Dept of Computer Science, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA 70148, USA.
BMC Bioinformatics. 2011 Oct 18;12 Suppl 10(Suppl 10):S21. doi: 10.1186/1471-2105-12-S10-S21.
Nanopore transduction detection (NTD) offers prospects for a number of highly sensitive and discriminative applications, including: (i) single nucleotide polymorphism (SNP) detection; (ii) targeted DNA re-sequencing; (iii) protein isoform assaying; and (iv) biosensing via antibody or aptamer coupled molecules. Nanopore event transduction involves single-molecule biophysics, engineered information flows, and nanopore cheminformatics. The NTD Nanoscope has seen limited use in the scientific community, however, due to lack of information about potential applications, and lack of availability for the device itself. Meta Logos Inc. is developing both pre-packaged device platforms and component-level (unassembled) kit platforms (the latter described here). In both cases a lipid bi-layer workstation is first established, then augmentations and operational protocols are provided to have a nanopore transduction detector. In this paper we provide an overview of the NTD Nanoscope applications and implementations. The NTD Nanoscope Kit, in particular, is a component-level reproduction of the standard NTD device used in previous research papers.
The NTD Nanoscope method is shown to functionalize a single nanopore with a channel current modulator that is designed to transduce events, such as binding to a specific target. To expedite set-up in new lab settings, the calibration and troubleshooting for the NTD Nanoscope kit components and signal processing software, the NTD Nanoscope Kit, is designed to include a set of test buffers and control molecules based on experiments described in previous NTD papers (the model systems briefly described in what follows). The description of the Server-interfacing for advanced signal processing support is also briefly mentioned.
SNP assaying, SNP discovery, DNA sequencing and RNA-seq methods are typically limited by the accuracy of the error rate of the enzymes involved, such as methods involving the polymerase chain reaction (PCR) enzyme. The NTD Nanoscope offers a means to obtain higher accuracy as it is a single-molecule method that does not inherently involve use of enzymes, using a functionalized nanopore instead.
纳米孔转导检测（NTD）为许多高度敏感和有区别的应用提供了前景，包括：（i）单核苷酸多态性（SNP）检测；（ii）靶向 DNA 重测序；（iii）蛋白质同工型分析；以及（iv）通过抗体或适体偶联分子进行生物传感。纳米孔事件转导涉及单分子生物物理学、工程信息流和纳米孔化学信息学。然而，由于缺乏关于潜在应用的信息，以及该设备本身的不可用性，NTD Nanoscope 在科学界的应用受到限制。Meta Logos Inc. 正在开发预包装的设备平台和组件级（未组装）试剂盒平台（此处描述后者）。在这两种情况下，首先建立脂质双层工作站，然后提供增强功能和操作协议，以获得纳米孔转导检测器。在本文中，我们提供了 NTD Nanoscope 应用和实现的概述。特别是 NTD Nanoscope 试剂盒是以前研究论文中使用的标准 NTD 设备的组件级复制品。
NTD Nanoscope 方法被证明可以用设计用于转导事件（例如与特定靶标结合）的通道电流调制器功能化单个纳米孔。为了加快新实验室环境中的设置，NTD Nanoscope 试剂盒组件和信号处理软件的校准和故障排除，NTD Nanoscope 试剂盒被设计为包括一组基于先前 NTD 论文中描述的实验的测试缓冲液和控制分子（下面简要描述的模型系统）。还简要提到了用于高级信号处理支持的服务器接口的描述。
SNP 分析、SNP 发现、DNA 测序和 RNA-seq 方法通常受到涉及的酶（例如涉及聚合酶链反应（PCR）酶的方法）的错误率的准确性限制。NTD Nanoscope 提供了一种获得更高准确性的方法，因为它是一种单分子方法，不固有地涉及使用酶，而是使用功能化的纳米孔。
