60 results found
Cai S, Pataillot-Meakin T, Shibakawa A, et al., 2021, Single-molecule amplification-free multiplexed detection of circulating microRNA cancer biomarkers from serum, Nature Communications, ISSN: 2041-1723
Ying Y-L, Ivanov AP, Tabard-Cossa V, 2021, No small matter, NATURE CHEMISTRY, Vol: 13, Pages: 216-217, ISSN: 1755-4330
Nanopores in solid-state membranes are promising for a wide range of applications including DNA sequencing, ultra-dilute analyte detection, protein analysis, and polymer data storage. Techniques to fabricate solid-state nanopores have typically been time consuming or lacked the resolution to create pores with diameters down to a few nanometres, as required for the above applications. In recent years, several methods to fabricate nanopores in electrolyte environments have been demonstrated. These in situ methods include controlled breakdown (CBD), electrochemical reactions (ECR), laser etching and laser-assisted controlled breakdown (la-CBD). These techniques are democratising solid-state nanopores by providing the ability to fabricate pores with diameters down to a few nanometres (i.e. comparable to the size of many analytes) in a matter of minutes using relatively simple equipment. Here we review these in situ solid-state nanopore fabrication techniques and highlight the challenges and advantages of each method. Furthermore we compare these techniques by their desired application and provide insights into future research directions for in situ nanopore fabrication methods.
Tang L, Paulose Nadappuram B, Cadinu P, et al., 2021, Combined quantum tunnelling and dielectrophoretic trapping for molecular analysis at ultra-low analyte concentrations, Nature Communications, Vol: 12, Pages: 1-8, ISSN: 2041-1723
Quantum tunnelling offers a unique opportunity to study nanoscale objects with atomic resolution using electrical readout. However, practical implementation is impeded by the lack of simple, stable probes, that are required for successful operation. Existing platforms offer low throughput and operate in a limited range of analyte concentrations, as there is no active control to transport molecules to the sensor. We report on a standalone tunnelling probe based on double-barrelled capillary nanoelectrodes that do not require a conductive substrate to operate unlike other techniques, such as scanning tunnelling microscopy. These probes can be used to efficiently operate in solution environments and detect single molecules, including mononucleotides, oligonucleotides, and proteins. The probes are simple to fabricate, exhibit remarkable stability, and can be combined with dielectrophoretic trapping, enabling active analyte transport to the tunnelling sensor. The latter allows for up to 5-orders of magnitude increase in event detection rates and sub-femtomolar sensitivity.
Ren R, Wang X, Cai S, et al., 2020, Selective sensing of proteins using aptamer functionalised nanopore extended field-effect transistors, Small Methods, Vol: 4, Pages: 1-8, ISSN: 2366-9608
The ability to sense proteins and protein‐related interactions at the single‐molecule level is becoming of increasing importance to understand biological processes and diseases better. Single‐molecule sensors, such as nanopores have shown substantial promise for the label‐free detection of proteins; however, challenges remain due to the lack of selectivity and the need for relatively high analyte concentrations. An aptamer‐functionalized nanopore extended field‐effect transistor (nexFET) sensor is reported here, where protein transport can be controlled via the gate voltage that in turn improves single‐molecule sensitivity and analyte capture rates. Importantly, these sensors allow for selective detection, based on the choice of aptamer chemistry, and can provide a valuable addition to the existing methods for the analysis of proteins and biomarkers in biological fluids.
Xue L, Yamazaki H, Ren R, et al., 2020, Solid-state nanopore sensors (Sep, 10.1038/s41578-020-0229-6, 2020), NATURE REVIEWS MATERIALS, Vol: 5, Pages: 952-952, ISSN: 2058-8437
Nanopore-based sensors have established themselves as a prominent tool for solution-based, single-molecule analysis of the key building blocks of life, including nucleic acids, proteins, glycans and a large pool of biomolecules that have an essential role in life and healthcare. The predominant molecular readout method is based on measuring the temporal fluctuations in the ionic current through the pore. Recent advances in materials science and surface chemistries have not only enabled more robust and sensitive devices but also facilitated alternative detection modalities based on field-effect transistors, quantum tunnelling and optical methods such as fluorescence and plasmonic sensing. In this Review, we discuss recent advances in nanopore fabrication and sensing strategies that endow nanopores not only with sensitivity but also with selectivity and high throughput, and highlight some of the challenges that still need to be addressed.
