179 results found
Wang X, Thomas T-M, Ren R, et al., 2023, Nanopore Detection Using Supercharged Polypeptide Molecular Carriers., J Am Chem Soc
The analysis at the single-molecule level of proteins and their interactions can provide critical information for understanding biological processes and diseases, particularly for proteins present in biological samples with low copy numbers. Nanopore sensing is an analytical technique that allows label-free detection of single proteins in solution and is ideally suited to applications, such as studying protein-protein interactions, biomarker screening, drug discovery, and even protein sequencing. However, given the current spatiotemporal limitations in protein nanopore sensing, challenges remain in controlling protein translocation through a nanopore and relating protein structures and functions with nanopore readouts. Here, we demonstrate that supercharged unstructured polypeptides (SUPs) can be genetically fused with proteins of interest and used as molecular carriers to facilitate nanopore detection of proteins. We show that cationic SUPs can substantially slow down the translocation of target proteins due to their electrostatic interactions with the nanopore surface. This approach enables the differentiation of individual proteins with different sizes and shapes via characteristic subpeaks in the nanopore current, thus facilitating a viable route to use polypeptide molecular carriers to control molecular transport and as a potential system to study protein-protein interactions at the single-molecule level.
Wojciak-Stothard B, Ainscough AJ, Smith TJ, et al., 2022, An organ-on-chip model of pulmonary arterial hypertension identifies a BMPR2-SOX17-prostacyclin signalling axis, Communications Biology, Vol: 5, Pages: 1-15, ISSN: 2399-3642
Pulmonary arterial hypertension (PAH) is an unmet clinical need. The lack of models of human disease is a key obstacle to drug development. We present a biomimetic model of pulmonary arterial endothelial-smooth muscle cell interactions in PAH, combining natural and induced bone morphogenetic protein receptor 2 (BMPR2) dysfunction with hypoxia to induce smooth muscle activation and proliferation, which is responsive to drug treatment. BMPR2- and oxygenation-specific changes in endothelial and smooth muscle gene expression, consistent with observations made in genomic and biochemical studies of PAH, enable insights into underlying disease pathways and mechanisms of drug response. The model captures key changes in the pulmonary endothelial phenotype that are essential for the induction of SMC remodelling, including a BMPR2-SOX17-prostacyclin signalling axis and offers an easily accessible approach for researchers to study pulmonary vascular remodelling and advance drug development in PAH.
Fried JP, Swett JL, Nadappuram BP, et al., 2022, Localised solid-state nanopore fabrication via controlled breakdown using on-chip electrodes, Nano Research, Vol: 15, Pages: 9881-9889, ISSN: 1998-0124
Controlled breakdown has recently emerged as a highly accessible technique to fabricate solid-state nanopores. However, in its most common form, controlled breakdown creates a single nanopore at an arbitrary location in the membrane. Here, we introduce a new strategy whereby breakdown is performed by applying the electric field between an on-chip electrode and an electrolyte solution in contact with the opposite side of the membrane. We demonstrate two advantages of this method. First, we can independently fabricate multiple nanopores at given positions in the membrane by localising the applied field to the electrode. Second, we can create nanopores that are self-aligned with complementary nanoelectrodes by applying voltages to the on-chip electrodes to locally heat the membrane during controlled breakdown. This new controlled breakdown method provides a path towards the affordable, rapid, and automatable fabrication of arrays of nanopores self-aligned with complementary on-chip nanostructures.
Tang L, Yi L, Jiang T, et al., 2022, Measuring conductance switching in single proteins using quantum tunneling, Science Advances, Vol: 8, Pages: 1-8, ISSN: 2375-2548
Interpreting the electrical signatures of single-proteins in electronic junctions has facilitated a better understanding of the intrinsic properties of proteins that are fundamental to chemical- and biological processes. Often such information is not accessible using ensemble and even single-molecule approaches. However, the fabrication of nanoscale single-protein junctions remains challenging as they often require sophisticated methods to ensure only a single protein is detected. We report on the fabrication of tunneling probes, direct measurement, and active control (switching) of single-protein conductance with an external field in solution. The probes allowed us to bridge a single streptavidin molecule to two independently addressable, biotin terminated electrodes and measure single protein tunneling response over long periods (up to 2 hours). We show that charge transport through the protein has multiple conductive pathways that depend on the magnitude of the applied bias. These findings open the door for the reliable fabrication of protein-based junctions, a better understanding of electronic properties of single protein molecules, and can enable their use in future protein-embedded bioelectronics applications.
