Latest Articles Include:
- The rise and rise of graphene
- UNKNOWN 5(11):755 (2010)
This year's Nobel Prize in Physics can be seen as part of the larger story of hexagonally bonded carbon. - Who or what is 'the public'?
- UNKNOWN 5(11):757-758 (2010)
It is essential to recognize the heterogeneous nature of 'the public' in engagement activities and to treat people as citizens rather than as mere laypersons, consumers or stakeholders. - Our choice from the recent literature
- UNKNOWN 5(11):759 (2010)
Scanning probe microscopy: Full speed ahead Nanobiomagnetometry: Quantum jump for sensors Solar cells: Quantum dots beat the limit Nanofluidics: A repulsive trap - DNA nanotechnology: Steps towards automated synthesis
- UNKNOWN 5(11):760-761 (2010)
A DNA walker moving along a DNA track can perform a series of organic reactions in a single solution without external intervention. - Magnetoelectrics: Making metallic memories
- UNKNOWN 5(11):761-762 (2010)
A phase transition at the surface of a thin film of iron can be exploited to create a metallic non-volatile memory. - Biosensing: Plasmons offer a helping hand
- UNKNOWN 5(11):762-763 (2010)
Arrays of metallic nanostructures allow chiral biomolecules to be detected and characterized with increased sensitivity. - Electron microscopy: A new spin on electron beams
- UNKNOWN 5(11):764-765 (2010)
Ideas about angular momentum that have been borrowed from optics could allow the magnetic and spin structures of materials to be studied on atomic scales with electron vortex beams. - DNA sequencing: Detecting methylation with force
- UNKNOWN 5(11):765-766 (2010)
An atomic force microscope with antibodies attached to its tip can be used to determine methylation patterns in individual DNA strands by making hundreds of force spectroscopy measurements. - Biomolecular computing: Learning through play
- UNKNOWN 5(11):767-768 (2010)
Solutions of DNA-based molecules can be taught to play a simple game in a process that does not require the operator to be familiar with the underlying molecular programming. - Exciton-like trap states limit electron mobility in TiO2 nanotubes
- UNKNOWN 5(11):769-772 (2010)
Nature Nanotechnology | Letter Exciton-like trap states limit electron mobility in TiO2 nanotubes * Christiaan Richter1 Search for this author in: * NPG journals * PubMed * Google Scholar * Charles A. Schmuttenmaer1charles.schmuttenmaer@yale.edu Search for this author in: * NPG journals * PubMed * Google Scholar * Affiliations * Contributions * Corresponding authorsJournal name:Nature NanotechnologyVolume: 5 ,Pages:769–772Year published:(2010)DOI:doi:10.1038/nnano.2010.196Received21 May 2010Accepted07 September 2010Published online17 October 2010 Abstract * Abstract * Author information * Supplementary information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Nanoparticle films have become a promising low-cost, high-surface-area electrode material for solar cells and solar fuel production1, 2. Compared to sintered nanoparticle films, oriented polycrystalline titania nanotubes offer the advantage of directed electron transport, and are expected to have higher electron mobility3, 4, 5, 6, 7. However, macroscopic measurements have revealed their electron mobility to be as low as that of nanoparticle films8, 9. Here, we show, through time-resolved terahertz spectroscopy10, that low mobility in polycrystalline TiO2 nanotubes is not due to scattering from grain boundaries or disorder-induced localization as in other nanomaterials11, 12, but instead results from a single sharp resonance arising from exciton-like trap states. If the number of these states can be lowered, this could lead to improved electron transport in titania nanotubes and significantly better solar cell performance. View full text Subject terms: * Electronic properties and devices * Nanoparticles Figures at a glance * Figure 1: Scanning electron microscopy images of TiO2 nanotube arrays fabricated by anodization. * Figure 2: Frequency-dependent photoconductivities. ,, Real () and imaginary () photoconductivities of rutile single crystal (green), Degussa P25 nanoparticle film (black) and nanotube sample (blue). All samples were stained with N3 dye, and the terahertz spectra were taken within 10 ps after photoexcitation with a 400-nm pulse. The data (open circles) are fit by the standard Drude model for the single crystal, the