Artificial Nanotube Gels for Mutation Detection

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DESCRIPTION (provided by applicant): Our vision is to combine nanotechnology with proven genetic screening technology to provide non-invasive, low cost, rapid screening for specific molecular signatures of cancer. Highly sensitive and specific, DOVAM-S (Detection of Virtually All Mutations-SSCP) is capable of screening several human genes for mutations with virtually 100% accuracy. The key technology to be demonstrated is a nanofabricated, electrophoretic microdevice for detecting mutations and polymorphisms of virtually all types. With this technology, cost-effective screening for cancer predisposition could be implemented in the relatively near term. Based on the unique properties of carbon nanotubes, we envision an integrated nano-DOVAM-S system with significantly reduced reagent volumes, shortened amplification and separation times, and automated readout and interpretation of results. In this proposal, we present this vision, and the necessary steps toward a proof-of-concept demonstration: first proving that SSCP is possible with carbon nanotube arrays, followed by protocol development and comparison with standard DOVAM-S in clinical mutation screening experiments. Other efforts to develop on-chip DNA analysis technology lack the essential advantages that distinguish DOVAM-S from competing approaches to mutation screening. These are a virtually 100% detection rate and the ability to multiplex samples. In order to be effective, mutation screening by DOVAM-S requires electrophoretic separation of single- stranded DNA with and without mutations. Our approach is to use carbon nariotubes as a solid-state nanometer-scale sieve for electrophoretic separation of single-strand DNA, replacing the cross-linked polymers used in conventional gel electrophoresis. Competing efforts to provide on-chip DNA analysis retain the use of cross-linked polymers, and many are based on hybridization reactions, which cannot attain the 100% detection of mutations that has been demonstrated in the DOVAM-S approach advocated here. Nano-DOVAM- S will be validated using the human factor VIII and IX genes and the ATM gene, mutated in certain cancers.