Wang X, Wilkinson MD, Lin X, et al., 2020, Correction: Single-molecule nanopore sensing of actin dynamics and drug binding, Chemical Science, Vol: 11, Pages: 8036-8038, ISSN: 2041-6520
Correction for ‘Single-molecule nanopore sensing of actin dynamics and drug binding’ by Xiaoyi Wang et al., Chem. Sci., 2020, 11, 970–979, DOI: 10.1039/C9SC05710B.
Clark R, Nawawi MA, Dobre A, et al., 2020, The effect of structural heterogeneity upon the microviscosity of ionic liquids, CHEMICAL SCIENCE, Vol: 11, Pages: 6121-6133, ISSN: 2041-6520
Cadinu P, Kang M, Paulose Nadappuram B, et al., 2020, Individually addressable multi-nanopores for single-molecule targeted operations, Nano Letters, Vol: 20, Pages: 2012-2019, ISSN: 1530-6984
The fine-tuning of molecular transport is a ubiquitous problem of single-molecule methods. The latter is evident even in powerful single-molecule methods such as nanopore sensing, where the quest for resolving more detailed biomolecular features is often limited by insufficient control of the dynamics of individual molecules within the detection volume of the nanopore. In this work, we introduce and characterize a reconfigurable multi-nanopore architecture that enables additional channels to manipulate the dynamics of DNA molecules in a nanopore. We show that the fabrication process of this device, consisting of four adjacent, individually addressable nanopores located at the tip of a quartz nanopipette, is fast and highly reproducible. By individually tuning the electric field across each nanopore, these devices can operate in several unique cooperative detection modes that allow moving, sensing, and trapping DNA molecules with high efficiency and increased temporal resolution.
Wang X, Wilkinson MD, Lin X, et al., 2020, Single-molecule nanopore sensing of actin dynamics and drug binding, Chemical Science, Vol: 11, Pages: 970-979, ISSN: 2041-6520
Actin is a key protein in the dynamic processes within the eukaryotic cell. To date, methods exploring the molecular state of actin are limited to insights gained from structural approaches, providing a snapshot of protein folding, or methods that require chemical modifications compromising actin monomer thermostability. Nanopore sensing permits label-free investigation of native proteins and is ideally suited to study proteins such as actin that require specialised buffers and cofactors. Using nanopores, we determined the state of actin at the macromolecular level (filamentous or globular) and in its monomeric form bound to inhibitors. We revealed urea-dependent and voltage-dependent transitional states and observed unfolding process within which sub-populations of transient actin oligomers are visible. We detected, in real-time, filament-growth, and drug-binding at the single-molecule level demonstrating the promise of nanopores sensing for in-depth understanding of protein folding landscapes and for drug discovery.
Zhang Y, Takahashi Y, Hong SP, et al., 2019, High-resolution label-free 3D mapping of extracellular pH of single living cells, Nature Communications, Vol: 10, Pages: 1-9, ISSN: 2041-1723
Dynamic mapping of extracellular pH (pHe) at the single-cell level is critical for understanding the role of H+ in cellular and subcellular processes, with particular importance in cancer. While several pHe sensing techniques have been developed, accessing this information at the single-cell level requires improvement in sensitivity, spatial and temporal resolution. We report on a zwitterionic label-free pH nanoprobe that addresses these long-standing challenges. The probe has a sensitivity >0.01 units, 2 ms response time, and 50 nm spatial resolution. The technology was incorporated into a double-barrel nanoprobe integrating pH sensing with feedback-controlled distance sensing via Scanning Ion Conductance Microscopy. This allows for the simultaneous 3D topographical imaging and pHe monitoring of living cancer cells. These classes of nanoprobes were used for real-time high spatiotemporal resolution pHe mapping at the subcellular level and revealed tumour heterogeneity of the peri-cellular environments of melanoma and breast cancer cells.
