SEQ is developing single-molecule detection, identification, manipulation and chemistry capabilities for the purpose of creating a high-speed, low cost DNA sequencer. This sequencing method consists of the isolation and processive exonucleolytic digestion of individual, long (50 kb) strands of DNA. The cleaved nucleotides are immobilized on a surface, in order, and subsequently detected and identified. Importantly, and in contrast to other sequencing methods, SEQ's approach uses native DNA. The present application seeks funding for those aspects of the scheme that require additional research and invention prior to a proof-of-principle demonstration; these are: 1) nucleotide photophysics and photochemistry, 2) nucleotide-surface binding and its effect on nucleotide photophysics and chemistry, and 3) exonuclease processivity and its cleavage-time distribution. When integrated with the advanced engineering portions of the sequencing scheme, the capabilities represented by the accomplishment of the individual specific aims of this application will enable a native-DNA single molecule sequencer. At that time, resolution of the majority of the present uncertainties regarding the efficiency and economy of such a sequencer will be answerable.
