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: 10482189
• 负责人: Steven Brueck
• 金额: $ 94.39万
• 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/10482189
• 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; Preparation; Process; Protocols documentation; RNA; RNA Transport; Sampling; Signal Transduction; Silicon Dioxide; 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; lithography; monolayer; 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传输和拉曼测序技术 在耦合的纳米通道/纳米孔系统中散射读数。 抽象的 Armonica Technologies，Inc。提议开发一种新颖，高通量，无标签，高度 基于廉价的纳米级图案和自我的准确，长阅读的DNA测序平台 集会。该平台由纳米通道组成（约100nm的横截面尺寸）；曲折 （复杂的3D）纳米孔由胶体纳米颗粒的自组装形成；纳米颗粒屏障 放置在纳米通道上；以及在 纳米通道屋顶。在运行中，单链或双链DNA部分伸展到 纳米通道中的线性构型在融合到通道并强迫的障碍物中被阻塞 （通过电场）通过屋顶上的曲折纳米孔转移。屋顶上的MIM结构 局部增强了施加激光源的电磁场，使表面增强了 反stokes拉曼散射（secars）在单个基地通过时检测 电磁热点，从而提供了单个碱基灵敏度和空间定位。独特的 单个碱基和表观遗传变体的拉曼光谱允许无标签的测序。光学的 检测允许大规模平行操作，因为唯一的要求是通过 不仅仅是光学波长，在制造中很容易完成。一个重要特征的 平台是多孔屋顶允许引入寡核苷酸，小蛋白质和DNA- 结合/DNA处理酶，允许可选操作并修改DNA 纳米通道。该阶段项目的目标是：制定用于电泳控制的协议 ssDNA易位；为了设计结构以确保ssDNA经过MIM热点；到 序列ssDNA的一小部分并评估错误率；并开发平行的光学读数，AI 分析数据和适当的存储协议。