Upton RL, Fedosyuk A, Edel JB, et al., 2021, Carbon Nanofiber/SiO2 Nanoparticle/HDPE Composites as Physically Resilient and Submersible Water-Repellent Coatings on HDPE Substrates, ACS APPLIED NANO MATERIALS, Vol: 4, Pages: 10090-10102
- Author Web Link
- Citations: 2
Ren R, Sun M, Goel P, et al., 2021, Single-molecule binding assay using nanopores and dimeric NP conjugates, Advanced Materials, Vol: 33, ISSN: 0935-9648
The ability to measure biomarkers, both specifically and selectively at the single-molecule level in biological fluids, has the potential to transform the diagnosis, monitoring, and therapeutic intervention of diseases. The use of nanopores has been gaining prominence in this area, not only for sequencing but more recently in screening applications. The selectivity of nanopore sensing can be substantially improved with the use of tags, but substantial challenges remain, especially when trying to differentiate between bound from unbound targets. Here we design highly sensitive and selective molecular probes made from NPs designed specifically for nanopores that self-assemble and dimerise upon binding to a biological target. We show that both single and paired NPs can be successfully resolved while improving the time and sensitivity of the biomarker detection. Nanopore sensing with NP conjugates can be used for applications such as antigen/antibody detection for sepsis screening and miRNA sequence analysis relevant to prostate cancer. We believe that such technology opens the doors to developing a highly sensitive and selective strategy for diagnosis and screening of diseases without the need for sample processing or amplification while requiring minimal sample volume.
Fried JP, Swett JL, Nadappuram BP, et al., 2021, Understanding electrical conduction and nanopore formation during controlled breakdown, Small, Vol: 17, Pages: 1-9, ISSN: 1613-6810
Controlled breakdown has recently emerged as a highly appealing technique to fabricate solid-state nanopores for a wide range of biosensing applications. This technique relies on applying an electric field of approximately 0.4–1 V nm−1 across the membrane to induce a current, and eventually, breakdown of the dielectric. Although previous studies have performed controlled breakdown under a range of different conditions, the mechanism of conduction and breakdown has not been fully explored. Here, electrical conduction and nanopore formation in SiNx membranes during controlled breakdown is studied. It is demonstrated that for Si-rich SiNx, oxidation reactions that occur at the membrane-electrolyte interface limit conduction across the dielectric. However, for stoichiometric Si3N4 the effect of oxidation reactions becomes relatively small and conduction is predominately limited by charge transport across the dielectric. Several important implications resulting from understanding this process are provided which will aid in further developing controlled breakdown in the coming years, particularly for extending this technique to integrate nanopores with on-chip nanostructures.
Oh S-H, Altug H, Jin X, et al., 2021, Nanophotonic biosensors harnessing van der Waals materials, NATURE COMMUNICATIONS, Vol: 12, ISSN: 2041-1723
- Author Web Link
- Citations: 45
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, Vol: 12, ISSN: 2041-1723
MicroRNAs (miRNAs) play essential roles in post-transcriptional gene expression and are also found freely circulating in bodily fluids such as blood. Dysregulated miRNA signatures have been associated with many diseases including cancer, and miRNA profiling from liquid biopsies offers a promising strategy for cancer diagnosis, prognosis and monitoring. Here, we develop size-encoded molecular probes that can be used for simultaneous electro-optical nanopore sensing of miRNAs, allowing for ultrasensitive, sequence-specific and multiplexed detection directly in unprocessed human serum, in sample volumes as small as 0.1 μl. We show that this approach allows for femtomolar sensitivity and single-base mismatch selectivity. We demonstrate the ability to simultaneously monitor miRNAs (miR-141-3p and miR-375-3p) from prostate cancer patients with active disease and in remission. This technology can pave the way for next generation of minimally invasive diagnostic and companion diagnostic tests for cancer.
Al Sulaiman D, Gatehouse A, Ivanov AP, et al., 2021, Length-Dependent, Single-Molecule Analysis of Short Double-Stranded DNA Fragments through Hydrogel-Filled Nanopores: A Potential Tool for Size Profiling Cell-Free DNA, ACS APPLIED MATERIALS & INTERFACES, Vol: 13, Pages: 26673-26681, ISSN: 1944-8244
- Author Web Link
- Citations: 5
Fried JP, Swett JL, Nadappuram BP, et al., 2021, In situ solid-state nanopore fabrication., Chemical Society Reviews, ISSN: 0306-0012
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.
Zhao M, Yu J, Zhang X, et al., 2021, Tuning interfacial energy barriers in heterojunctions for anti‐interference sensing, Advanced Functional Materials, Vol: 31, ISSN: 1616-301X
Analytes with similar redox properties are normally difficult to distinguish through classic electrochemical methods. This becomes especially true for the on‐site detection in seawater where the high salinity and complex chemical components can impose severe interference. Hereby introducing numerous nanoscale heterojunctions in the Cu/CuO/reduced graphene oxide (rGO)/polypyrrole (PPy) and Cu/CuO/rGO/chitosan electrochemical sensors, tunable interfacial energy barriers to exponentially regulate the electrochemical signal can be constructed. Importantly, these energy barriers are independent to redox but closely related to the electrostatic interaction from absorbed charged analytes such as Hg2+ and Cu2+. Moreover, the similar sensing principle is also valid for the energy barriers in p‐n junctions as demonstrated in the Ni/NiO/ZnO/PPy sensor. The good anti‐interference properties and ultrahigh sensitivity of this sensing mode offers new opportunities in trace analyte detection in harsh environments such as seawater.
