Carbon Nanotubes: A New Synthetic Nanopore for Sequencing

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DESCRIPTION (provided by applicant): Nanopore sequencing offers the possibility of rapid single molecule sequencing with long reads, almost no sample preparation, and direct electronic readout from a small, computer-chip-like device. Nanopores are orifices that are so small that electrophoretic translocation of DNA through them necessarily occurs one base at a time. All nanopores require some means of localizing DNA with atomic precision as well as controlling its speed of translocation through the pore. Here, we introduce an entirely new type of nanopore for the DNA translocation, the single walled carbon nanotube (SWCNT). SWCNTs are relatively homogeneous on an atomic scale, easy to manufacture with no special nanofabrication, and can form excellent electrodes, simplifying tunneling readout and opening the possibility of electrochemical readout. Their high aspect ratio (channel length/channel diameter) might permit trapping of the DNA in the tube, opening a new avenue for control of translocation speed. Molecular dynamics simulations have predicted that single-stranded DNA can be driven through a 2 nm diameter SWCNT by an electric field. We have confirmed this prediction experimentally, building devices in which a single SWCNT connects two fluid reservoirs and using PCR to verify DNA translocation. Arizona State University will direct the project and focus on device fabrication and DNA translocation. Oak Ridge National Laboratory will focus on multiscale modeling of ion and DNA transport through SWCNTs. Columbia University will focus on the construction of nm-scale gaps in SWCNTs. At the end of the two-year project we will: (a) Have developed robust device fabrication procedures and made devices available to the research community; (b) We will have obtained an understanding of the factors controlling the transport of ions and DNA through the tubes; (c) We will have identified factors that affect the speed of DNA translocation and the length of polymers that can be passed in one read; and (d) We will have built prototype devices in which a tunnel gap is integrated into a single SWCNT nanopore device. These developments should accelerate development of nanopore technology towards the production of a cheap, fast, and reliable DNA sequencing chip. PUBLIC HEALTH RELEVANCE: If successful, the new technology could enable ultra-low cost, single molecule sequencing with long reads, making whole-genome studies available to the general population. Making a search of whole genomes for rare variants economically feasible has many implications for medicine.