Wang X, Wilkinson MD, Lin X, et al., 2019, Single-molecule nanopore sensing of actin dynamics and drug binding, Publisher: Cold Spring Harbor Laboratory
<jats:title>Abstract</jats:title><jats:p>Actin is a key protein in the dynamic processes within the eukaryotic cell. To date, methods exploring the molecular state of actin are limited to insights gained from structural approaches, providing a snapshot of protein folding, or methods that require chemical modifications compromising actin monomer thermostability. Nanopore sensing permits label-free investigation of native proteins and is ideally suited to study proteins such as actin that require specialised buffers and cofactors. Using nanopores we determined the state of actin at the macromolecular level (filamentous or globular) and in its monomeric form bound to inhibitors. We revealed urea-dependent and voltage-dependent transitional states and observed unfolding process within which sub-populations of transient actin oligomers are visible. We detected, in real-time, drug-binding and filament-growth events at the single-molecule level. This enabled us to calculate binding stoichiometries and to propose a model for protein dynamics using unmodified, native actin molecules, demostrating the promise of nanopores sensing for in-depth understanding of protein folding landscapes and for drug discovery.</jats:p>
Cai S, Sze JYY, Ivanov AP, et al., 2019, Small molecule electro-optical binding assay using nanopores., Nat Commun, Vol: 10
The identification of short nucleic acids and proteins at the single molecule level is a major driving force for the development of novel detection strategies. Nanopore sensing has been gaining in prominence due to its label-free operation and single molecule sensitivity. However, it remains challenging to detect small molecules selectively. Here we propose to combine the electrical sensing modality of a nanopore with fluorescence-based detection. Selectivity is achieved by grafting either molecular beacons, complementary DNA, or proteins to a DNA molecular carrier. We show that the fraction of synchronised events between the electrical and optical channels, can be used to perform single molecule binding assays without the need to directly label the analyte. Such a strategy can be used to detect targets in complex biological fluids such as human serum and urine. Future optimisation of this technology may enable novel assays for quantitative protein detection as well as gene mutation analysis with applications in next-generation clinical sample analysis.
Much of the functionality of multi-cellular systems arises from the spatial organisation and dynamic behaviours within and between cells. Current single-cell genomic methods only provide a transcriptional “snapshot” of individual cells. The real-time analysis and perturbation of living cells would generate a step-change in single-cellanalysis. Here we describe minimally invasive nanotweezers that can be spatially controlled to extract samples from living cells with single-molecule precision. They consist of two closely spaced electrodes with gaps as small as 10-20 nm, which can be usedfor the dielectrophoretic trapping of DNA and proteins.Aside from trapping single molecules, we also extract nucleic acids for gene expression analysis from living cells, without affecting their viability. Finally, we report on the trapping, and extraction of a single mitochondrion. This work bridges the gap between single-molecule/organelle manipulation and cell biology and can ultimately enable a better understanding of living cells.
Xue L, Cadinu P, Paulose Nadappuram B, et al., 2018, Gated single-molecule transport in double-barreled nanopores, ACS Applied Materials and Interfaces, Vol: 10, Pages: 38621-38629, ISSN: 1944-8244
Single-molecule methods have been rapidly developing with the appealing prospect of transforming conventional ensemble-averaged analytical techniques. However, challenges remain especially in improving detection sensitivity and controlling molecular transport. In this article, we present a direct method for the fabrication of analytical sensors that combine the advantages of nanopores and field-effect transistors for simultaneous label-free single-molecule detection and manipulation. We show that these hybrid sensors have perfectly aligned nanopores and field-effect transistor components making it possible to detect molecular events with up to near 100% synchronization. Furthermore, we show that the transport across the nanopore can be voltage-gated to switch on/off translocations in real time. Finally, surface functionalization of the gate electrode can also be used to fine tune transport properties enabling more active control over the translocation velocity and capture rates.