Vilar Compte R, Summers P, Lewis B, et al., 2021, Visualising G-quadruplex DNA dynamics in live cells by fluorescence lifetime imaging microscopy, Nature Communications, Vol: 12, ISSN: 2041-1723
Guanine rich regions of oligonucleotides fold into quadruple-stranded structures called G-quadruplexes (G4s). Increasing evidence suggests that these G4 structures form in vivo and play a crucial role in cellular processes. However, their direct observation in live cells remains a challenge. Here we demonstrate that a fluorescent probe (DAOTA-M2) in conjunction with fluorescence lifetime imaging microscopy (FLIM) can identify G4s within nuclei of live and fixed cells. We present a FLIM-based cellular assay to study the interaction of non-fluorescent small molecules with G4s and apply it to a wide range of drug candidates. We also demonstrate that DAOTA-M2 can be used to study G4 stability in live cells. Reduction of FancJ and RTEL1 expression in mammalian cells increases the DAOTA-M2 lifetime and therefore suggests an increased number of G4s in these cells, implying that FancJ and RTEL1 play a role in resolving G4 structures in cellulo.
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.
Ma Y, Sikdar D, He Q, et al., 2020, Self-assembling two-dimensional nanophotonic arrays for reflectivity-based sensing, Chemical Science, Vol: 11, Pages: 9563-9570, ISSN: 2041-6520
We propose a nanoplasmonic platform that can be used for sensing trace levels of heavy metals in solutions via simple optical reflectivity measurements. The considered example is a lead sensor, which relies on the lead-mediated assembly of glutathione-functionalized gold nanoparticles (NPs) at a self-healing water/DCE liquid | liquid interface (LLI). Capillary forces tend to trap each NP at the LLI while the negatively charged ligands prevent the NPs settling too close to each other. In the presence of lead, due to chelation between the lead ion and glutathione ligand, the NPs assemble into a dense quasi-2D interfacial array. Such a dense assembly of plasmonic NPs can generate a remarkable broad-band reflectance signal, which is absent when NPs are adsorbed at the interface far apart from each other. The condensing effect of the LLI and the plasmonic coupling effect among the NP array gives rise to a dramatic enhancement of the reflectivity signals. Importantly, we show that our theory of the optical reflectivity from such an array of NPs works in perfect harmony with the physics and chemistry of the system with the key parameter being the interparticle distance at the interface. As a lead sensor, the system is fast, stable, and can achieve detection limits down to 14 ppb. Future alternative recognizing ligands can be used to build sister platforms for detecting other heavy metals.
Xue L, Yamazaki H, Ren R, et al., 2020, Solid-state nanopore sensors, Nature Reviews Materials, Vol: 5, Pages: 931-951, 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
The behaviour of two molecular rotors, one charged – 3,3′-diethylthiacarbocyanine iodide (Cy3) and one neutral – 8-[4-decyloxyphenyl]-4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY-C10), have been studied in various ionic liquids. The fluorescent decay lifetime has been used to elucidate the structure of the immediate region around the rotor. The neutral BODIPY-C10 was found to prefer the non-polar alkyl chain environment, leading to two trends in the lifetime of the dye: one when it was fully partitioned into the non-polar domain, and one when it also sampled polar moieties. The positively charged Cy3 dye showed a complex relationship between the bulk viscosity of the ionic liquid and lifetime of the molecular rotor. This was attributed to a combination of polarity related spectral changes, changes in anion cages around the dye, and temperature dependent fluorescent lifetimes alongside the dependence of the rotor upon the viscosity.
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.
Ma Y, Sikdar D, Fedosyuk A, et al., 2020, Electrotunable nanoplasmonics for amplified surface enhanced Raman spectroscopy, ACS Nano, Vol: 14, Pages: 328-336, ISSN: 1936-0851
Tuning the properties of optical metamaterials in real time is one of the grand challenges of photonics. Being able to do so will enable a new class of photonic materials for use in applications such as surface enhanced Raman spectroscopy and reflectors/absorbers. One strategy to achieving this goal is based on the electrovariable self-assembly and disassembly of two-dimensional nanoparticle arrays at a metal liquid interface. As expected the structure results in plasmonic coupling between NPs in the array but perhaps as importantly between the array and the metal surface. In such a system the density of the nanoparticle array can be controlled by the variation of electrode potential. Due to the additive effect, we show that less than 1 V variation of electrode potential can give rise to a dramatic simultaneous change in optical reflectivity from ~93 % to ~1 % and the amplification of the SERS signal by up to 5 orders of magnitude. The process allows for reversible tunability. These concepts are demonstrated in this manuscript, using a platform based on the voltage-controlled assembly of 40 nm Au-nanoparticle arrays at a TiN/Ag electrode in contact with an aqueous electrolyte. We show that all the physics underpinning the behaviour of this platform works precisely as suggested by the proposed theory, setting the electrochemical nanoplasmonics as a promising new direction in photonics research.
