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| Open AccessHigh-throughput mechanical phenotyping and transcriptomics of single cells
The molecular system regulating cell surface mechanics remains largely unexplored at single-cell resolution. Here, the authors report a high-throughput single-cell assay, ELASTomics, which integrates mechanical phenotyping with unbiased transcriptomics.
- Akifumi Shiomi
- , Taikopaul Kaneko
- & Hirofumi Shintaku
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Article
| Open AccessRectifying artificial nanochannels with multiple interconvertible permeability states
Transmembrane channels have inspired the development of biomimetic channels. Here, the authors present a class of artificial nanochannels based on DNAzyme-functionalized glass nanopipettes to allow for the control of channel permeability.
- Ruocan Qian
- , Mansha Wu
- & Yi Lu
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Article
| Open AccessNanopore analysis of salvianolic acids in herbal medicines
Natural herbs, which contain pharmacologically active compounds, have been historically used as medicines but the analysis of their chemical components is time-consuming and complex. Here, the authors report a phenylboronic acid appended Mycobacterium smegmatis porin A (MspA) nanopore for sensing a variety of bioactive compounds based on salvianolic acid, without the need for sample separation or purification.
- Pingping Fan
- , Shanyu Zhang
- & Shuo Huang
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Article
| Open AccessNanopore analysis of cis-diols in fruits
Fruits contain a large variety of cis-diols but their rapid and direct analysis without complex sample pretreatment was not achieved. Here, the authors report a Mycobacterium smegmatis porin A nanopore modified with a phenylboronic acid adapter for recognition of 1,2-diphenols, alditols, α-hydroxy acids and saccharides in fruits.
- Pingping Fan
- , Zhenyuan Cao
- & Shuo Huang
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Article
| Open AccessSingle-molecule RNA sizing enables quantitative analysis of alternative transcription termination
The development of RNA technologies demands accurate assessment of transcript size and heterogeneity. Here, authors report a nanopore-based approach to study full-length RNA transcripts at the single-molecule level, identify premature transcription termination and study rolling-circle transcription.
- Gerardo Patiño-Guillén
- , Jovan Pešović
- & Ulrich Felix Keyser
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Article
| Open AccessHydrophobically gated memristive nanopores for neuromorphic applications
Designing efficient nanoscale and adaptable bioinspired memristors remains a challenge. Here, the authors develop a bioinspired hydrophobically gated memristive nanopore capable of learning, forgetting, and retaining memory through an electrowetting mechanism.
- Gonçalo Paulo
- , Ke Sun
- & Alberto Giacomello
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Article
| Open AccessMultiplexed detection of viral antigen and RNA using nanopore sensing and encoded molecular probes
Fast discrimination of SARS-CoV-2 variants in clinical samples remains a challenge. Here, authors report on single molecule nanopore sensing combined with DNA molecular probes to simultaneously detect various antigens and RNA mutations of SARS-CoV-2 variants in patient samples.
- Ren Ren
- , Shenglin Cai
- & Joshua B. Edel
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Article
| Open AccessEnzymatic synthesis and nanopore sequencing of 12-letter supernumerary DNA
Unnatural base pairing xenonucleic acids (XNAs) can be used to expand life’s alphabet beyond ATGC. Here, authors show strategies for enzymatic synthesis and next-generation nanopore sequencing of XNA base pairs for reading and writing 12-letter DNA (ATGCBSPZXKJV).
- Hinako Kawabe
- , Christopher A. Thomas
- & Jorge A. Marchand
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Article
| Open AccessFeasibility of an implantable bioreactor for renal cell therapy using silicon nanopore membranes
An implantable bioartificial kidney with a cell-containing bioreactor could be used to treat end-stage renal disease. Here the authors demonstrate the feasibility of an implantable bioreactor by maintaining human cell viability and functionality after implantation in a xenograft model.
- Eun Jung Kim
- , Caressa Chen
- & Shuvo Roy
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Article
| Open AccessStable trapping of multiple proteins at physiological conditions using nanoscale chambers with macromolecular gates
The possibility to trap biomolecules is important for analysing them by optical methods. Here we show how nanoscale chambers with macromolecular gates can be used to trap hundreds of proteins in a volume of one attoliter at physiological conditions without exposing them to any direct forces.
