Ångström- and Nano-scale Pore-Based Nucleic Acid Sequencing of Current and Emergent Pathogens

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.

A workflow for accurate metabarcoding using nanopore MinION sequencing

“…Given some of the weaknesses in RCA, exploration of other isothermal amplification procedures such as LAMP (Mori & Notomi, 2009; Shepherd et al., 2020), multiple displacement amplification (Hansen et al., 2018) or recombinase polymerase amplification (Donoso & Valenzuela, 2018) is recommended. ASHURE is not limited to the RCA workflow and can be adapted for these other protocols.…”

A Critical Review on the Sensing, Control, and Manipulation of Single Molecules on Optofluidic Devices

“…If a nanopore is made sensitive enough that it produces distinguishable current modulation as different bases of nucleic acids pass through the pore, it is possible to sequence the nucleic acids by analyzing the nanopore current trace, which is the core idea of nucleic acid sequencing [38,389] The principle of nanopore sequencing is illustrated in Figure 8b [389]. With the extensive efforts of numerous researchers around the world, it was feasible to develop a nucleic acid sequencing tool based on nanopores [380,390,391]. Nanopore-based nucleic acid sequencing is a vast topic, and readers are referred to explore the independent reviews on this topic for further details [17,380].…”

Plasmonic Photochemistry as a Tool to Prepare Metallic Nanopores with Controlled Diameter for Optimized Detection of Single Entities

“…It is important to stress that, although the preparation of a single nanopore with a diameter of a few nm has already been reported in the literature, [9,[56][57][58][59][60] the controllable preparation of a metallic (plasmonic) nanopore array with a diameter between tens of nm down to 5 nm is still very challenging. [61] The method proposed here enables a controlled diameter reduction of the nanopore (1 nm min −1 with Ag growth) both in single pore configuration and in arrays with arbitrary pores shapes and arrangements.…”