Fast DNA Sequencing Using Near-field Microwave Sensors
Lead Research Organisation:
University College London
Department Name: London Centre for Nanotechnology
Abstract
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.
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.
Technical Summary
This project aims to demonstrate a fundamentally novel approach for single-molecule sensing based on the interaction of molecules with electromagnetic fields oscillating at microwave frequencies, an area where no preliminary data exists. Microwaves interact with molecules and compounds and can be used for molecular "fingerprinting". By coupling a microwave source to a suitable aperture (tip), it is possible to push this interaction several orders of magnitude below the diffraction limit, enabling probing down to single-molecule level, in the so-called near-field regime.
By realising atomically-thin, planar conductive tips encapsulated between two insulating layers precisely aligned with a nanopore, we aim to sequence unamplified DNA by probing individual bases via their interaction with the highly localised electromagnetic fields produced by the tips. Little is known of the electromagnetic properties of individual DNA bases at microwave frequencies, however theoretical studies based on DFT suggest that each of the four bases forming the DNA has a different polarizability (with G>A>T>C), due to deformability of charge distribution.
The sensor will operate at frequencies up to 20 GHz, i.e. oscillating at ~4 orders of magnitude faster than the translocation speed of the DNA bases (~1 MHz), potentially enabling real-time sequencing and avoiding the complexities of an enzyme-base slowing system. This single proof-of-concept design has the potential to yield transformative improvements in DNA sequencing accuracy and speed and lends itself to many possible modalities and applications of single-molecule sensing, including, for instance, of peptides - thus it has the potential to be a platform for next-generation tools.
By realising atomically-thin, planar conductive tips encapsulated between two insulating layers precisely aligned with a nanopore, we aim to sequence unamplified DNA by probing individual bases via their interaction with the highly localised electromagnetic fields produced by the tips. Little is known of the electromagnetic properties of individual DNA bases at microwave frequencies, however theoretical studies based on DFT suggest that each of the four bases forming the DNA has a different polarizability (with G>A>T>C), due to deformability of charge distribution.
The sensor will operate at frequencies up to 20 GHz, i.e. oscillating at ~4 orders of magnitude faster than the translocation speed of the DNA bases (~1 MHz), potentially enabling real-time sequencing and avoiding the complexities of an enzyme-base slowing system. This single proof-of-concept design has the potential to yield transformative improvements in DNA sequencing accuracy and speed and lends itself to many possible modalities and applications of single-molecule sensing, including, for instance, of peptides - thus it has the potential to be a platform for next-generation tools.