Fast DNA Sequencing Using Near-field Microwave Sensors

在生命系统中，DNA是将信息从父母传递给孩子的核酸。确定四种携带信息的碱基（分别表示为A、C、G、T）的顺序称为“排序”。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20年前人类基因组首次测序的开创性工作以来，测序技术取得了巨大进步，大大减少了时间和复杂性。便携式测序设备现已商业化，对于西非埃博拉病毒的现场监测和快速识别SARS-CoV-2 （covid - 19）变体等至关重要。这些便携式设备是基于溶解离子（带电原子）通过一个被称为“纳米孔”的小孔的运动，其尺寸约为几纳米，即一米的十亿分之一。如果DNA链存在，它们也可以通过孔流动，暂时阻止离子的流动。构成DNA的四种碱基中的每一种都以略微不同的方式改变着离子流，因此，通过监测离子流随时间的变化，就有可能确定DNA中碱基的序列。纳米孔测序正在彻底改变我们对DNA进行测序的方式，但存在一些与离子电流方法基本相关的局限性。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，因此不可能实时读取序列。相反，必须使用复杂的基于酶的机制来减缓DNA的转运。在这个项目中，我们希望通过结合固态纳米孔和一种识别DNA链内四种碱基的新方法来实现实时测序率的革命性变化。为此，我们将使用微波——以千兆赫频率振荡的电磁波。微波是移动电话、wi-fi和蓝牙网络以及GPS卫星中用于传输大量信息的信息和通信技术的核心。微波也与物质相互作用，可以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原子精确的纳米制造和高频电子提供的测量精度。该装置将由一个原子级薄的导体（石墨烯）组成，形状像一个领结，中间有一个小间隙。导体充当波导，使微波在传感器的两端之间传播。领结的中心将小心翼翼地与纳米孔对齐，这样，当DNA通过孔时，它就会与领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）中的每一种碱基对传播的微波产生不同的传输和反射，从而使碱基序列能够被读取。这种方法用快速通信工程技术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，其速度有可能提高1000倍。开发的传感器技术将具有测序之外的功能，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技术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.