Nanopore analytics: sensing of single molecules
TL;DR: In nanopore analytics, individual molecules pass through a single nanopore giving rise to detectable temporary blockades in ionic pore current, which ranges from nucleic acids, peptides, proteins, and biomolecular complexes to organic polymers and small molecules.
Abstract: In nanopore analytics, individual molecules pass through a single nanopore giving rise to detectable temporary blockades in ionic pore current. Reflecting its simplicity, nanopore analytics has gained popularity and can be conducted with natural protein as well as man-made polymeric and inorganic pores. The spectrum of detectable analytes ranges from nucleic acids, peptides, proteins, and biomolecular complexes to organic polymers and small molecules. Apart from being an analytical tool, nanopores have developed into a general platform technology to investigate the biophysics, physicochemistry, and chemistry of individual molecules (critical review, 310 references).
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University of Cambridge1, Istituto Italiano di Tecnologia2, Lancaster University3, University of Manchester4, Catalan Institution for Research and Advanced Studies5, Technical University of Denmark6, Nokia7, Queen Mary University of London8, University of Trento9, fondazione bruno kessler10, Technische Universität München11, Polytechnic University of Milan12, Centre national de la recherche scientifique13, University of Trieste14, University of Ioannina15, University of Geneva16, Trinity College, Dublin17, Texas Instruments18, University of Paris19, Spanish National Research Council20, Leiden University21, Delft University of Technology22, University of Patras23, École Normale Supérieure24, Radboud University Nijmegen25, Nest Labs26, Airbus UK27, Seoul National University28, Yonsei University29, University of Oxford30, Chalmers University of Technology31, University of Groningen32, STMicroelectronics33, Chemnitz University of Technology34, Max Planck Society35, Aalto University36
TL;DR: An overview of the key aspects of graphene and related materials, ranging from fundamental research challenges to a variety of applications in a large number of sectors, highlighting the steps necessary to take GRMs from a state of raw potential to a point where they might revolutionize multiple industries are provided.
Abstract: We present the science and technology roadmap for graphene, related two-dimensional crystals, and hybrid systems, targeting an evolution in technology, that might lead to impacts and benefits reaching into most areas of society. This roadmap was developed within the framework of the European Graphene Flagship and outlines the main targets and research areas as best understood at the start of this ambitious project. We provide an overview of the key aspects of graphene and related materials (GRMs), ranging from fundamental research challenges to a variety of applications in a large number of sectors, highlighting the steps necessary to take GRMs from a state of raw potential to a point where they might revolutionize multiple industries. We also define an extensive list of acronyms in an effort to standardize the nomenclature in this emerging field.
2,560 citations
TL;DR: A platform for the rapid electronic detection of probe-hybridized microRNAs from cellular RNA is presented, in which a target microRNA is first hybridized to a probe and enriched through binding to the viral protein p19.
Abstract: Small RNA molecules have an important role in gene regulation and RNA silencing therapy, but it is challenging to detect these molecules without the use of time-consuming radioactive labelling assays or error-prone amplification methods. Here, we present a platform for the rapid electronic detection of probe-hybridized microRNAs from cellular RNA. In this platform, a target microRNA is first hybridized to a probe. This probe:microRNA duplex is then enriched through binding to the viral protein p19. Finally, the abundance of the duplex is quantified using a nanopore. Reducing the thickness of the membrane containing the nanopore to 6 nm leads to increased signal amplitudes from biomolecules, and reducing the diameter of the nanopore to 3 nm allows the detection and discrimination of small nucleic acids based on differences in their physical dimensions. We demonstrate the potential of this approach by detecting picogram levels of a liver-specific miRNA from rat liver RNA.
664 citations
TL;DR: In single-channel electrophysiological measurements, the authors found similarities to the response of natural ion channels, such as conductances on the order of 1 nanosiemens and channel gating, and show that the synthetic channels can be used to discriminate single DNA molecules.
Abstract: We created nanometer-scale transmembrane channels in lipid bilayers by means of self-assembled DNA-based nanostructures. Scaffolded DNA origami was used to create a stem that penetrated and spanned a lipid membrane, as well as a barrel-shaped cap that adhered to the membrane, in part via 26 cholesterol moieties. In single-channel electrophysiological measurements, we found similarities to the response of natural ion channels, such as conductances on the order of 1 nanosiemens and channel gating. More pronounced gating was seen for mutations in which a single DNA strand of the stem protruded into the channel. Single-molecule translocation experiments show that the synthetic channels can be used to discriminate single DNA molecules.
653 citations
TL;DR: Past and current studies related to nucleic acid biophysics are surveyed, and will hopefully provoke a discussion of immediate and future prospects for the field.
568 citations
TL;DR: It is shown that coating nanopores with fluid bilayer lipids allows the pore diameters to be fine-tuned in sub-nanometre increments, and incorporation of mobile ligands in the lipid conferred specificity and slowed down the translocation of targeted proteins sufficiently to time-resolve translocation events of individual proteins.