Drude–Smith model for the nanoparticles, and a Lorentz oscillator plus power law conductivity for the nanotubes. All spectra are scaled to the maximum of their respective σ1(ω) for comparison. * Figure 3: Photoconductivity of a TiO2 nanotube sample. ,, Real () and imaginary () photoconductivities of a TiO2 nanotube sample (400 °C anneal for 1 h, stained with N3 dye). Data (dotted lines) and best fits to the data (solid lines) are shown. The spectra are offset by 2 S m−1 from each other and labelled with the time in picoseconds after photoexcitation (0.2–21 ps) by a 400-nm pulse. Similar plots for samples annealed at higher temperature (475 °C) and photoexcited at both 400 and 800 nm may be seen in the Supplementary Information. * Figure 4: Fitting parameter γ as a function of time after photoexcitation. Black filled circles represent data for a sample annealed at 400 °C, and red squares a sample annealed at 475 °C. The open symbols are those at a delay time of 1 ps. Author information * Abstract * Author information * Supplementary information Affiliations * Department of Chemistry, Yale University, 225 Prospect St., New Haven, Connecticut 06520-8107 USA * Christiaan Richter & * Charles A. Schmuttenmaer Contributions C.R. and C.A.S. conceived and designed the experiments, analysed the data and co-wrote the paper. C.R. performed the experiments. Competing financial interests The authors declare no competing financial interests. Corresponding authors Correspondence to: * Christiaan Richter (Present address: Rochester Institute of Technology, Chemical and Biomedical Engineering, 160 Lomb Memorial Drive, Rochester, New York 14623-5603 USA) or * Charles A. Schmuttenmaer (charles.schmuttenmaer@yale.edu) Supplementary information * Abstract * Author information * Supplementary information PDF files * Supplementary information (1,393 KB) Supplementary information Additional data - Training a molecular automaton to play a game
- UNKNOWN 5(11):773-777 (2010)
Nature Nanotechnology | Letter Training a molecular automaton to play a game * Renjun Pei1 Search for this author in: * NPG journals * PubMed * Google Scholar * Elizabeth Matamoros1 Search for this author in: * NPG journals * PubMed * Google Scholar * Manhong Liu1, 5 Search for this author in: * NPG journals * PubMed * Google Scholar * Darko Stefanovic3, 4 Search for this author in: * NPG journals * PubMed * Google Scholar * Milan N. Stojanovic1, 2mns18@columbia.edu Search for this author in: * NPG journals * PubMed * Google Scholar * Affiliations * Contributions * Corresponding authorJournal name:Nature NanotechnologyVolume: 5 ,Pages:773–777Year published:(2010)DOI:doi:10.1038/nnano.2010.194Received25 March 2010Accepted02 September 2010Published online24 October 2010 Abstract * Abstract * Author information * Supplementary information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Research at the interface between chemistry and cybernetics has led to reports of 'programmable molecules', but what does it mean to say 'we programmed a set of solution-phase molecules to do X'? A survey of recently implemented solution-phase circuitry1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 indicates that this statement could be replaced with 'we pre-mixed a set of molecules to do X and functional subsets of X'. These hard-wired mixtures are then exposed to a set of molecular inputs, which can be interpreted as being keyed to human moves in a game, or as assertions of logical propositions. In nucleic acids-based systems, stemming from DNA computation16, 17, 18, 19, 20, these inputs can be seen as generic oligonucleotides. Here, we report using reconfigurable21, 22, 23 nucleic acid catalyst-based units to build a multipurpose reprogrammable molecular automaton that goes beyond single-purpose 'hard-wired' molecular automata. The automaton covers all ! possible responses to two consecutive sets of four inputs (such as four first and four second moves for a generic set of trivial two-player two-move games). This is a model system for more general molecular field programmable gate array (FPGA)-like devices that can be programmed by example, which means that the operator need not have any knowledge of molecular computing methods. View full text Subject terms: * Molecular machines and motors * Nanobiotechnology Figures at a glance * Figure 1: Schematic presentation of