- Justas Svirelis
- , Zeynep Adali
- & Andreas Dahlin
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Article
| Open AccessStructure and dynamics of an archetypal DNA nanoarchitecture revealed via cryo-EM and molecular dynamics simulations
DNA can be folded into rationally designed, unique, and functional materials. Here the authors analyse an archetypal DNA nanoarchitecture with single particle cryo-electron microscopy and molecular dynamics simulations.
- Katya Ahmad
- , Abid Javed
- & Stefan Howorka
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Article
| Open AccessMoS2 nanopore identifies single amino acids with sub-1 Dalton resolution
Protein sequencing is one of the key aims of the nanopore field. Working toward this goal, here the authors report the direct identification of single amino acids in MoS2 nanopores with sub-1 Dalton resolution, as well as the discrimination of the amino acid isomers and amino acid phosphorylation.
- Fushi Wang
- , Chunxiao Zhao
- & Jiandong Feng
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Article
| Open AccessHigh-resolution discrimination of homologous and isomeric proteinogenic amino acids in nanopore sensors with ultrashort single-walled carbon nanotubes
Ultrashort single-walled carbon nanotubes inserted in lipid bilayers can be used as nanopore sensors. Here, the authors demonstrate the high-resolution discrimination of homologous and isomeric proteinogenic amino acids with such carbon-based nanopores.
- Weichao Peng
- , Shuaihu Yan
- & Yuliang Zhao
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Article
| Open AccessSwitchable biomimetic nanochannels for on-demand SO2 detection by light-controlled photochromism
Conventional nanochannel sensors are passively responsive and may be slowly damaged by analytes present in the environment before detection. Here, authors developed a light-controlled inert/active-switchable biomimetic nanochannel sensor to achieve SO2 on-demand detection and long-term preservation.
- Dan Zhang
- , Yongjie Sun
- & Xuanjun Zhang
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Article
| Open AccessSingle-molecule fingerprinting of protein-drug interaction using a funneled biological nanopore
Efficient screening of protein-drug interactions (PDIs) has been impeded by the limitations of current biophysical approaches. Here, the authors present a funneled YaxAB nanopore sensor which allows label-free, single-molecule detection of proteins and PDIs.
- Ki-Baek Jeong
- , Minju Ryu
- & Seung-Wook Chi
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Article
| Open AccessIdentification of tagged glycans with a protein nanopore
The structural complexity of glycans seriously challenges the currently available analytical methods. Here, the authors report the identification of glycan isomers, glycans with varying chain lengths, and distinct branched glycans, via a glycan derivatization strategy and nanopore sensing.
- Minmin Li
- , Yuting Xiong
- & Guangyan Qing
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Article
| Open AccessA generalizable nanopore sensor for highly specific protein detection at single-molecule precision
Sensitive and accurate approaches for protein detection have many potential applications. Here the authors show how engineered protein nanopore sensors, consisting of a monobody fused to a single-polypeptide nanopore, can be used for highly specific detection of proteins in complex biofluids.
- Mohammad Ahmad
- , Jeung-Hoi Ha
- & Liviu Movileanu
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Article
| Open AccessSimultaneous profiling of histone modifications and DNA methylation via nanopore sequencing
The interplay between histone modifications and DNA methylation plays a crucial role in establishing and maintaining the epigenomic landscape. Here, the authors develop a nanopore sequencing based method for mapping histone modifications and DNA methylation from native, long, single DNA molecules.
- Xue Yue
- , Zhiyuan Xie
- & Yimeng Yin
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Article
| Open AccessLamellar carbon nitride membrane for enhanced ion sieving and water desalination
Traditional carbon nitride membranes are generally presented with random stacking behavior leading to undesired separation performance. Here, authors create lamellar membranes via polycation pillaring to afford adaptive subnanochannels, overcoming the selectivity-permeability trade-off in forward osmosis.
