(14c) Microarray Diagnostic Formats: Meaning, Metrics and Money

The capture of genetic material (DNA and RNA) from various life science samples ? from food to microbiology to environment to medicine ? is very important in identifying disease, genetics, and bio-hazards. DNA diagnostics constitute the class of techniques used. DNA microarrays are one recently developed miniaturized diagnostic device where thousands of DNA samples can be identified simultaneously with small sample size and high throughput. The method involves capture of one strand of DNA target by its complementary DNA probe partner on a surface. Captured DNA signal is then measured with optical or radiometric methods. We study how DNA and proteins interact with device capture surfaces in microarray diagnostic assays, and have used many methods to understand how to optimize surface capture and diagnostic assay performance. Multiple surface analysis methods include x-ray photoelectron spectroscopy (XPS), surface optical methods (SPR), 32P-radiolabeling, and fluorescence assays on surfaces of different chemistries. Higher DNA probe surface density does not improve partner DNA signal capture. Immobilized DNA for this duplex capture produces steric and electrostatic interference on surfaces that blocks DNA target analyte capture. But, reduced DNA probe density, allowing higher hybridization efficiencies, produces lower overall assay signal. DNA assay performance depends on understanding these effects in microarray microspot devices. Recent work from the Grainger group in this regard: P. Gong, G.M. Harbers, D.W. Grainger, ?Multi-technique Comparison of Immobilized and Hybridized Oligonucleotide Surface Density on Commercial Amine-Reactive Microarray Slides,? Analy. Chem. 78:7, 2342-2351 (2006). C-Y Lee, P. Gong, L.J. Gamble, D.G. Castner, D.W. Grainger, ?Hybridization Behavior of Mixed DNA/Alkylthiol Monolayers on Gold: Characterization by SPR and 32P Radiometric Assay,? Analy. Chem., 78, 3316-3325 (2006). P. Gong, C-Y Lee, G.M. Harbers, D.G. Castner, D.W. Grainger, L.J. Gamble, ?Comparison of Immobilized DNA Orientation and Density Using NEXAFS, XPS, and Fluorescence Intensity Measurements on Gold? Analy. Chem., 78, 3326-3334 (2006) C-Y Lee, L.J. Gamble, D.W. Grainger, D.G. Castner, ?Mixed DNA/Oligoethylene glycol functionalized gold surfaces improve DNA hybridization in complex media,? BioInterphases, 1, 83-92 2006. P. Wu, D.W. Grainger, ?Comparison of hydroxylated print additives on antibody microarray performance,? J. Proteome Res., 5(11) 2956-2965, 2006. D. Dandy, P. Wu, D.W. Grainger, ?Assay feature size influences nucleic acid capture in DNA microarrays,? Proc Natl Acad Sci U S A 2007 104(20):8223-8 D. Xue, P. Gong, D.W. Grainger, C.M. Elliott, V. Disette, C.A. Bignozzi, S. Caramori, ?Electrochemical detection of DNA hybridization through catalytic oxidation of Co(II) complexes by covalently bound or intercalated Ru(II) complexes,? J Am Chem Soc 2007 129(7):1854-5 C-Y Lee, Phuong-Cac T. Nguyen,1,2 D.W. Grainger, L.J. Gamble, D.G. Castner, Structure and DNA Hybridization Properties of Mixed Nucleic Acid/Maleimide-ethylene glycol Monolayers, Anal Chem 2007 Jun 15;79(12):4390-4400 C.Y. Lee, G. M. Harbers, D.W. Grainger, L. J. Gamble, D. G. Castner, ?Fluorescence, XPS and ToF-SIMS Surface Chemical State Image Analysis of DNA Microarrays, J Am Chem Soc 2007 published on line Jul 11;