the game of tit-for-tat. , Example of the game of tit-for-tat perfectly played. The second player (automaton) achieves its goal, marking a fresh quadrant after each of the first player's moves. The first player's new moves are represented by a blue filled circle and previous moves by a black filled circle. The automaton's new moves are represented by a red open circle and previous moves by a black open circle. In this simple game, the second player's strategy is entirely determined by its response to the first player's first move. , One strategy, 'counterclockwise', is shown; we use mnemonic names to describe strategies, and 'counterclockwise' indicates that the automaton's responses lag behind human moves. –, Training procedure for the 'counterclockwise' strategy. Training consists of splitting a solution-phase automaton into four wells (representing the four quadrants) and going through a procedure as follows: a human (trainer) points to the well, and says 'if on the first move I p! lay in this well (n = 1, 2, 3 or 4), you will play here', simultaneously injecting a solution keyed to the human's move (that is, containing tmn, where m = 1 or 2 for the first or the second move) into the 'here' well n. For the second move, the procedure is similar. The procedure is repeated for all moves in the strategy. At the end of the procedure (addition of the training oligonucleotides t12, t22, t23 into well 1, t14, t21, t24 into well 2, t11, t21, t24 into well 3 and t13, t22, t23 into well 4), the automaton is ready, and will play back the game according to the trained strategy. * Figure 2: Basic molecular logic units and their activation during training and game play. , A two-input AND gate (i11ANDt11) is turned, upon addition of a training input (t11), into a single-input YES gate (YESi11). The training input is the complement of an oligonucleotide (inh11) that is pre-complexed with the gate, inhibiting the enzymatic activity of the deoxyribozyme. The single-input YES gate is activated by the play input i11 to cleave the double end-labelled substrate. , A three-input ANDAND gate (i11ANDi22ANDt22) is turned into a two-input AND gate (i11ANDi22) by a training input (t22) complementary to an oligonucleotide (inh22) that is pre-complexed with the gate. The two-input AND gate is activated by the play inputs i11 and i22 to cleave the double end-labelled substrate. * Figure 3: Demonstration of training and play-back. , Layout of molecular logic in a well before training; all four wells contain identical molecular logic units. , Layout of molecular logic in the four wells of the automaton trained according to a 'counterclockwise' strategy (only the trimmed gates are shown, for simplicity of presentation). , Representative game-play for the 'counterclockwise' strategy. The automaton was trained by a 'counterclockwise' strategy as shown in Fig. 1. In board representation, the human's new moves are represented by blue filled circles, previous moves by black filled circles, and the automaton's new moves are represented by red open circles and previous moves by black open circles. Inputs triggering these moves are also indicated. In bar graph representation, the experimental results for 30 min after the addition of inputs into all wells are shown with well numbers on the horizontal axis and fluorescence change (ΔF) on the vertical axis. Readouts for new moves are given in red; in ! the second-move displays, old (first) move readouts are given in black. Author information * Abstract * Author information * Supplementary information Affiliations * Division of Experimental Therapeutics, Department of Medicine, Columbia University, New York, USA * Renjun Pei, * Elizabeth Matamoros, * Manhong Liu & * Milan N. Stojanovic * Department of Biomedical Engineering, Columbia University, New York, USA * Milan N. Stojanovic * Department of Computer Science, University of New Mexico, Albuquerque, New Mexico, USA * Darko Stefanovic * Center for Biomedical Engineering, University of New Mexico, Albuquerque, New Mexico, USA * Darko Stefanovic * Present address: School of Chemistry and Biotechnology, Yunnan University of Nationalities, Yunnan, China * Manhong Liu Contributions R.P. supervised and coordinated experimental efforts, optimized gates, performed the majority of experiments, analysed results and participated in writing the paper. E.M. participated in the initial ideation of the game, performed experiments and analysed results. M.L. performed experiments and analysed results. D.S. performed the game strategy analysis computationally, ran simulations and participated in writing the paper. M.N.S. initiated the project, proposed the game with E.M., and wrote the initial version of the paper. Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * Milan N. Stojanovic (mns18@columbia.edu) Supplementary information * Abstract * Author information * Supplementary information PDF files * Supplementary information (10,799 KB) Supplementary information Additional data - Autonomous multistep organic synthesis in a single isothermal solution mediated by a DNA walker
- UNKNOWN 5(11):778-782 (2010)
Nature Nanotechnology | Letter Autonomous multistep organic synthesis in a single isothermal solution mediated by a DNA walker * Yu He1 Search for this author in: * NPG journals * PubMed * Google Scholar * David R. Liu1drliu@fas.harvard.edu Search for this author in: * NPG journals * PubMed * Google Scholar * Affiliations * Contributions * Corresponding authorJournal name:Nature NanotechnologyVolume: 5 ,Pages:778–782Year published:(2010)DOI:doi:10.1038/nnano.2010.190Received19 April 2010Accepted23 August 2010Published online10 October 2010 Abstract * Abstract * Author information * Supplementary information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Multistep synthesis in the laboratory typically requires numerous reaction vessels, each containing a different set of reactants. In contrast, cells are capable of performing highly efficient and selective multistep biosynthesis under mild conditions with all reactants simultaneously present in solution1, 2, 3, 4. If the latter approach could be applied in the laboratory, it could improve the ease, speed and efficiency of multistep reaction sequences. Here, we show that a DNA mechanical device—a DNA walker moving along a DNA track—can be used to perform a series of amine acylation reactions in a single solution without any external intervention. The products of these reactions are programmed by the sequence of the DNA track, but they are not related to the structure of DNA. Moreover, they are formed with speeds and overall yields that are significantly greater than those previously achieved by multistep DNA-templated small-molecule synthesis. View full text Subject terms: * Molecular machines and motors * Nanobiotechnology Figures at a glance * Figure 1: Overview of the DNAsome system. , The system described in this work comprises six DNA or DNA-linked molecules. Three substrates (–) and an initiator () can hybridize on a single-stranded DNA track (). Each substrate has an amino acid NHS ester at its 5′ end and two ribonucleotides (green dot) in the middle of its DNA sequence. The DNA walker () contains a 3′ amine group and an RNA-cleaving DNAzyme (purple line) that can cleave the ribonucleotides in the substrates. , DNAsome-mediated multistep synthesis of a triamide product. All steps take place in a single solution under one set of reaction conditions without external intervention. * Figure 2: Analysis of reaction products generated by the DNAsome system. , Mass spectroscopy analysis of the three-step DNAsome-mediated reaction sequence. See main text for a detailed description of reaction conditions. , Mass spectrometry analysis of the experiment in repeated using substrates lacking amino-acid NHS esters. See Supplementary Information for all expected and observed masses. * Figure 3: Mass spectroscopy analysis of reactions identical to the one shown in Fig. 2a, but using different DNA tracks or with no DNA track. , The DNA tracks are I–C1–C3–C2 (), I–C2–C3–C1 (), I–C3–C2–C1 () and no DNA track (). See Supplementary Information for all expected and observed masses. Author information * Abstract * Author information * Supplementary information Affiliations * Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA * Yu He & * David R. Liu Contributions Y.H. and D.L. conceived and designed the project, analysed the data and wrote the manuscript. Y.H. performed the experiments. Competing financial interests D.L. is a consultant for Ensemble Discovery, a company that uses DNA-templated synthesis for industrial applications. Corresponding author Correspondence to: * David R. Liu (drliu@fas.harvard.edu) Supplementary information * Abstract * Author information * Supplementary information PDF files * Supplementary information (1,205 KB) Supplementary information Additional data - Ultrasensitive detection and characterization of biomolecules using superchiral fields
