Fast DNA Sequencing Using Near-field Microwave Sensors

DNA是在生命系统中将信息从父母传递给孩子的核酸。确定四个携带信息的碱基（表示为A、C、G、T）的顺序被称为“测序”。这种测序是现代分子生物学和遗传流行病学的核心，在诊断和精准医学方面具有巨大的应用潜力。自从大约20年前人类基因组首次测序的开创性工作以来，测序技术已经取得了巨大的进步，大大减少了时间和复杂性。便携式测序设备现已上市，并已成为西非埃博拉病毒现场监测和SARS-CoV-2（COVID-19）变种快速鉴定等工作的基础，这些便携式设备基于溶解离子（带电原子）通过称为“纳米孔”的小孔的运动，纳米孔的尺寸约为几纳米，即十亿分之一米。如果DNA链存在，它们也可以流过孔，暂时阻止离子的流动。形成DNA的四种碱基中的每一种都以略微不同的方式改变离子流，因此，通过监测离子流如何随时间变化，可以确定DNA内碱基的序列。纳米孔测序正在彻底改变我们对DNA进行测序的方式，但受到一些限制，这些限制从根本上与离子电流方法有关。特别是，尽管DNA可以以高速（每秒约100万个碱基）通过孔，但不可能如此快速地监测离子的运动，因此不可能在真实的时间内读取序列。相反，必须使用复杂的基于酶的机制来减缓DNA的传输。在这个项目中，我们希望通过将固态纳米孔与识别DNA链内四种碱基的新方法相结合，实现实时测序速率的变革。为此，我们将使用微波-以GHz频率振荡的电磁波。微波是移动的电话、wi-fi和蓝牙网络以及全球定位系统卫星中用于携带大量信息的信息和通信技术的核心。微波还可以与物质相互作用，通过测量分子独特的电磁指纹来探测分子。我们提出的传感器将结合联合收割机原子精度的纳米纤维与高频电子提供的测量精度。该设备将由一个原子级薄的导体（石墨烯）组成，形状像一个蝴蝶结，在其中心有一个小间隙。导体充当波导，使微波能够在传感器的两端之间传播。蝴蝶结的中心将与纳米孔仔细对齐，这样，当DNA通过孔时，它与蝴蝶结尖端形成的电磁场相互作用。我们希望构成DNA的四种碱基（A、C、G和T）中的每一种都能引起传播微波的不同透射和反射，从而使碱基序列得以读取。这种方法取代了目前用于纳米孔传感的缓慢的，基于离子运动的电化学与快速通信工程技术，具有1000倍的速度增加的潜力。开发的传感器技术将具有超越测序的能力，因为它可以应用于分析与生物化学和医学相关的其他分子。由于我们的传感器与电子芯片制造技术的兼容性以及微波电子器件在无线通信中的普遍使用，我们设想与现有技术无缝集成，以实现便携式测序和传感工具。

DNA is the nucleic acid that passes information from parent to child in living systems. Determining the order of the four information-carrying bases, (denoted A,C,G,T) is known as "sequencing". Such sequencing is at the core of modern molecular biology and genetic epidemiology and has huge potential for applications in diagnosis and precision medicine. Since the pioneering work that led to the first sequencing of the human genome about 20 years ago, sequencing technology has made enormous progress, significantly reducing time and complexity. Portable sequencing devices are now commercially available and have been fundamental, for example, for field-surveillance of Ebola virus in West Africa and rapid identification of SARS-CoV-2 (COVID19) variants.These portable devices are based on the motion of dissolved ions (charged atoms) through a tiny hole called a "nanopore", whose dimensions are in the order of a few nanometers, i.e. billionths of a metre. If DNA strands are present, they can also be made to flow through the pore, temporarily blocking the flow of ions. Each of the four bases forming the DNA modifies the ion flow in a slightly different way and therefore, by monitoring how the flow of ions changes over time it is possible to determine the sequence of the bases within the DNA. Nanopore sequencing is revolutionising the way we sequence DNA, but suffers from some limitations which are fundamentally linked to the ion current approach. In particular, although DNA can pass through the pore at a high speed (~1 million bases per second) it is not possible to monitor the motion of ions this quickly and therefore it is not possible to read the sequence in real time. Instead complex enzyme-based mechanisms must be used to slow down the DNA transit.In this project, we hope to achieve a transformative change in real-time sequencing rates by combining solid-state nanopores with a new way of identifying the four bases within DNA strands. To do so, we will use microwaves - electromagnetic waves oscillating at GHz frequencies. Microwaves are at the core of the information and communication technologies used in mobile phones, wi-fi and Bluetooth networks and GPS satellites to carry large amounts of information. Microwaves also interact with matter and can be used to probe molecules by measuring their unique electromagnetic fingerprints. Our proposed sensors will combine atomically-precise nanofabrication with the measurement accuracy offered by high frequency electronics. The device will consist of an atomically-thin conductor (graphene) shaped as a bowtie with a small gap at its centre. The conductor acts as a waveguide, enabling microwave propagation between the two ends of the sensor. The centre of the bowtie will be carefully aligned with a nanopore, so that, when DNA passes through the pore, it interacts with the electromagnetic field formed at the bowtie tips. We hope that each of the four bases forming the DNA (A, C, G and T) will cause different transmission and reflection of the propagating microwaves, allowing the sequence of bases to be read. This approach replaces the slow, ion-motion based electrochemistry currently used for nanopore sensing with fast communication-engineering technologies, with potential for a 1000-fold increase in speed.The sensor technology developed will have capabilities beyond sequencing, as it can be applied to analyse other molecules relevant for biochemistry and medicine. Thanks to the compatibility of our sensors with electronic chip fabrication technology and the ubiquitous use of microwave electronics for wireless communication, we envisage a seamless integration with already existing technology to realise portable sequencing and sensing tools.