Abstract
State-of-the-art nanopore sequencing enables rapid and real-time identification of novel pathogens, which has wide application in various research areas and is an emerging diagnostic tool for infectious diseases including COVID-19. Nanopore translocation enables de novo sequencing with long reads (> 10 kb) of novel genomes, which has advantages over existing short-read sequencing technologies. Biological nanopore sequencing has already achieved success as a technology platform but it is sensitive to empirical factors such as pH and temperature. Alternatively, ångström- and nano-scale solid-state nanopores, especially those based on two-dimensional (2D) membranes, are promising next-generation technologies as they can surpass biological nanopores in the variety of membrane materials, ease of defining pore morphology, higher nucleotide detection sensitivity, and facilitation of novel and hybrid sequencing modalities. Since the discovery of graphene, atomically-thin 2D materials have shown immense potential for the fabrication of nanopores with well-defined geometry, rendering them viable candidates for nanopore sequencing membranes. Here, we review recent progress and future development trends of 2D materials and their ångström- and nano-scale pore-based nucleic acid (NA) sequencing including fabrication techniques and current and emerging sequencing modalities. In addition, we discuss the current challenges of translocation-based nanopore sequencing and provide an outlook on promising future research directions.
Highlights
Emerging nanopore translocation technologies are promising routes for rapid and efficient genetic identification and sequencing of novel pathogens, a prerequisite for public health responses to emerging infectious diseases, and the development of targeted therapeutics and vaccines
The COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, a positive single-stranded RNA virus) has created an unprecedented demand for genetic sequencing and testing
Oxford Nanopore Technologies (ONT), which is a commercial front-runner in translocationbased sequencers, introduced a kit for their MinION system for detecting SARS-CoV-2 by combining nanopore translocation technology with LAMP to validate results from LAMP, since it is prone to false-positives [2]
Summary
Emerging nanopore translocation technologies are promising routes for rapid and efficient genetic identification and sequencing of novel pathogens, a prerequisite for public health responses to emerging infectious diseases, and the development of targeted therapeutics and vaccines. TCIM has high access resistance that makes the sensing length of nanopore larger compared to the actual membrane thickness To overcome these challenges, an alternative or complementary modality is to measure the in-plane transverse current (TCS) during NA translocation, which is modulated by the changes in the local density of states near the nanopore, in order to identify individual nucleotides [50]. The output conductance and the SNR depend on various experimental conditions including the dynamic conformational and charge states of the target NA, the electrolyte concentration, solution temperature, bias voltage, pH, bubble formation in the nanopore channel, nanopore size, morphology and chemical functionalization or presence of dangling bonds of nanopore surfaces [62]–[64] As discussed, these sources of noise in the output conductance require appropriate modulation and control to achieve the highest SNR, ultimate spatial-temporal resolution, and error-free nanopore sequencing, which warrants further research. These 2D material heterostructures have been explored primarily via computational modelling, and there exist many 2D materials combinations and heterostructure permutations which exhibit immense potential for future NA sequencing architectures
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