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 已成为纳米级信息处理机器编程的强大基质。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读取。然而，由于典型的小分子荧光报告基因的光谱重叠，可以并行检测的独特输出的数量是有限的，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，我们提出了一种多路复用的无测序读出方法，该方法可以通过高度并行的方式实时动态测量 DSD 电路活动，使用纳米孔传感器阵列技术（Oxford Nanopore Technologies 的 MinION 设备）直接检测条形码输出链。这些结果将 DSD 输出带宽增加了一个数量级，超过了目前荧光光谱法的可行带宽。