Single molecule DNA/RNA transport and Raman scattering readout in a coupled nanochannel/nanopore sequencing system.

Single molecule DNA/RNA transport and Raman Scattering readout in a couplednanochannel/nanopore sequencing system Armonica Technologies, Inc. is proposing to develop a novel, high-throughput, label-free, highly accurate, long-read DNA sequencing platform based on inexpensive nanoscale patterning and self- assembly. The platform consists of nanochannels (cross section dimensions of ~ 100 nm); tortuous (convoluted, 3D) nanopores formed by self-assembly of colloidal nanoparticles; nanoparticle barriers placed across the nanochannels; and a metal-insulator-metal (MIM) field enhancement structure atop the nanochannel roof. In operation, single- stranded- or double-stranded-DNA is partially stretched into a linear configuration in the nanochannels, is blocked at barriers incorporated into the channels and forced (by electric field) to translocate through the tortuous nanopores in the roof. The MIM structure on the roof locally enhances the electromagnetic fields of applied laser sources allowing surface enhanced coherent anti-Stokes Raman scattering (SECARS) detection of individual bases as they pass through the electromagnetic hot spots, thus providing single base sensitivity and spatial localization. The distinct Raman spectra of the individual bases allow label-free sequencing. Optical detection allows massively parallel operation since the only requirement is separation of the pores by more than an optical wavelength, which is easily accomplished in the fabrication. An important feature of the platform is that the porous roofs allow introduction of oligonucleotides, small proteins, and DNA-binding/DNA processing enzymes, permitting optional manipulation and modification of the DNA in the nanochannels. The goals of this Phase I project are: to optimize the MIM structure for single base sensitivity and spatial localization; to demonstrate single base sensitivitySingle molecule DNA/RNA transport and Raman scattering readoutin a coupled nanochannel/nanopore sequencing system. Rapid, label-free, highly accurate, long-read DNA sequencing has important implications for genomic and medical applications. A novel nanostructured platform consisting of nanochannels, tortuous (3D convolved) nanopores, nanopore barriers and metal (plasmonic/metamaterial) antennas is proposed allowing massively parallel optical readout with dramatically faster throughput and improved accuracy than current technologies. Readout of the DNA bases is by label-free, surface-enhanced coherenet anti-Stokes Raman scattering, a highly specific process that uniquely identifies the DNA bases including epigenetic and isotopic variations, allowing sequencing of cellular DNA with minimal pre-processing.