Nanopore-based technologies beyond DNA sequencing

Ying, Yi‐Lun; Hu, Zheng‐Li; Zhang, Shengli; Qing, Yujia; Fragasso, Alessio; Maglia, Giovanni; Meller, A.; Bayley, Hagan; Dekker, Cees; Long, Yi‐Tao

doi:10.1038/s41565-022-01193-2

Cited by 196 publications

(176 citation statements)

References 150 publications

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“…[47][48][49][50] The most successful application of nanopore technology, however, is in the field nucleic acid sequencing, as demonstrated by the commercialization of nanopore sequencing devices from Oxford Nanopore Technologies Ltd. 51 This technology relies on the integration of biological nanopores with advanced electronics and some recent applications of biological nanopores were reviewed recently. 11,52 In this section, we highlight recent work enabling high-throughput single entity detection with nanopores and implications for single-entity research. We present key aspects to allow for highthroughput analysis and discuss the integration of nanopores with microfluidic/optical setups, and the application of machine-learning algorithms to process nanopore data and to enable high-resolution single-entity analysis.…”

Section: Nanopore Working Principlementioning

confidence: 99%

“…They exploit the high-throughput and selective transport and screening of chemical species offered by the electric field and molecular confinement in nanopores and nanopipettes. While scholarly reviews of nanopore electrochemistry have been published recently, [10][11][12][13] we highlight here the present state-of-the art and the importance of nanopores as a platform that provides high-throughput electroanalysis. Electrochemical nanoimpacts is another platform providing high-throughput electroanalysis at the level of individual nanoparticles (NPs).…”

Section: Introductionmentioning

confidence: 99%

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The new era of high throughput nanoelectrochemistry

Valavanis

Ciocci

et al. 2022

Preprint

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Scanning electrochemical probe microscopies (SEPMs) have played a key role in advancing small-scale electrochemistry. SEPMs use an electrochemical probe (micro/nanoelectrode or pipet) to quantify and map local interfacial fluxes of electroactive species and have found increasingly wide applications. Our contribution to the Fundamental and Applied Reviews in Analytical Chemistry 2019 discussed how advances in SEPMs converged towards nanoscale electrochemical mapping. This inflection in experimental capability has opened up myriad opportunities for SEPMs in many types of systems, from material and energy sciences to the life sciences. The enhancement in the spatial resolution of imaging techniques, and instrumental developments, have resulted in significant increases in the size of electrochemical datasets from a typical experiment and served to speed up measurement throughput. Next generation nanoelectrochemistry will thus see an emphasis on “big data”, its analysis, storage and curation, high throughput analysis and parallelization, “intelligent” instruments and experiments, active control of nanoscale systems, and the integration of nanoelectrochemistry and nanoscale micro(spectro)scopy. For this review article, we focus on recent advances in frontier nanoscale electrochemistry, analysis and imaging techniques that are already addressing some of these key targets, and are well-placed to embrace other aspects in the near future. Our goal is to provide an overview of the present state-of-the-art in high throughput nanoelectrochemistry and imaging, and signpost promising new avenues for nanoscale electrochemical methods.

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Section: Nanopore Working Principlementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

The new era of high throughput nanoelectrochemistry

Valavanis

Ciocci

et al. 2022

Preprint

View full text Add to dashboard Cite

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“…Over the past decade, nanopores have enabled real-time, single-molecule analysis of small molecules, proteins, or nucleic acids. − For example, accurate, ultralong genome reads provided by the MinION (Oxford Nanopore Technologies) sequencer have become commercially available . Nearly all of today’s nanopore implementations can be categorized into two types: synthetic and biological. , The bulk of synthetic nanopores are solid-state nanopores, typically made by beam milling on silicon chips to achieve pores with controllable geometry .…”

Section: Introductionmentioning

confidence: 99%

Functionalized DNA-Origami-Protein Nanopores Generate Large Transmembrane Channels with Programmable Size-Selectivity

et al. 2022

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The DNA-origami technique has enabled the engineering of transmembrane nanopores with programmable size and functionality, showing promise in building biosensors and synthetic cells. However, it remains challenging to build large (>10 nm), functionalizable nanopores that spontaneously perforate lipid membranes. Here, we take advantage of pneumolysin (PLY), a bacterial toxin that potently forms wide ring-like channels on cell membranes, to construct hybrid DNA−protein nanopores. This PLY-DNA-origami complex, in which a DNA-origami ring corrals up to 48 copies of PLY, targets the cholesterol-rich membranes of liposomes and red blood cells, readily forming uniformly sized pores with an average inner diameter of ∼22 nm. Such hybrid nanopores facilitate the exchange of macromolecules between perforated liposomes and their environment, with the exchange rate negatively correlating with the macromolecule size (diameters of gyration: 8−22 nm). Additionally, the DNA ring can be decorated with intrinsically disordered nucleoporins to further restrict the diffusion of traversing molecules, highlighting the programmability of the hybrid nanopores. PLY-DNA pores provide an enabling biophysical tool for studying the cross-membrane translocation of ultralarge molecules and open new opportunities for analytical chemistry, synthetic biology, and nanomedicine.

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“…A survey of synthesis methods of lipid bilayer membranes can be found in [ 3 ]. This research path also includes functionalization mechanisms mimicking those of biological membranes—for instance incorporating artificial ion channels [ 4 ], ion pumps [ 5 ], nuclear pore complexes [ 6 , 7 ], etc. Albeit enormous advances have been achieved in this area, they stopped short in front of the most formidable task of them all: how to create a new synthetic living cell out of the non-living building blocks—“synthetic biogenesis” [ 8 ].…”

Section: Introductionmentioning

confidence: 99%

Bio-Inspired Nanomembranes as Building Blocks for Nanophotonics, Plasmonics and Metamaterials

2022

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Nanomembranes are the most widespread building block of life, as they encompass cell and organelle walls. Their synthetic counterparts can be described as freestanding or free-floating structures thinner than 100 nm, down to monatomic/monomolecular thickness and with giant lateral aspect ratios. The structural confinement to quasi-2D sheets causes a multitude of unexpected and often counterintuitive properties. This has resulted in synthetic nanomembranes transiting from a mere scientific curiosity to a position where novel applications are emerging at an ever-accelerating pace. Among wide fields where their use has proven itself most fruitful are nano-optics and nanophotonics. However, the authors are unaware of a review covering the nanomembrane use in these important fields. Here, we present an attempt to survey the state of the art of nanomembranes in nanophotonics, including photonic crystals, plasmonics, metasurfaces, and nanoantennas, with an accent on some advancements that appeared within the last few years. Unlimited by the Nature toolbox, we can utilize a practically infinite number of available materials and methods and reach numerous properties not met in biological membranes. Thus, nanomembranes in nano-optics can be described as real metastructures, exceeding the known materials and opening pathways to a wide variety of novel functionalities.

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Nanopore-based technologies beyond DNA sequencing

Cited by 196 publications

References 150 publications

The new era of high throughput nanoelectrochemistry

The new era of high throughput nanoelectrochemistry

Functionalized DNA-Origami-Protein Nanopores Generate Large Transmembrane Channels with Programmable Size-Selectivity

Bio-Inspired Nanomembranes as Building Blocks for Nanophotonics, Plasmonics and Metamaterials

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