 myocardial infarction (MI) survivors without ventricular tachyarrhythmia during a 6-month follow-up and a group of 136 survivors of ventricular tachyarrhythmia/fibrillation. QTd did not differ in patients with and without ventricular tachyarrhythmia/fibrillation. Eleven ventricular tachyarrhythmia/fibrillation survivors without structural heart disease had the lowest QTd (P < or = 0.02). The strongest factor determining QTd and the magnitude of its measurement error was the lead array (P = 0.0001). Measurement errors had two components. The smallest relative errors were in the total body surface mapping array with one component related to interobserver reproducibility (9.1 +/- 7.6%), and the other component related to accuracy of measurement of the QT interval (36 +/- 16%). The authors estimated that a difference of QTd of at least 50 ms between study groups is required in a 12-lead ECG to draw any conclusions from the studies. In patients with structural heart disease, QTd from limited arrays of ECG leads was not a reliable measure. It correlated with the presence of structural heart disease, but not with arrhythmogenicity. An array consisting of ECG leads covering the entire chest allowed better reproducibility and measurement accuracy of QTd.

Aged↗