- Yang Wang
- , Tingting Lian
- & Markus Antonietti
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Article
| Open AccessA click chemistry amplified nanopore assay for ultrasensitive quantification of HIV-1 p24 antigen in clinical samples
Accurate detection of antigen p24 for HIV−1 early diagnosis remains challenging. Here the authors present a click chemistry amplified nanopore (CAN) assay that allows p24 quantification at ultralow concentration range in clinical samples.
- Xiaojun Wei
- , Xiaoqin Wang
- & Chang Liu
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Article
| Open AccessCholesterol-stabilized membrane-active nanopores with anticancer activities
Bacterial cells utilize cholesterol-enhanced pore formation to specifically target eukaryotic cells. Here, the authors present a class of bio-inspired, cholesterol-enhanced nanopores which display anticancer activities in vitro.
- Jie Shen
- , Yongting Gu
- & Huaqiang Zeng
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Article
| Open AccessAssembly of transmembrane pores from mirror-image peptides
Alpha-helix nanopores have a range of potential applications and the inclusion of non-natural amino acids allows for modification. Here, the authors report on the creation of alpha-helix pores using D-amino acids and show the pores formed, have different properties to the L-counterparts and were resistant to proteases.
- Smrithi Krishnan R
- , Kalyanashis Jana
- & Kozhinjampara R. Mahendran
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Article
| Open AccessA nanopore interface for higher bandwidth DNA computing
Toe-hold-mediated strand displacement (DSD) is a widely used molecular tool in applications such as DNA computing and nucleic acid diagnostics. Here the authors characterize dozens of orthogonal barcode sequences that can be used for monitoring the output kinetics of multiplexed DSD reactions in real-time using a commercially-available portable nanopore array device.
- Karen Zhang
- , Yuan-Jyue Chen
- & Jeff Nivala
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Article
| Open AccessMultifunctional graphene heterogeneous nanochannel with voltage-tunable ion selectivity
Nanoporous 2D materials have shown promising potential for ion sieving applications due to their physical and chemical properties. Here authors develop a heterogeneous graphene-based polyethylene terephthalate nanochannel with ion sieving ability that is controlled by adjusting the applied voltage.
- Shihao Su
- , Yifan Zhang
- & Jianming Xue
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Article
| Open AccessGenome-wide mapping of individual replication fork velocities using nanopore sequencing
Theulot et al. introduce NanoForkSpeed, a nanopore sequencing-based method to map individual replication fork velocities on entire genomes. NFS shows that fork speed is uniform across yeast chromosomes except for a marked slowdown at pausing sites.
- Bertrand Theulot
- , Laurent Lacroix
- & Benoît Le Tallec
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Article
| Open AccessOn the origins of conductive pulse sensing inside a nanopore
Conductive events during nanopore sensing, are seen typically under low salt conditions and widely thought to arise from counterions brought into the pore via analyte. Here, authors show that an imbalance of ionic fluxes lead to conductive events.
- Lauren S. Lastra
- , Y. M. Nuwan D. Y. Bandara
- & Kevin J. Freedman
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Article
| Open AccessA reversibly gated protein-transporting membrane channel made of DNA
Artificial systems to control the transport of molecules across biomembranes can be useful for biosensing or drug delivery. Here, the authors assemble a DNA channel enabling the precisely timed, stimulus-controlled transport of functional proteins across bilayer membranes.
- Swarup Dey
- , Adam Dorey
- & Hao Yan
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Article
| Open AccessDisentangling the recognition complexity of a protein hub using a nanopore
Nanopores are powerful tools for sampling protein-peptide interactions. Here, the authors convert a protein-based nanopore into a sensitive biosensor to characterize the complex binding of WDR5 protein to a 14-residue ligand.
- Lauren Ashley Mayse
- , Ali Imran
- & Liviu Movileanu
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Matters Arising
| Open AccessInconsistencies in the specific nucleobase pairing motif prone to photodimerization in a MOF nanoreactor
- Pascale Clivio
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Article
| Open AccessProtein identification by nanopore peptide profiling
Peptide mass fingerprinting is a traditional approach for protein identification by mass spectrometry. Here, the authors provide evidence that peptide mass fingerprinting is also feasible using FraC nanopores, demonstrating protein identification based on nanopore measurements of digested peptides.
