The challenge when employing solid-state nanopores as single-molecule sensors in a given assay is the specificity of the ionic current signal during the translocation of target molecules. Here we present the capture and translocation characteristics of short structurally defined DNA molecules that could serve as effective surrogate labels in biosensing applications. We produced T-shaped or Y-shaped DNA molecules with a 50 bp double-stranded DNA (dsDNA) backbone and a 25 bp dsDNA branch in the middle, as improved labels over short linear DNA fragments. We show that molecular topologies can be distinguished from linear DNA by analyzing ionic current blockades produced as these DNA labels translocate through nanopores fabricated by controlled breakdown on 10-nm-thick SiN membranes and ranging in diameter from 4 to 10 nm. Event signatures are shown to be a direct result of the structure of the label and lead to an increased signal-to-noise ratio over that of short linear dsDNA, in addition to well resolved dwell times for the pore size in this range. These results show that structurally defined branched DNA molecules can be robustly detected for a broad range of pore size, and thus represent promising candidates as surrogate labels in a variety of nanopore-based molecular or immunoassay schemes.

中文翻译：

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固态纳米孔中短分支DNA标记的捕获和转运特性

在给定的测定中采用固态纳米孔作为单分子传感器时的挑战是靶分子移位过程中离子电流信号的特异性。在这里，我们介绍了可以在生物传感应用中充当有效替代标记的短结构定义的DNA分子的捕获和转运特性。我们生产的T形或Y形DNA分子具有50 bp的双链DNA（dsDNA）骨架和中间的25 bp dsDNA分支，作为对短线性DNA片段的改良标记。我们表明，通过分析这些DNA标记通过在10 nm厚的SiN膜上的受控击穿而制造的纳米孔，其直径从4到10 nm不等，所形成的纳米孔易位，可以通过分析产生的离子电流阻断来将分子拓扑结构与线性DNA区分开。结果表明，事件签名是标记结构的直接结果，并且与短线性dsDNA相比，信噪比提高了，此外，该范围内孔径的驻留时间得到了很好的解决。这些结果表明，可以在很宽的孔径范围内稳健地检测到结构确定的分支DNA分子，因此在各种基于纳米孔的分子或免疫测定方案中，它们都有望作为替代标记。