Al Sulaiman D, Cadinu P, Ivanov AP, et al., 2018, Chemically modified hydrogel-filled nanopores: a tunable platform for single-molecule sensing, Nano Letters: a journal dedicated to nanoscience and nanotechnology, Vol: 18, Pages: 6084-6093, ISSN: 1530-6984
Label-free, single-molecule sensing is an ideal candidate for biomedical applications that rely on the detection of low copy numbers in small volumes and potentially complex biofluids. Among them, solid-state nanopores can be engineered to detect single molecules of charged analytes when they are electrically driven through the nanometer-sized aperture. When successfully applied to nucleic acid sensing, fast transport in the range of 10–100 nucleotides per nanosecond often precludes the use of standard nanopores for the detection of the smallest fragments. Herein, hydrogel-filled nanopores (HFN) are reported that combine quartz nanopipettes with biocompatible chemical poly(vinyl) alcohol hydrogels engineered in-house. Hydrogels were modified physically or chemically to finely tune, in a predictable manner, the transport of specific molecules. Controlling the hydrogel mesh size and chemical composition allowed us to slow DNA transport by 4 orders of magnitude and to detect fragments as small as 100 base pairs (bp) with nanopores larger than 20 nm at an ionic strength comparable to physiological conditions. Considering the emergence of cell-free nucleic acids as blood biomarkers for cancer diagnostics or prenatal testing, the successful sensing and size profiling of DNA fragments ranging from 100 bp to >1 kbp long under physiological conditions demonstrates the potential of HFNs as a new generation of powerful and easily tunable molecular diagnostics tools.
Ivanov AP, Edel JB, 2018, Scissoring genes with light, NATURE CHEMISTRY, Vol: 10, Pages: 800-801, ISSN: 1755-4330
Cadinu P, Campolo G, Pud S, et al., 2018, Double barrel nanopores as a new tool for controlling single-molecule transport, Nano Letters, Vol: 18, Pages: 2738-2745, ISSN: 1530-6984
The ability to control the motion of single biomolecules is key to improving a wide range of biophysical and diagnostic applications. Solid-state nanopores are a promising tool capable of solving this task. However, molecular control and the possibility of slow readouts of long polymer molecules are still limited due to fast analyte transport and low signal-to-noise ratios. Here, we report on a novel approach of actively controlling analyte transport by using a double-nanopore architecture where two nanopores are separated by only a ∼ 20 nm gap. The nanopores can be addressed individually, allowing for two unique modes of operation: (i) pore-to-pore transfer, which can be controlled at near 100% efficiency, and (ii) DNA molecules bridging between the two nanopores, which enables detection with an enhanced temporal resolution (e.g., an increase of more than 2 orders of magnitude in the dwell time) without compromising the signal quality. The simplicity of fabrication and operation of the double-barrel architecture opens a wide range of applications for high-resolution readout of biological molecules.
Peveler WJ, Noimark S, Al-Azawi H, et al., 2018, Covalently attached antimicrobial surfaces using BODIPY: improving efficiency and effectiveness, ACS Applied Materials and Interfaces, Vol: 10, Pages: 98-104, ISSN: 1944-8244
The development of photoactivated antimicrobial surfaces that kill pathogens through the production of singlet oxygen has proved very effective in recent years, with applications in medical devices and hospital touch surfaces, to improve patient safety and well being. However, many of these surfaces require a swell-encapsulation-shrink strategy to incorporate the photoactive agents in a polymer matrix, and this is resource intensive, given that only the surface fraction of the agent is active against bacteria. Furthermore, there is a risk that the agent will leach from the polymer and thus raises issues of biocompatibility and patient safety. Here, we describe a more efficient method of fabricating a silicone material with a covalently attached monolayer of photoactivating agent that uses heavy-atom triplet sensitization for improved singlet oxygen generation and corresponding antimicrobial activity. We use boron-dipyrromethane with a reactive end group and incorporated Br atoms, covalently attached to poly(dimethylsiloxane). We demonstrate the efficacy of this material in producing singlet oxygen and killing Staphylococcus aureus and suggest how it might be easily modifiable for future antimicrobial surface development.
Kunstmann-Olsen C, 2018, Joshua Edel, Aleksandar Ivanov, and MinJun Kim (Eds): Nanofluidics, 2nd Edn, Chromatographia, Vol: 81, Pages: 173-173, ISSN: 0009-5893
Sze JYY, Ivanov AP, Cass AEG, et al., 2017, Single molecule multiplexed nanopore protein screening in human serum using aptamer modified DNA carriers, Nature Communications, Vol: 8, Pages: 1-10, ISSN: 2041-1723
The capability to screen a range of proteins at the single-molecule level with enhanced selectivity in biological fluids has been in part a driving force in developing future diagnostic and therapeutic strategies. The combination of nanopore sensing and nucleic acid aptamer recognition comes close to this ideal due to the ease of multiplexing, without the need for expensive labelling methods or extensive sample pre-treatment. Here, we demonstrate a fully flexible, scalable and low-cost detection platform to sense multiple protein targets simultaneously by grafting specific sequences along the backbone of a double-stranded DNA carrier. Protein bound to the aptamer produces unique ionic current signatures which facilitates accurate target recognition. This powerful approach allows us to differentiate individual protein sizes via characteristic changes in the sub-peak current. Furthermore, we show that by using DNA carriers it is possible to perform single-molecule screening in human serum at ultra-low protein concentrations.
