Automated DNA sequencing has been based on gel electrophoresis techniques developed in the 1970's with fluorescence detection replacing radioactivity detection. The first fluorescence based sequencers, including the original Ll-COR systems operating in 1986, were based on the detection of visible fluorescence using gas lasers and vacuum detectors. Recently, the use of solid-state optical components has provided a highly sensitive, yet economical detection system based on near-infrared fluorescence. Near-infrared fluorescence is not limited to DNA sequencing based on electrophoresis. Single molecule detection techniques as well as base addition/subtraction sequencing schemes are examples of strategies that would be enhanced by near-infrared fluorescence. In phase l of this effort we will address the feasibility of the design and synthesis of infrared (IR) dye labeled biomolecules by concentrating on the synthesis of IR-labeled phosphoramidites and nucleoside triphosphates. These labeled biomolecules would reduce the cost of sequencing by allowing additional sequencing strategies such as primer walking using hexamer primers. investigation into appropriate dye structures that provide adequate conjugation to the nucleic acid substrate; compatibility to DNA synthesis protocols; and compatibility with different DNA polymerases would be carried out.
Success of Phase l objectives would initially lead to the commercialization of additional lower cost alternatives to DNA sequencing via electrophoresis by using the near- infrared fluorescence detection capabilities of the Ll-COR Model 4000 DNA Sequencer. Subsequent success in Phase II would lead to the commercialization of improved DNA sequencing technology not necessarily limited to electrophoretic separation.