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.
Ma Y, Sikdar D, Fedosyuk A, et al., 2019, An auxetic thermo-responsive nanoplasmonic optical switch., ACS Applied Materials and Interfaces, ISSN: 1944-8244
Development and use of metamaterials have been gaining prominence in large part due to the possibility of creating platforms with 'disruptive' and unique optical properties. However, to date the majority of such systems produced using micro or nanotechnology, are static and can only perform certain target functions. Next-generation multifunctional smart optical metamaterials are expected to have tuneable elements with the possibility of controlling the optical properties in real time via variation in parameters such as pressure, mechanical stress, voltage, or through non-linear optical effects. Here, we address this challenge by developing a thermally controlled optical switch, based on the self-assembly of poly(N-isopropylacrylamide)-functionalised gold nanoparticles on a planar macroscale gold substrate. We show that such meta-surfaces can be tuned to exhibit substantial changes in the optical properties both in terms of wavelength and intensity, through the temperature-controlled variation of the interparticle distance within the nanoparticle monolayer as well as its separation from the substrate. This change is based on temperature induced auxetic expansion and contraction of the functional ligands. Such a system has potential for numerous applications, ranging from thermal sensors to regulated light harnessing.
Kubánková M, Lin X, Albrecht T, et al., 2019, Rapid fragmentation during seeded lysozyme aggregation revealed at the single molecule level, Analytical Chemistry, Vol: 91, Pages: 6880-6886, ISSN: 0003-2700
Protein aggregation is associated with neurodegenerative disorders such as Alzheimer's and Parkinson's diseases. The poorly understood pathogenic mechanism of amyloid diseases makes early stage diagnostics or therapeutic intervention a challenge. Seeded polymerization that reduces the duration of the lag phase and accelerates fibril growth is a widespread model to study amyloid formation. Seeding effects are hypothesized to be important in the "infectivity" of amyloids and are linked to the development of systemic amyloidosis in vivo. The exact mechanism of seeding is unclear yet critical to illuminating the propagation of amyloids. Here we report on the lateral and axial fragmentation of seed fibrils in the presence of lysozyme monomers at short time scales, followed by the generation of oligomers and growth of fibrils.
Cai S, Sze YYJ, Ivanov A, et al., 2019, Small molecule electro-optical binding assay using nanopores, Nature Communications, Vol: 10, Pages: 1-9, ISSN: 2041-1723
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.
Paulose Nadappuram B, Cadinu P, Barik A, et al., 2019, Nanoscale tweezers for single-cell biopsies, Nature Nanotechnology, Vol: 14, Pages: 80-88, ISSN: 1748-3387
Much of the functionality of multicellular systems arises from the spatial organization 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-cell analysis. 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 used for 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.
Ma Y, Zagar C, Klemme DJ, et al., 2018, A tunable nanoplasmonic mirror at an electrochemical interface, ACS Photonics, Vol: 5, Pages: 4604-4616, ISSN: 2330-4022
Designing tunable optical metamaterials is one of the great challenges in photonics. Strategies for reversible tuning of nanoengineered devices are currently being sought through electromagnetic or piezo effects. For example, bottom-up self-assembly of nanoparticles at solid | liquid or liquid | liquid interfaces can be used to tune optical responses by varying their structure either chemically or through applied voltage. Here, we report on a fully reversible tunable-color mirror based on a TiN-coated Ag substrate immersed in an aqueous solution of negatively charged Au-nanoparticles (NPs). Switching electrode potential can be used to fully control the assembly/disassembly of NPs at the electrode | electrolyte interface within a 0.6 V wide electrochemical window. The plasmon coupling between the electrode and the adsorbed NP array at high positive potentials produces a dip in the optical reflectance spectrum, creating the "absorber" state. Desorption of NPs at low potentials eliminates the dip, returning the system to the reflective "mirror" state. The intensity and wavelength of the dip can be finely tuned through electrode-potential and electrolyte concentration. The excellent match between the experimental data and the theory of optical response for such system allows us to extract valuable information on equilibrium and kinetic properties of NP-assembly/disassembly. Together with modeling of the latter, this study promotes optimization of such meta-surfaces for building electrotunable reflector devices.
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.
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