- UNKNOWN 5(11):783-787 (2010)
Nature Nanotechnology | Letter Ultrasensitive detection and characterization of biomolecules using superchiral fields * E. Hendry1 Search for this author in: * NPG journals * PubMed * Google Scholar * T. Carpy2 Search for this author in: * NPG journals * PubMed * Google Scholar * J. Johnston2, 3 Search for this author in: * NPG journals * PubMed * Google Scholar * M. Popland2 Search for this author in: * NPG journals * PubMed * Google Scholar * R. V. Mikhaylovskiy1 Search for this author in: * NPG journals * PubMed * Google Scholar * A. J. Lapthorn2 Search for this author in: * NPG journals * PubMed * Google Scholar * S. M. Kelly4 Search for this author in: * NPG journals * PubMed * Google Scholar * L. D. Barron2 Search for this author in: * NPG journals * PubMed * Google Scholar * N. Gadegaard3 Search for this author in: * NPG journals * PubMed * Google Scholar * M. Kadodwala2malcolmk@chem.gla.ac.uk Search for this author in: * NPG journals * PubMed * Google Scholar * Affiliations * Contributions * Corresponding authorJournal name:Nature NanotechnologyVolume: 5 ,Pages:783–787Year published:(2010)DOI:doi:10.1038/nnano.2010.209Received07 July 2010Accepted20 September 2010Published online31 October 2010 Abstract * Abstract * Author information * Supplementary information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg The spectroscopic analysis of large biomolecules is important in applications such as biomedical diagnostics and pathogen detection1, 2, and spectroscopic techniques can detect such molecules at the nanogram level or lower. However, spectroscopic techniques have not been able to probe the structure of large biomolecules with similar levels of sensitivity. Here, we show that superchiral electromagnetic fields3, generated by the optical excitation of plasmonic planar chiral metamaterials4, 5, are highly sensitive probes of chiral supramolecular structure. The differences in the effective refractive indices of chiral samples exposed to left- and right-handed superchiral fields are found to be up to 106 times greater than those observed in optical polarimetry measurements, thus allowing picogram quantities of adsorbed molecules to be characterized. The largest differences are observed for biomolecules that have chiral planar sheets, such as proteins with high β-sheet content, w! hich suggests that this approach could form the basis for assaying technologies capable of detecting amyloid diseases and certain types of viruses. View full text Subject terms: * Nanobiotechnology * Photonic structures and devices Figures at a glance * Figure 1: Changes induced in the chiral plasmonic resonances of the PCM are readily detected using CD spectroscopy. , CD spectra collected from LH/RH PCMs immersed in distilled water. The three modes that show the largest sensitivity to changes in the local refractive index of the surrounding medium have been labelled I, II and III. Shown to the right of each spectrum is an electron micrograph of the PCM displaying the gammadion structure and periodicity. , Influence of the adsorbed proteins haemoglobin, β-lactoglobulin and thermally denatured β-lactoglobulin on the CD spectra of the PCMs. Red spectra were collected in Tris buffer before protein adsorption (solid line, LH PCM; dashed line, RH PCM), and black spectra were collected after protein adsorption. Magnitudes and directions of ΔλRH/LH values of mode II for β-lactoglobulin adsorption have been highlighed. , Haemoglobin (upper) and β-lactoglobulin (lower) (α-helix, cyan cylinder; β-sheet, ribbons), shown adopting a well-defined arbitrary structure with respect to a surface. The figure illustrates the more anisotropic nature ! of adsorbed β-lactoglobulin. * Figure 2: Finite element modelling of the local electromagnetic fields around the PCMs. , Comparison between experimental and modelled CD spectra. –, Left-hand panels: time-averaged electric field strength at the wavelengths marked by arrows in , when excited by LH circularly polarized light. All fields are calculated at the substrate interface of the sample and normalized by the incident electric