Crick CR, Albella P, Kim H-J, et al., 2017, Low-Noise Plasmonic Nanopore Biosensors for Single Molecule Detection at Elevated Temperatures, ACS Photonics, Vol: 4, Pages: 2835-2842, ISSN: 2330-4022
Advanced single molecular analysis is a key stepping stone for the rapid sensing and characterization of biomolecules. This will only be made possible through the implementation of versatile platforms, with high sensitivities and the precise control of experimental conditions. The presented work details an advancement of this technology, through the development of a low-noise Pyrex/silicon nitride/gold nanopore platform. The nanopore is surrounded by a plasmonic bullseye structure and provides targeted and controllable heating via laser irradiation, which is directed toward the center of the pore. The device architecture is investigated using multiwavelength laser heating experiments and 'individual DNA molecules are detected under controlled heating. The plasmonic features, optimized through numerical simulations, are tuned to the wavelength of incident light, ensuring a platform that provides substantial heating with high signal-to-noise.
Ren R, Zhang Y, Paulose Nadappuram B, et al., 2017, Nanopore extended field effect transistor for selective single molecule biosensing, Nature Communications, Vol: 8, Pages: 1-9, ISSN: 2041-1723
There has been a significant drive to deliver nanotechnological solutions to biosensing, yet there remains an unmet need in the development of biosensors that are affordable, integrated, fast, capable of multiplexed detection, and offer high selectivity for trace analyte detection in biological fluids. Herein, some of these challenges are addressed by designing a new class of nanoscale sensors dubbed nanopore extended field-effect transistor (nexFET) that combine the advantages of nanopore single-molecule sensing, field-effect transistors, and recognition chemistry. We report on a polypyrrole functionalized nexFET, with controllable gate voltage that can be used to switch on/off, and slow down single-molecule DNA transport through a nanopore. This strategy enables higher molecular throughput, enhanced signal-to-noise, and even heightened selectivity via functionalization with an embedded receptor. This is shown for selective sensing of an anti-insulin antibody in the presence of its IgG isotype.
Cadinu P, Paulose Nadappuram B, Lee DJ, et al., 2017, Single molecule trapping and sensing using dual nanopores separated by a zeptoliter nanobridge, Nano Letters, Vol: 17, Pages: 6376-6384, ISSN: 1530-6984
There is a growing realization, especially within the diagnostic and therapeutic community, that the amount of information enclosed in a single molecule can not only enable a better understanding of biophysical pathways, but also offer exceptional value for early stage biomarker detection of disease onset. To this end, numerous single molecule strategies have been proposed, and in terms of label-free routes, nanopore sensing has emerged as one of the most promising methods. However, being able to finely control molecular transport in terms of transport rate, resolution, and signal-to-noise ratio (SNR) is essential to take full advantage of the technology benefits. Here we propose a novel solution to these challenges based on a method that allows biomolecules to be individually confined into a zeptoliter nanoscale droplet bridging two adjacent nanopores (nanobridge) with a 20 nm separation. Molecules that undergo confinement in the nanobridge are slowed down by up to 3 orders of magnitude compared to conventional nanopores. This leads to a dramatic improvement in the SNR, resolution, sensitivity, and limit of detection. The strategy implemented is universal and as highlighted in this manuscript can be used for the detection of dsDNA, RNA, ssDNA, and proteins.
