Programmable DNA Nanoswitch Sensing with Solid-State Nanopores

Sensing performance of solid-state
nanopores is limited by the
fast kinetics of small molecular targets. To address this challenge,
we translate the presence of a small target to a large conformational
change of a long polymer. In this work, we explore the performance
of solid-state nanopores for sensing the conformational states of
molecular nanoswitches assembled using the principles of DNA origami.
These programmable single-molecule switches show great potential in
molecular diagnostics and long-term information storage. We investigate
the translocation properties of linear and looped nanoswitch topologies
using nanopores fabricated in thin membranes, ultimately comparing
the performance of our nanopore platform for detecting the presence
of a DNA analogue to a sequence found in a Zika virus biomarker gene
with that of conventional gel electrophoresis. We found that our system
provides a high-throughput method for quantifying several target concentrations
within an order of magnitude by sensing only several hundred molecules
using electronics of moderate bandwidth that are conventionally used
in nanopore sensing systems.

固态纳米孔的传感性能受限于小分子目标的快速动力学。为应对此挑战，我们将小目标的检出转化为长聚合物的大构象变化。在本研究中，我们探讨了利用DNA折纸原理组装的分子纳米开关构象状态的固态纳米孔传感性能。这些可编程的单分子开关在分子诊断和长期信息存储方面展现出巨大的潜力。我们通过在薄膜中制备的纳米孔，研究了线性及环状纳米开关拓扑结构的转运特性，并最终将我们纳米孔平台检测DNA类似物存在的能力与传统的凝胶电泳方法进行了比较。我们发现，我们的系统通过仅感知数百个分子，便能够以高吞吐量方式量化数个数量级内的目标浓度，且使用的是在纳米孔传感系统中传统上广泛应用的、带宽适中的电子设备。