The principal goal of this research is to further develop laser desorption/ionization time-of-flight mass spectrometry into a practical technique for high-speed DNA sequencing and sizing. Specific technical aims include unit base resolution in mixtures of DNA oligomers containing up to 300 nucleotides with sensitivity levels of less than or equal to one femtomole component. A reduction in molecular fragmentation and adduct formation in addition to multiply charged ions and dimer ions is also required. Central to the success of the desorption/ionization of fragile DNA oligomers is the nature of the matrix and its preparation with the oligonucleotides which must be optimized in order to achieve the technical goals. Proposed work will emphasize novel preparation techniques using ultraviolet-sensitive matrices such as 3-hydroxypicolinic acid as well as cryogenic frozen solutions for new matrices. Several improvements in instrumentation will be studied to further improve performance with existing and new sample preparation methods. While most of the research will be directed toward improving the performance of the basic mass spectrometry for oligonucleotides, a small fraction of the effort will be devoted to demonstrating genomics applications, including those where the high speed of the mass spectrometry can be used to advantage even with the current state-of-the-art technology.
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