Abstract: Synthetic nanopores have been used to study individual biomolecules in high throughput, but their performance as sensors does not match that of biological ion channels. Challenges include control of nanopore diameters and surface chemistry, modification of the translocation times of single-molecule analytes through nanopores, and prevention of non-specific interactions with pore walls. Here, inspired by the olfactory sensilla of insect antennae, we show that coating nanopores with a fluid lipid bilayer tailors their surface chemistry and allows fine-tuning and dynamic variation of pore diameters in subnanometre increments. Incorporation of mobile ligands in the lipid bilayer conferred specificity and slowed the translocation of targeted proteins sufficiently to time-resolve translocation events of individual proteins. Lipid coatings also prevented pores from clogging, eliminated non-specific binding and enabled the translocation of amyloid-beta (Ab) oligomers and fibrils. Through combined analysis of their translocation time, volume, charge, shape and ligand affinity, different proteins were identified.
547 citations
Cites background or methods from "Nanopore analytics: sensing of sing..."
...Moreover, for a protein with known charge, translocation experiments combined with equation (3), make it possible to determine – non-optically – the lateral diffusion constants of lipids and therefore the fluidity of bilayers within seconds (Table 2)....
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...456, equation (3) predicted a translocation time for streptavidin of 126 ± 29 μs in POPC-coated pores and of 91 ± 21 μs in DΔPPC-coated pores....
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...The excellent agreement between the data (black squares) and the predicted td values (red curve) supports the simple model used for the derivation of equation (3)....
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...Equation (3) made it possible to compare theoretically predicted td values with experimentally determined values for proteins with known net charge....
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...Based on these assumptions, we derived equation (3) to predict td values theoretically (for a detailed derivation and additional assumptions made, see Supplementary Section S8):...
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References
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TL;DR: The extracellular patch clamp method, which first allowed the detection of single channel currents in biological membranes, has been further refined to enable higher current resolution, direct membrane patch potential control, and physical isolation of membrane patches.
Abstract: 1. The extracellular patch clamp method, which first allowed the detection of single channel currents in biological membranes, has been further refined to enable higher current resolution, direct membrane patch potential control, and physical isolation of membrane patches. 2. A description of a convenient method for the fabrication of patch recording pipettes is given together with procedures followed to achieve giga-seals i.e. pipette-membrane seals with resistances of 10(9) - 10(11) omega. 3. The basic patch clamp recording circuit, and designs for improved frequency response are described along with the present limitations in recording the currents from single channels. 4. Procedures for preparation and recording from three representative cell types are given. Some properties of single acetylcholine-activated channels in muscle membrane are described to illustrate the improved current and time resolution achieved with giga-seals. 5. A description is given of the various ways that patches of membrane can be physically isolated from cells. This isolation enables the recording of single channel currents with well-defined solutions on both sides of the membrane. Two types of isolated cell-free patch configurations can be formed: an inside-out patch with its cytoplasmic membrane face exposed to the bath solution, and an outside-out patch with its extracellular membrane face exposed to the bath solution. 6. The application of the method for the recording of ionic currents and internal dialysis of small cells is considered. Single channel resolution can be achieved when recording from whole cells, if the cell diameter is small (less than 20 micrometer). 7. The wide range of cell types amenable to giga-seal formation is discussed.
17,136 citations
TL;DR: Monolayers of alkanethiolates on gold are probably the most studied SAMs to date and offer the needed design flexibility, both at the individual molecular and at the material levels, and offer a vehicle for investigation of specific interactions at interfaces, and of the effect of increasing molecular complexity on the structure and stability of two-dimensional assemblies.
