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Virus detection using logic tags, molecular beacons and coffee stains
Rick Hasleton
Departments of Biomedical Engineering
Vanderbilt University
The detection of viruses remains an important medical challenge. In this seminar I describe the development of three different virus detection technologies each appropriate for a different setting: a clinical laboratory, a pediatrician’s office and a low resource environment.
In high resource settings, such as a hospital laboratory, the most important criteria are very low limit of detection and high specificity. As long as these are met, less rapid results are tolerated. A commonly used test in this setting is an antibody-based ELISA. The level of detection of this test is limited by the innate presence of non-specific interactions between antibodies and non-viral targets. The first technology I will describe is an application of DNA computing, designed to increase the limit of detection of antibody-based methods. The approach combines DNA reporter tags whose sequences enable logical operations among tags and facilitate subtraction of non-specific antibody interactions prior to PCR amplification.
The second technology, based on molecular beacons, is perhaps best-suited to the virus detection challenges found in a pediatrician’s office. In this low laboratory resource setting, the primary focus is rapid assessment with perhaps lower sensitivity. We are developing a method to detect viral RNA using molecular beacons arrayed on a moveable gold-plated wire. When no viral targets are present, the fluorophores on the molecular beacons are quenched by their close proximity to the gold wire, and no fluorescence is produced. In the presence of viral targets, the molecular beacons capture viral targets and, through a change in fluorescence, signal the presence of virus. In this design, processing is achieved by wire motion through processing solutions residing in small capillary tubes. This mechanically extracts, processes and enables detection of viral targets contained in a patient sample.
The third technology, based on changes in coffee ring patterns, is designed for environments with few resources and little expertise. In a low resource setting, a major criteria is simplicity of design. Complex designs drive up the cost of manufacturing and limit distribution. But even clearing this hurtle is no guarantee, since complex designs also fail with improper use by unskilled end-users. We are developing a simple diagnostic design based on the radial microfluidics responsible for coffee ring stains. The proposed diagnostic design is inexpensive to manufacture, is simple to operate and can be readily interpreted by an unskilled end-user.
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