In this proposal, the investigators introduce new concepts that should make the sequencing of individual DNA fragments by fluorescently identifying individual base pairs a more practical reality. The investigators propose new integrated optical and fluid flow control devices for use in continuous flow sequencing. They will improve delivery of the laser excitation to fluorescently labeled DNA nucleotides with an optical waveguide integrated into the same substrate as a capillary structure in which the fluid flow is confined. This waveguide confines the laser beam to a well-defined, propagation path within the substrate and enables the realization of extremely small (sub-femtoliter) interaction volumes. This waveguide-capillary structure is suitable for the detection of extremely minute quantities of fluorophors down to a single molecule. Beam confinement in the waveguide is similar to confinement in silica optical fibers although in their realization a rectangular ridge waveguide is used. By using planar processing nanofabrication techniques, submicrometer lengths and subfemtoliter volumes are accessible. In the system, all molecules in the flow are constrained to pass through the interaction volume. The integrated structure should have several advantages over published methods of single molecule detection in flowing liquids. With this pilot program, the investigators will develop the concepts leading to a new type of robust high speed sequencing device, with several orders of magnitude higher sequencing rates than present techniques.