- Florian Leonardus Rudolfus Lucas
- , Roderick Corstiaan Abraham Versloot
- & Giovanni Maglia
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Article
| Open AccessProgrammable nano-reactors for stochastic sensing
Monitoring single molecule chemical reactions can be difficult and nanopore based strategies which have shown promise are technically challenging. Here, the authors report on a technique which allows for the direct observation of different reactions and demonstrate the ability to distinguish clinically relevant analogues.
- Wendong Jia
- , Chengzhen Hu
- & Shuo Huang
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Article
| Open AccessDigital immunoassay for biomarker concentration quantification using solid-state nanopores
The concentration of a biomarker in solution can be determined by counting single molecules. Here the authors report a digital immunoassay scheme with solid-state nanopore readout to quantify a target protein and use this to measure thyroid-stimulating hormone from human serum.
- Liqun He
- , Daniel R. Tessier
- & Vincent Tabard-Cossa
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Article
| Open AccessCombining machine learning and nanopore construction creates an artificial intelligence nanopore for coronavirus detection
Rapid, accurate and specific point-of-care diagnostics can help manage and contain fast-spreading infections. Here, the authors present a nanopore-based system that uses artificial intelligence to discriminate between four coronaviruses in saliva, with little need for sample pre-processing.
- Masateru Taniguchi
- , Shohei Minami
- & Kazunori Tomono
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Article
| Open AccessTowards explicit regulating-ion-transport: nanochannels with only function-elements at outer-surface
Function elements are key components for nanochannel systems for artificial regulation of ion transport. Here, the authors investigate the independent role of function elements at the outer surface of nanochannel systems, without function elements at inner walls, in promoting osmotic energy conversion and biochemical sensing.
- Qun Ma
- , Yu Li
- & Fan Xia
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Article
| Open AccessSlowing down DNA translocation through solid-state nanopores by edge-field leakage
Solid-state nanopores can serve as single molecule sensors for DNA sequencing, but the current designs suffer from fast DNA translocation so low detectivity. Wang et al. slow down and control the translocation speed by 5 orders of magnitude using a leakage field generated at the nanopore tip.
- Ceming Wang
- , Sebastian Sensale
- & Hsueh-Chia Chang
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Article
| Open AccessHigh-frequency gas effusion through nanopores in suspended graphene
Atomically thin porous graphene is promising for filtration and sieving applications. Here the authors, using a laser-actuated micro-drum device of bilayer graphene with controlled number of nanopores, and measuring the permeation rate of different gases, show that it can also be used for permeation-based sensing.
- I. E. Rosłoń
- , R. J. Dolleman
- & P. G. Steeneken
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Article
| Open AccessRational design of DNA nanostructures for single molecule biosensing
A key attribute for modern healthcare is the ability to detect low concentrations of biomarkers. Here, the authors use nanopores and DNA origami with target-specific aptamers for detection of CRP.
- Mukhil Raveendran
- , Andrew J. Lee
- & Paolo Actis
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Article
| Open AccessHigh permeability sub-nanometre sieve composite MoS2 membranes
Molybdenum disulfide membranes are attractive for filtration of nanoscale species but should be optimized for application. Here, the authors report composite membranes with tunable surface charge, pore size and interlayer spacing, achieving efficient filtration of small-molecule dyes and osmosis.
- Bedanga Sapkota
- , Wentao Liang
- & Meni Wanunu
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Article
| Open AccessControlled packing and single-droplet resolution of 3D-printed functional synthetic tissues
Precise patterning of lipid-stabilised aqueous droplets is a key challenge in building synthetic tissue designs. Here, the authors show how the interactions between pairs of droplets direct the packing of droplets within 3D-printed networks, enabling the formation of synthetic tissues with high-resolution features.
- Alessandro Alcinesio
- , Oliver J. Meacock
- & Hagan Bayley
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Article
| Open AccessGiant single molecule chemistry events observed from a tetrachloroaurate(III) embedded Mycobacterium smegmatis porin A nanopore
Engineered biological nanopores enable observation of single molecule chemistry events; however a cylindrical pore geometry can have undesired effects. The authors report a conical biological pore which was embedded with tetrachloroaurate(III) to allow for discrimination between different biothiols.