Abstract: The field of self-assembled monolayers (SAMs) has witnessed tremendous growth in synthetic sophistication and depth of characterization over the past 15 years.1 However, it is interesting to comment on the modest beginning and on important milestones. The field really began much earlier than is now recognized. In 1946 Zisman published the preparation of a monomolecular layer by adsorption (self-assembly) of a surfactant onto a clean metal surface.2 At that time, the potential of self-assembly was not recognized, and this publication initiated only a limited level of interest. Early work initiated in Kuhn’s laboratory at Gottingen, applying many years of experience in using chlorosilane derivative to hydrophobize glass, was followed by the more recent discovery, when Nuzzo and Allara showed that SAMs of alkanethiolates on gold can be prepared by adsorption of di-n-alkyl disulfides from dilute solutions.3 Getting away from the moisture-sensitive alkyl trichlorosilanes, as well as working with crystalline gold surfaces, were two important reasons for the success of these SAMs. Many self-assembly systems have since been investigated, but monolayers of alkanethiolates on gold are probably the most studied SAMs to date. The formation of monolayers by self-assembly of surfactant molecules at surfaces is one example of the general phenomena of self-assembly. In nature, self-assembly results in supermolecular hierarchical organizations of interlocking components that provides very complex systems.4 SAMs offer unique opportunities to increase fundamental understanding of self-organization, structure-property relationships, and interfacial phenomena. The ability to tailor both head and tail groups of the constituent molecules makes SAMs excellent systems for a more fundamental understanding of phenomena affected by competing intermolecular, molecular-substrates and molecule-solvent interactions like ordering and growth, wetting, adhesion, lubrication, and corrosion. That SAMs are well-defined and accessible makes them good model systems for studies of physical chemistry and statistical physics in two dimensions, and the crossover to three dimensions. SAMs provide the needed design flexibility, both at the individual molecular and at the material levels, and offer a vehicle for investigation of specific interactions at interfaces, and of the effect of increasing molecular complexity on the structure and stability of two-dimensional assemblies. These studies may eventually produce the design capabilities needed for assemblies of three-dimensional structures.5 However, this will require studies of more complex systems and the combination of what has been learned from SAMs with macromolecular science. The exponential growth in SAM research is a demonstration of the changes chemistry as a disciAbraham Ulman was born in Haifa, Israel, in 1946. He studied chemistry in the Bar-Ilan University in Ramat-Gan, Israel, and received his B.Sc. in 1969. He received his M.Sc. in phosphorus chemistry from Bar-Ilan University in 1971. After a brief period in industry, he moved to the Weizmann Institute in Rehovot, Israel, and received his Ph.D. in 1978 for work on heterosubstituted porphyrins. He then spent two years at Northwestern University in Evanston, IL, where his main interest was onedimensional organic conductors. In 1985 he joined the Corporate Research Laboratories of Eastman Kodak Company, in Rochester, NY, where his research interests were molecular design of materials for nonlinear optics and self-assembled monolayers. In 1994 he moved to Polytechnic University where he is the Alstadt-Lord-Mark Professor of Chemistry. His interests encompass self-assembled monolayers, surface engineering, polymers at interface, and surfaces phenomena. 1533 Chem. Rev. 1996, 96, 1533−1554
7,465 citations
TL;DR: It is shown that an electric field can drive single-stranded RNA and DNA molecules through a 2.6-nm diameter ion channel in a lipid bilayer membrane, which could in principle provide direct, high-speed detection of the sequence of bases in single molecules of DNA or RNA.
Abstract: We show that an electric field can drive single-stranded RNA and DNA molecules through a 2.6-nm diameter ion channel in a lipid bilayer membrane. Because the channel diameter can accommodate only a single strand of RNA or DNA, each polymer traverses the membrane as an extended chain that partially blocks the channel. The passage of each molecule is detected as a transient decrease of ionic current whose duration is proportional to polymer length. Channel blockades can therefore be used to measure polynucleotide length. With further improvements, the method could in principle provide direct, high-speed detection of the sequence of bases in single molecules of DNA or RNA.
3,251 citations
01 Jan 1996
TL;DR: The action potential is triggered when the membrane potential, which was at the resting level, depolarizes and reaches the threshold of excitation, which triggers the action potential.
Abstract: Excitability. Excitability of cell membranes is crucial for signaling in many types of cell. Excitation in the physiological sense means that the cell membrane potential undergoes characteristic changes which, in most cases, go in the depolarizing direction. Single depolarization from the resting potential to potentials near 0 mV has generally been called an action potential. A schematic representation of a neuronal action potential is given in Fig. 12.1 A. The action potential is triggered when the membrane potential, which was at the resting level, depolarizes and reaches the threshold of excitation. This depolarization, which triggers the action potential, is generated by depolarizing synaptic currents, or depolarizing current coming from a membrane region that is already excited (propagation of an action potential), or by pacemaker currents mediated by pacemaker channels, or by current injected externally by an electrode. The duration of different types of action potential varies from seconds to less than 1 ms.
3,016 citations
Harvard University1, University of California, Santa Cruz2, University of British Columbia3, University of Oxford4, University of Washington5, University of California, San Diego6, Oak Ridge National Laboratory7, Arizona State University8, Brown University9, Case Western Reserve University10, Boston University11, University of North Carolina at Chapel Hill12, North Carolina State University13, National Institutes of Health14
TL;DR: A nanopore-based device provides single-molecule detection and analytical capabilities that are achieved by electrophoretically driving molecules in solution through a nano-scale pore, a unique analytical capability that makes inexpensive, rapid DNA sequencing a possibility.
Abstract: A nanopore-based device provides single-molecule detection and analytical capabilities that are achieved by electrophoretically driving molecules in solution through a nano-scale pore. The nanopore provides a highly confined space within which single nucleic acid polymers can be analyzed at high throughput by one of a variety of means, and the perfect processivity that can be enforced in a narrow pore ensures that the native order of the nucleobases in a polynucleotide is reflected in the sequence of signals that is detected. Kilobase length polymers (single-stranded genomic DNA or RNA) or small molecules (e.g., nucleosides) can be identified and characterized without amplification or labeling, a unique analytical capability that makes inexpensive, rapid DNA sequencing a possibility. Further research and development to overcome current challenges to nanopore identification of each successive nucleotide in a DNA strand offers the prospect of 'third generation' instruments that will sequence a diploid mammalian genome for ∼$1,000 in ∼24 h.
2,512 citations