Nanoscale Optofluidic Pathogen Detection

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DESCRIPTION (provided by applicant): The need to rapidly diagnose emerging viral threats along with the potential for associating individual or multiple point polymorphisms with disease states and pharmacological responses has lead to a recent interest in the development of new high-throughput nucleic acid biosensors. In this application, R21 support is requested for the development of "Nanoscale Optofluidic Sensor Arrays" which represent a new paradigm in high fidelity, high throughput, and unlabeled biosensing. The technique relies on shrinking the fluidic system down to the same scale as the wavelength of light and using the properties of a unique silicon nanophotonic structure to gain access to the evanescent field and to provide spatial localization of the reaction site. As is demonstrated this technique: (1) has attogram level detection sensitivity without the need for target labeling, (2) enables independent functionalization of individual nano-sensing sites with sub-micron spacing (3) ensures each solution phase nucleic acid target has multiple opportunities to hybridize with its surface immobilized complement (4) allows for inherent two dimensional multiplexing and (5) enforces reaction specificity through a unique electrokinetic stringency technique. Though broadly applicable to a wide range of nucleic acid applications, here we propose to demonstrate the platform through the specific detection of viral pathogens (focusing on the four serotypes of Dengue virus which has been identified by the Center of Disease Control and Prevention as one of the emerging diseases of our century) multiplexed simultaneously against a series of independent samples. This exploratory work builds on the PI's and Co-PI's background in integrated microfluidic devices, nanoscale optofluidic integration, high-throughput nucleic acid screening and RNA based viral pathogen biosensors. In this work we will focus on the experimental development of the sensor platform in preparation for an R01 application in which the device will be applied to clinical diagnostics and will incorporate sample preparation steps such as immunomagnetic separation, RNA extraction and pre- concentration prior to sensor analysis. Dengue virus is a major public health concern in tropical and subtropical areas. It causes an estimated 50 million illnesses annually, including 250,000-500,000 cases of Dengue Hemorrhagic Fever with 5-10% of mortality. Development of the Nanoscale Optofluidic Sensor Array could provide a technique by which viral pathogens like, but not limited to Dengue, can be detected at very low quantities in a highly parallel format. The near term major application will be as an early stage detection platform.