Data content for SI Figures in PLOS ONE paper "Nanopore-based Target Sequence Detection"

Abstract from the paper: The promise of portable diagnostic devices relies on three basic requirements: comparable sensitivity to established platforms, inexpensive manufacturing and cost of operations, and the ability to survive rugged field conditions. Solid state nanopores can meet all these requirements, but to achieve high manufacturing yields at low costs, assays must be tolerant to fabrication imperfections and to nanopore enlargement during operation. This paper presents a model for molecular engineering techniques that meets these goals with the aim of detecting target sequences within DNA. In contrast to methods that require precise geometries, we demonstrate detection using a range of pore geometries. As a result, our assay model tolerates any pore-forming method and in-situ pore enlargement. Using peptide nucleic acid (PNA) probes modified for conjugation with synthetic bulk-adding molecules, pores ranging 15-50 nm in diameter are shown to detect individual PNA-bound DNA. Detection of the CFTRDeltaF508 gene mutation, a codon deletion responsible for ~66% of all cystic fibrosis chromosomes, is demonstrated with a 26-36 nm pore size range by using a size-enhanced PNA probe. A mathematical framework for assessing the statistical significance of detection is also presented.论文摘要：便携式诊断设备的应用前景需满足三项核心要求：与成熟检测平台相当的灵敏度、低廉的制造成本与运营成本，以及可耐受严苛现场环境的能力。固态纳米孔（solid state nanopores）可满足上述所有要求，但为实现低成本下的高制造良率，检测分析方法必须能够耐受制造缺陷以及运行过程中的纳米孔孔径扩大问题。本文提出一种适配上述目标的分子工程技术模型，用于检测DNA内部的靶标序列。与依赖精确孔几何结构的现有方法不同，本研究展示了可通过一系列不同孔几何结构实现检测的方案。据此，本检测分析模型可兼容任意造孔方法与原位孔径扩大现象。本研究使用经修饰可与合成体积增容分子结合的肽核酸（peptide nucleic acid, PNA）探针，证实直径15~50 nm的纳米孔可检测单个结合了PNA的DNA分子。此外，本研究采用尺寸增容型PNA探针，在26~36 nm的孔径范围内实现了对CFTRΔF508基因突变的检测——该突变属于密码子缺失型突变，约占所有囊性纤维化染色体的66%。本研究同时提出了用于评估检测结果统计学显著性的数学框架。