New methods for sequencing genornic DNA rapidly and accurately in a large number of individuals are needed to better understand the role of genetic variation in common disease. Sequencing-by-synthesis (SBS) is one of the most promising contemporary methods for fast, high-throughput, and low cost genomic DNA sequencing applications. The Base Addition Sequence Scheme (BASS) involves the repetitive cycles of incorporation of 3'-O-labile nucleotide terminators, in situ identification of the incorporated base, and deprotection to yield a 3'-OH group to allow the next cycle of DNA synthesis. The use of DNA templates attached to a solid support eliminates the need for electrophoresis, which resolves the nested DNA fragments by their respective size. We anticipate that formatting the sequencing chemistry into a high density array will increase throughput of the technology, shorten the time required to effect the examination, and lower the cost per read significantly. The aim of this proposal is the development of novel protecting groups with two distinct properties; (a) fluorescence and (b) photolability. That is, the protecting groups would be identified immediately after incorporation of the appropriate nucleotide by laser-induced fluorescence and efficiently removed (>99.9%) upon UV irradiation. To achieve this goal, we propose an exploration of two strategies: syntheses and structural identification of (i) novel fluorescent, 3'-O-photolabile nucleosides, and (ii) novel FRET 3'-Ophotolabile nucleosides bearing an acceptor dye such as fluorescein, rhodarnine, BODIPY, or sulfonated pyrene. Both strategies have the distinct advantage of in situ monitoring of the deprotection step, thus ensuring efficient removal of the protecting group before starting the next BASS cycle. The outcome of this research will provide a basis of a phase II grant for the development of a powerful rapid, high throughput, and low cost DNA sequencing technology.
Thesaurus Terms: chemical synthesis, fluorescence, fluorescence resonance energy transfer, nucleic acid sequence, nucleoside analog, photochemistry, technology /technique development
