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A Quantitative Analytical Tool for Producing DNA-Based Diagnostic Arrays--Atom Sciences, Inc., 114 Ridgeway Center, Oak Ridge, TN 37830-6926; 423-483-1113
Dr. Tom J. Whitaker, Principal Investigator
Dr. Tom J. Whitaker, Business Official
DOE Grant No. DE-FG02-98ER82536
Amount: $560,566
Arrays of oligodeoxynucleotides (ODN’s), or "DNA chips," offer miniaturization and shorter analysis times for many DNA analytical applications including genetic diagnostics, sequencing of short DNA’s, and ODN fingerprinting of clones in support of mapping. However, the difficulty of applying quality control steps has hampered the full acceptance of these arrays. Development of high-resolution, quantitative method to analyze the (ODN’s) on an array would allow a systematic approach to the quality control issue. This project will develop a broadly useful quality control methodology along with instrumentation that DNA chip manufacturers can use for quality assessment and control (QA/QC). The core strategy is to label the ODNs with tin (Sn). Then, during the array manufacturing, QA/QC is achieved by quantifying the amount of Sn-ODN in micro-spots of the array. This measurement is accomplished by using standard ion-sputtering followed by resonance ionization mass-spectrometry. In Phase I, DNA chips were prepared by immobilization chemistry and in situ synthesis, initial analyses of the Sn-ODN deposition were performed, and an improved calibration method was identified. Phase II will improve the ability to quantitatively measure ODNs precisely, by using enriched Sn isotopes in the calibration procedure. Several constituent steps will be automated, and the capability to resolve features down to a size of 20 m m features will be achieved.
Commercial Applications and other Benefits as described by the awardee: Several companies serving medical diagnostics and basic research markets are now producing ODN arrays. The inproved QA/QC capability provided by this project should directly benefit these ODN array manufacturers. It will allow them to improve their product in a systematic controlled fashion.