Label-free Real-time Single-molecule Assay Platform for Genomic Identification

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Clinical presentation, particularly early in the course of disease, is only rarely pathognomonic of infection with a specific infectious agent. As a result, diagnosis is complex with many different organisms causing similar symptoms. Given that effective intervention requires accurate diagnosis and that the probability of success diminishes over time, tests that enable rapid, efficient differential diagnosis have potential to decrease morbidity, mortality, and social and economic costs of infectious diseases. Polymerase chain reaction (PCR) is not well suited to highly multiplexed microbiological analyses because primer interactions can reduce sensitivity and the repertoire of reporter systems is typically limited to 10 to 20 targets. DNA microarrays allow extensive multiplexing but existing assays are less sensitive than agent-specific PCR and require amplification, fluorescent labeling and several hours for processing. Next generation sequencing has unlimited multiplex potential. However, current platforms require hours to days for sample processing and bioinformatic analysis and are too complex for most point-of-care applications. In this project we will develop a single-molecule field-effect transistor (smFET) diagnostic assay platform. This application draws on our recent work, in which we have shown that the conductance of a carbon nanotube with a single covalently tethered DNA probe molecule is exquisitely sensitive to the increased charge that results from hybridization of a complementary DNA strand. smFET arrays on active complementary metal-oxide-semiconductor (CMOS) substrates will allow genomic materials to be assayed to concentrations approaching 1 fM (or 600 molecule per mL), comparable to qPCR, but while allowing multiplexing comparable to microarrays. We will specifically apply this technology to a genomic diagnostic platform that will allow efficient, low-cost differential diagnosis of infectious diseases. Our objectives we will be to optimize and develop the sensor to detect target concentration as low as 1 fM and develop approaches to distinguish mismatches through analysis of binding kinetics; integrate these devices onto CMOS measurement substrates, further improving electronic performance and allowing parallel multiplexing; test the platform with clinical samples in a staged strategy that begins in minimal biocontainment with nucleic acid templates, proceeds to work with potentially infectious materials in biocontainment; reduce the form factor for the device to that of a portable USB stick; and build software and bioinformatics infrastructure to support this platform for deployment in the field and clinics.