- Jiao Cao
- , Wendong Jia
- & Shuo Huang
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Article
| Open AccessA large size-selective DNA nanopore with sensing applications
Artificial nanopores can perform selective gating of molecules analogous to transmembrane proteins. Here, the authors design a DNA origami pore with a controllable lid for size-selective gating and translocation of macromolecules and evaluate its biosensing properties by single particle assay.
- Rasmus P. Thomsen
- , Mette Galsgaard Malle
- & Jørgen Kjems
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Article
| Open AccessActive DNA unwinding and transport by a membrane-adapted helicase nanopore
Active translocation of DNA through nanopores usually needs enzyme assistance. Here authors present a nanopore derived from helicase E1 of bovine papillomavirus (BPV) which acts as a conductive pore embedded in lipid membrane to allow the translocation of ssDNA and unwinding of dsDNA.
- Ke Sun
- , Changjian Zhao
- & Jia Geng
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Article
| Open AccessSingle-molecule sensing of peptides and nucleic acids by engineered aerolysin nanopores
Aerolysin pores have potential to improve the accuracy of DNA sequencing and single-molecule proteomics. Here, the authors rationally design a set of mutated pores to achieve a more accurate detection of peptides and nucleic acids.
- Chan Cao
- , Nuria Cirauqui
- & Matteo Dal Peraro
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Article
| Open AccessMeasurements of the size and correlations between ions using an electrolytic point contact
The size of an ion affects everything from the structure of water to life itself. Here, a sub-nanometer diameter pore sputtered through a thin silicon nitride membrane is used to systematically test ion permeability by measuring the electrolytic current and current noise and show that the ions move with a grossly distorted hydration shell in a correlated way.
- Eveline Rigo
- , Zhuxin Dong
- & Gregory Timp
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Article
| Open AccessPhoto-induced ultrafast active ion transport through graphene oxide membranes
Ionic transport through subnanometer-sized channels in 2D material-based membranes can be exploited for energy and separation applications. Here the authors demonstrate the visible light activation of an ultrafast ionic flux against a concentration gradient in graphene oxide membranes.
- Jinlei Yang
- , Xiaoyu Hu
- & Wei Guo
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Article
| Open AccessFraC nanopores with adjustable diameter identify the mass of opposite-charge peptides with 44 dalton resolution
Using Fragaceatoxin C nanopores to study peptides below 1.6 kDa is challenging. Here the authors demonstrate that nanopores can be engineered to different sizes to detect a range of peptide lengths below the previous resolution limit, and show that the mass of a peptide can be identified by ionic current blockades.
- Gang Huang
- , Arnout Voet
- & Giovanni Maglia
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Article
| Open AccessDirect RNA sequencing on nanopore arrays redefines the transcriptional complexity of a viral pathogen
Here, Depledge et al. use nanopore arrays for direct RNA sequencing to profile the HSV-1 transcriptome in productively infected cells. Sequencing of individual RNAs reveals a highly complex viral transcriptome including mRNAs encoding new viral fusion proteins derived by read-through transcription.
- Daniel P. Depledge
- , Kalanghad Puthankalam Srinivas
- & Angus C. Wilson
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Article
| Open AccessDetecting topological variations of DNA at single-molecule level
Ultrathin nanopore membranes have the potential for detecting topological variation in DNA. Here the authors use barcoded DNA to characterise the translocation profiles of DNA with single strand gaps.
- Ke Liu
- , Chao Pan
- & Aleksandra Radenovic
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Article
| Open AccessThermostable virus portal proteins as reprogrammable adapters for solid-state nanopore sensors
Solid state nanopores are robust but the sizing can be variable, whereas protein nanopores are precisely sized but lack robustness. Here the authors cork a solid state nanopore with the DNA-translocating portal protein from the virus G20c to obtain a lipid-free hybrid nanopore that can sense various biopolymers.
- Benjamin Cressiot
- , Sandra J. Greive
- & Meni Wanunu