Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA.
Microsoft Research, Redmond, WA, USA.
Nat Commun. 2022 Aug 20;13(1):4904. doi: 10.1038/s41467-022-32526-3.
DNA has emerged as a powerful substrate for programming information processing machines at the nanoscale. Among the DNA computing primitives used today, DNA strand displacement (DSD) is arguably the most popular, with DSD-based circuit applications ranging from disease diagnostics to molecular artificial neural networks. The outputs of DSD circuits are generally read using fluorescence spectroscopy. However, due to the spectral overlap of typical small-molecule fluorescent reporters, the number of unique outputs that can be detected in parallel is limited, requiring complex optical setups or spatial isolation of reactions to make output bandwidths scalable. Here, we present a multiplexable sequencing-free readout method that enables real-time, kinetic measurement of DSD circuit activity through highly parallel, direct detection of barcoded output strands using nanopore sensor array technology (Oxford Nanopore Technologies' MinION device). These results increase DSD output bandwidth by an order of magnitude over what is currently feasible with fluorescence spectroscopy.
DNA 已成为在纳米尺度上对信息处理机器进行编程的强大基质。在当今使用的 DNA 计算原语中，DNA 链置换 (DSD) 可以说是最受欢迎的，基于 DSD 的电路应用范围从疾病诊断到分子人工神经网络。DSD 电路的输出通常使用荧光光谱法读取。然而，由于典型小分子荧光报告器的光谱重叠，可同时检测到的独特输出数量有限，需要复杂的光学设置或反应的空间隔离才能使输出带宽可扩展。在这里，我们提出了一种可复用的无测序读出方法，该方法通过使用纳米孔传感器阵列技术（Oxford Nanopore Technologies' MinION 设备）对条形码输出链进行高度平行的直接检测，实现了 DSD 电路活性的实时、动力学测量。这些结果使 DSD 输出带宽比目前使用荧光光谱法可行的带宽提高了一个数量级。
