Single molecule DNA/RNA sequencing technology based on a parallel Raman scattering readout in a coupled nanochannel/nanopore system

基于耦合纳米通道/纳米孔系统中并行拉曼散射读数的单分子 DNA/RNA 测序技术

• 批准号: 10682588
• 负责人: Steven Brueck
• 金额: $ 90.88万
• 依托单位: ARMONICA TECHNOLOGIES, INC.
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-03-17 至 2024-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10682588
• 关键词: 3-Dimensional; Adenine; Algorithms; Bacteriophage lambda; Behavior; Binding Proteins; Characteristics; Chemicals; Coupled; Cytosine; DNA; DNA Binding; DNA Damage; DNA Modification Process; DNA sequencing; Data Analyses; Data Storage and Retrieval; Deposition; Detection; Development; Dimensions; Electromagnetic Fields; Electromagnetics; Engineering; Ensure; Enzymes; Epigenetic Process; Film; Genomics; Goals; Grant; Hot Spot; Individual; Isotopes; Label; Lasers; Massive Parallel Sequencing; Measurement; Medical; Metals; Methylation; Modification; Molecular; Motion; Movement; Nanochip Analytical Device; Nanoporous; Nanostructures; Oligonucleotides; Optics; Particle Size; Pattern; Phase; Porosity; Preparation; Process; Protocols documentation; RNA; RNA Transport; Sampling; Signal Transduction; Silicon Dioxide; Single-Stranded DNA; Small Business Innovation Research Grant; Source; Speed; Stretching; Structure; Surface; System; Techniques; Technology; Time; Variant; atomic layer deposition; base; benzonitrile; colloidal nanoparticle; design; ds-DNA; electric field; fabrication; lithography; nanochannel; nanoparticle; nanopore; nanoscale; novel; operation; plasmonics; response; self assembly; sequencing platform; single molecule; transcriptome sequencing; vapor

Single molecule DNA/RNA transport and Raman sequencing technology based on parallel Raman scattering readout in a coupled nanochannel/nanopore system. Abstract 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 ~ 100nm); 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 and epigenetic variants 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, 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 II project are: to develop a protocol for electrophoretic control of the ssDNA translocation; to engineer the structure to ensurethat the ssDNA passes the MIM hot spot; to sequence a short section of ssDNA and evaluate error rates; and to develop parallel optical readout, AI analysis of the data and appropriate storage protocol.

基于平行拉曼的单分子DNA/RNA转运和拉曼测序技术