Nanowire Enhanced Substrates for Microarrays

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DESCRIPTION (provided by applicant): Existing substrates for fluorescent microarray applications have many limitations including poor sensitivity, low dynamic range, variable spot uniformity and large feature sizes on mechanically spotted arrays. Despite these limitations the fluorescent microarray has become a major tool for large-scale genomic analyses and the emerging proteomic industry. Thus far, attempts to introduce new substrates have been unsuccessful, largely because of reduced kinetic performance and the requirements for major changes to the basic array fabrication and analysis infrastructure. In this program we will develop a novel, nano-enabled microarray substrate that will overcome all the major limitations of existing microarray substrates and yet will be entirely incompatible with existing hybridization protocols, array fabrication and analysis infrastructure. This technology is based upon our ability to control and pattern the growth of SiO2 coated, nanometer diameter wires on the surface of a planar substrate. This novel material provides dramatic increases in effective surface area and yet retains the basic chemical characteristics required for surface functionalization and assay development. In Phase I we will optimize the material and develop methods for depositing and patterning it on planar surfaces compatible with conventional array fabrication and scanning instrumentation. We will link oligonucleotide probes to the enhanced surface using conventional chemistries and hybridize fluorescent targets to these probes using standard protocols. We will optimize the performance of the nanowire enhanced substrates to achieve a 100-fold increase in signal intensity per unit area with a concomitant increase in dynamic range. Furthermore, we will decrease feature sizes on spotted arrays to well below currently achievable levels and at the same time increase the uniformity of the spotted probe. Finally we will demonstrate the broad utility of this substrate by developing a protein binding assay on the nanowire enhanced surface. Preliminary experiments on non-optimized materials indicate that these milestones will be achievable. Our long term aims are to demonstrate the compatibility of this performance enhancing substrate with all array fabrication approaches, to increase the density of spotted arrays to those now achieved by lithographically synthesized formats and finally to manufacture well characterized high density DNA and protein arrays to carry out large scale genomic (proteomic) analyses on this substrate.