Lin X, Ivanov AP, Edel JB, 2017, Selective single molecule nanopore sensing of proteins using DNA aptamer-functionalised gold nanoparticles, Chemical Science, Vol: 8, Pages: 3905-3912, ISSN: 2041-6539
Single molecule detection methods, such as nanopore sensors have found increasing importance in applications ranging from gaining a better understanding of biophysical processes to technology driven solutions such as DNA sequencing. However, challenges remain especially in relation to improving selectivity to probe specific targets or to alternatively enable detection of smaller molecules such as small-sized proteins with a sufficiently high signal-to-noise ratio. In this article, we propose a solution to these technological challenges by using DNA aptamer-modified gold nanoparticles (AuNPs) that act as a molecular carrier through the nanopore sensor. We show that this approach offers numerous advantages including: high levels of selectivity, efficient capture from a complex mixture, enhanced signal, minimized analyte-sensor surface interactions, and finally can be used to enhance the event detection rate. This is demonstrated by incorporating a lysozyme binding aptamer to a 5 nm AuNP carrier to selectively probe lysozyme within a cocktail of proteins. We show that nanopores can reveal sub-complex molecular information, by discriminating the AuNP from the protein analyte, indicating the potential use of this technology for single molecule analysis of different molecular analytes specifically bound to AuNP.
Pitchford WH, Crick CR, Kim HJ, et al., 2017, Low Noise Nanopore Platforms Optimised for the Synchronised Optical and Electrical Detection of Biomolecules, RSC Nanoscience and Nanotechnology, Pages: 270-300, ISBN: 9781849734042
Nanopores are valuable tools for single-molecule sensing and biomolecular analysis. This can not only be seen from their prevalence in academic and industrial research, but in the growing capabilities at the cutting edge of the field. Recently the demand for improved structural resolution and accelerated analytical throughput has led to the incorporation of additional detection methods, such as fluorescence spectroscopy. The most frequently used solid-state nanopore platforms consist of a bulk silicon substrate and silicon nitride membrane. Although these platforms have many potential uses, they exhibit high photo-induced ionic current noise when probed with light. Due to the high translocation velocity of molecules, high bandwidth electrical measurements are essential for structural information to be investigated via resistive pulse sensing. Consequently, the applicability of Si substrate based nanopore sensors to synchronized optical and electrical measurements is limited at high-bandwidth and high-laser-power. This chapter describes the development and application of a unique low-noise nanopore platform, composed of a predominately Pyrex substrate and silicon nitride membrane. Proof-of-principle experiments are presented that show a Pyrex substrate greatly reduces ionic current noise arising from both platform capacitance and laser illumination. Furthermore, using confocal microscopy and a partially metallic nanopore as a zero mode waveguide, high signal-to-noise synchronized optical and electrical detection of dsDNA is demonstrated.
Kim M, Ivanov A, Edel J, 2017, Preface, ISBN: 9781849734042
Edel J, Ivanov A, Kim M, 2016, Nanofluidics (Second Edition), Publisher: Royal Society of Chemistry, ISBN: 9781849734042
Despite the growth of this field, there are surprisingly few books dedicated to nanofluidics. This book will fill the gap in the literature for a text focusing on bioanalytical applications.
Crick CR, Noimark S, Peveler WJ, et al., 2016, Advanced Compositional Analysis of Nanoparticle-polymer Composites Using Direct Fluorescence Imaging, Jove-Journal of Visualized Experiments, Vol: 113, ISSN: 1940-087X
The fabrication of polymer-nanoparticle composites is extremely important in the development of many functional materials. Identifying the precise composition of these materials is essential, especially in the design of surface catalysts, where the surface concentration of the active component determines the activity of the material. Antimicrobial materials which utilize nanoparticles are a particular focus of this technology. Recently swell encapsulation has emerged as a technique for inserting antimicrobial nanoparticles into a host polymer matrix. Swell encapsulation provides the advantage of localizing the incorporation to the external surfaces of materials, which act as the active sites of these materials. However, quantification of this nanoparticle uptake is challenging. Previous studies explore the link between antimicrobial activity and surface concentration of the active component, but this is not directly visualized. Here we show a reliable method to monitor the incorporation of nanoparticles into a polymer host matrix via swell encapsulation. We show that the surface concentration of CdSe/ZnS nanoparticles can be accurately visualized through cross-sectional fluorescence imaging. Using this method, we can quantify the uptake of nanoparticles via swell encapsulation and measure the surface concentration of encapsulated particles, which is key in optimizing the activity of functional materials.
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