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.

基于并行拉曼的单分子DNA/RNA转运及拉曼测序技术 在耦合的纳米通道/纳米孔系统中的散射读出。 摘要 Armonica Technologies，Inc.提出开发一种新的，高通量，无标记，高度 基于廉价的纳米级图案化和自组装的精确、长读段DNA测序平台， 组装件.该平台由纳米通道（横截面尺寸约100 nm）组成;曲折 （回旋3D）通过胶体纳米颗粒的自组装形成的纳米孔;纳米颗粒屏障 金属-绝缘体-金属（MIM）场增强结构， 纳米通道屋顶在操作中，单链或双链DNA被部分拉伸成单链DNA。 纳米通道中的线性构型在结合到通道中的屏障处被阻断， (by电场）以移位通过顶部中的曲折纳米孔。屋顶上的MIM结构 局部增强所施加的激光源的电磁场， 反斯托克斯拉曼散射（SECARS）检测单个碱基，因为它们通过 电磁热点，从而提供单碱基灵敏度和空间定位。鲜明的 单个碱基和表观遗传变体的拉曼光谱允许无标记测序。光学 检测允许大规模并行操作，因为唯一的要求是通过 比光学波长更长，在制造中容易实现。的重要特征 平台的一个重要特点是，多孔屋顶允许引入寡核苷酸、小蛋白质和DNA- 结合/DNA加工酶，允许任选地操纵和修饰DNA中的DNA。 纳米通道该第二阶段项目的目标是：开发用于电泳控制的协议， ssDNA易位;设计结构以确保ssDNA通过MIM热点; 测序一小段ssDNA并评估错误率;并开发并行光学读出，AI 数据分析和适当的存储协议。