High-density DNA probe arrays provide a massively parallel approach to nucleic acid sequence analysis that is transforming gene-based biomedical research and diagnostics. Light-directed combinatorial oligonucleotide synthesis has enabled the large-scale production of GeneChip probe arrays which contain several hundred of thousand oligonucleotide sequences on glass "chips" about one cm2 in size. Due to their very high information content, GeneChip probe arrays are finding widespread use in the hybridization-based detection and analysis of mutations and polymorphisms ("genotyping"), and in a wide range of gene expression studies. The manufacturing process integrates solid-phase photochemical oligonucleotide synthesis with lithographic techniques adapted from the microelectronics industry. The present-generation methodology employs MeNPOC photo-activatable nucleoside monomers with proximity photolithography, and is currently capable of printing individual 10 microns 2 probe features at a density of 10(6) probes/cm2.

The continual need for increased manufacturing capacity in the production of GeneChip™ DNA probe arrays, and the expanding use of these arrays into new areas of application such as molecular medicine, has stimulated the development of new chemistries and production methods with higher efficiency and resolution. For current production methods based on contact photolithography, modifications in substrate materials and photoactivated synthesis reagents have provided significant improvements in array performance and information content (≥4×106 sequences∕cm2). An alternative next-generation manufacturing process is also in development, which utilizes photoacid generating polymer films, and automated projection lithography systems. This process has the ability to fabricate arrays with 1 micron feature pitch and smaller, providing an unprecedented sequence density of 108∕cm2 and greater.

Reactive oxygen species are highly reactive molecules and have been implicated in the pathophysiology of many diseases, including diabetes mellitus, cancer, rheumatoid arthritis, and cardiovascular, renal, inflammatory, infectious, and neurologic diseases (1, 2 ). Cells and biological fluids have an array of protective antioxidant mechanisms, both for preventing the production of free radicals and for repairing oxidative damage (3 ). These antioxidant systems include enzymes, macromolecules, and small molecules, including ascorbic acid, ␣-tocopherol, ␤-carotene, ubiquinol-10, reduced lipoic acid (DHLA), reduced glutathione (GSH), methionine, uric acid, bilirubin, and some amino acids. Antioxidants within cells, cell membranes, and extracellular fluids can be up-regulated and mobilized to neutralize excessive and inappropriate formation of reactive oxygen species, but a deficiency of antioxidant defense may lead to a situation of increased oxidative stress.Assays that measure the combined antioxidant effect of the nonenzymatic defenses in biological fluids may be useful in providing an index of ability to resist oxidative damage. Several methods (4 -6 ) have been developed to assess the total antioxidant capacity of human serum or plasma because of the difficulty in measuring each antioxidant component separately and the interactions among different antioxidant components in the serum or plasma. However, the measured antioxidant capacity of a sample depends on which technology and which free radical generator or oxidant is used in the measurement. The ferric reducing ability of plasma (FRAP) assay uses an easily reduced oxidant in a redox-linked colorimetric method (6 ). Because the redox potential of the ferrous/ ferric couple is 0.77 V, any substance or antioxidant with a redox potential Ͻ0.77 V will drive the ferric reduction, assuming stability of redox product. According to a study by Cao and Prior (7 ), the FRAP assay does not measure serum proteins and excludes the low-molecular-weight SH-group-containing antioxidants, such as GSH, DHLA, and some amino acids. We developed a novel method for measuring the ubiquinone-9-reducing ability of plasma (URAP). This new method estimates antioxidant systems with redox potentials Յ0.1 V, which will drive the reduction of ubiquinone-9 (Fig. 1A).HPLC analysis was performed with an ESA Model 582 Solvent Delivery Module, AS1000 autosampler (Thermo Separation Products), and a reversed-phase Microsorb-MV column [150 ϫ 4.6 mm (i.d.); 5-m bead size] from Rainin. The mobile phase consisted of a mixture of anhydrous sodium acetate (4.2 g; Sigma), 15 mL of glacial acetic acid (Mallinckrodt), 15 mL of 2-propanol (Mallinckrodt), 720 mL of methanol (Fisher), and 250 mL of hexane (Fisher). The flow rate was 1.1 mL/min. The electrochemical detector with ESA Model 5200A CouloChem II has been described previously (8 ). The electrochemical cells were a postcolumn guard cell and analytical cell containing dual electrodes in series. The potential of the postcolumn guard cell was set at ϩ0...