Solid-state nanopore sensors for nucleic acid analysis

Nanopore DNA analysis is an emerging technique that involves electrophoretically driving DNA molecules through a nano-scale pore in solution and monitoring the corresponding change in ionic pore current. This versatile approach permits the label-free, amplification-free analysis of charged polymers (single stranded DNA, double stranded DNA and RNA) ranging in length from single nucleotides to kilobase long genomic DNA fragments with subnanometer resolution. Recent advances in nanopores suggest that this low-cost, highly scalable technology could lend itself to the development of third generation DNA sequencing technologies, promising rapid and reliable sequencing of the human diploid genome for under $1000. Here, we report the development of versatile, nano-manufactured Al2O3 solid-state nanopores and nanopore arrays for rapid, label-free, single-molecule detection and analysis of DNA and protein. This nano-scale technology has proven to be reliable, affordable, and mass producible, and allows for integration with VLSI processes. A detailed characterization of nanopore performance in terms of electrical noise, mechanical robustness and materials analysis is provided, and the functionality of this technology in experimental DNA biophysics is explored. A framework for the application of this technology to medical diagnostics and sequencing is also presented. Specifically, studies involved the detection of DNA-protein complexes, a viable strategy in screening methylation patterns in panels of genes for early cancer detection, and the creation of lipid bilayer coated nanopore sensors, useful in creating hybrid biological/solid-state nanopores for DNA sequencing applications. The concept of a gated nanopore is also presented with preliminary results. The fabrication of this novel system has been enabled by the recent discovery of graphene, a highly versatile material with remarkable electrical and mechanical properties. Direct modulation of the nanopore conductance was observed through the application of potentials to the graphene gate. These exciting results suggest this technology could potentially be useful in slowing down or trapping a DNA molecule in the pore, thereby enabling solid-state nanopore sequencing