field (E0). Right-hand panels: local optical chirality, C, as defined in equation (3), normalized by the magnitudes for LH circularly polarized plane waves. * Figure 3: Values of ΔΔλ and ΔλAV induced by the adsorption of chiral materials. , Plot of ΔλAV (I) for tryptophan and the six proteins. , Corresponding ΔΔλ values for I, II and III modes. Also shown are the effectively zero ΔΔλ values obtained from the (achiral) ethanol solvent. Author information * Abstract * Author information * Supplementary information Affiliations * School of Physics, University of Exeter, Stocker Road, Exeter EX4 4QL, UK * E. Hendry & * R. V. Mikhaylovskiy * School of Chemistry, Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK * T. Carpy, * J. Johnston, * M. Popland, * A. J. Lapthorn, * L. D. Barron & * M. Kadodwala * Division of Biomedical Engineering, School of Engineering, Rankine Building, University of Glasgow, Glasgow G12 8LT, UK * J. Johnston & * N. Gadegaard * College of Medical, Veterinary and Life Sciences, Institute of Molecular, Cell & Systems Biology, University of Glasgow, Glasgow G12 8QQ, UK * S. M. Kelly Contributions M.K. conceived and designed the experiments. T.C., J.J., M.P. and S.K. performed the experiments. R.V.M. and E.H. performed numerical simulations. J.J. and N.G. fabricated the PCMs. E.H., L.D.B. and M.K. analysed the data. A.L. and S.M.K. contributed materials/analysis tools. E.H., A.L., S.M.K., N.G., L.D.B. and M.K. co-wrote the paper. Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * M. Kadodwala (malcolmk@chem.gla.ac.uk) Supplementary information * Abstract * Author information * Supplementary information PDF files * Supplementary information (1,382 KB) Supplementary information Additional data - Nanomechanical recognition measurements of individual DNA molecules reveal epigenetic methylation patterns
- UNKNOWN 5(11):788-791 (2010)
Nature Nanotechnology | Letter Nanomechanical recognition measurements of individual DNA molecules reveal epigenetic methylation patterns * Rong Zhu1, 2 Search for this author in: * NPG journals * PubMed * Google Scholar * Stefan Howorka3, 4 Search for this author in: * NPG journals * PubMed * Google Scholar * Johannes Pröll5, 6 Search for this author in: * NPG journals * PubMed * Google Scholar * Ferry Kienberger1 Search for this author in: * NPG journals * PubMed * Google Scholar * Johannes Preiner1 Search for this author in: * NPG journals * PubMed * Google Scholar * Jan Hesse1, 3 Search for this author in: * NPG journals * PubMed * Google Scholar * Andreas Ebner1 Search for this author in: * NPG journals * PubMed * Google Scholar * Vassili Ph. Pastushenko1 Search for this author in: * NPG journals * PubMed * Google Scholar * Hermann J. Gruber1 Search for this author in: * NPG journals * PubMed * Google Scholar * Peter Hinterdorfer1, 2, 3peter.hinterdorfer@jku.at Search for this author in: * NPG journals * PubMed * Google Scholar * Affiliations * Contributions * Corresponding authorJournal name:Nature NanotechnologyVolume: 5 ,Pages:788–791Year published:(2010)DOI:doi:10.1038/nnano.2010.212Received31 March 2010Accepted01 October 2010Published online31 October 2010 Abstract * Abstract * Author information * Supplementary information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Atomic force microscopy1 (AFM) is a powerful tool for analysing the shapes of individual molecules and the forces acting on them. AFM-based force spectroscopy provides insights into the structural and energetic dynamics2, 3, 4 of biomolecules by probing the interactions within individual molecules5, 6, or between a surface-bound molecule and a cantilever that carries a complementary binding partner7, 8, 9. Here, we show that an AFM cantilever with an antibody tether can measure the distances between 5-methylcytidine bases in individual DNA strands with a resolution of 4 Å, thereby revealing the DNA methylation pattern, which has an important role in the epigenetic control of gene expression. The antibody is able to bind two 5-methylcytidine bases of a surface-immobilized DNA strand, and retracting the cantilever results in a unique rupture signature reflecting the spacing between two tagged bases. This nanomechanical approach might also allow related chemical patterns to be! retrieved from biopolymers at the single-molecule level. View full text Subject terms: * Nanobiotechnology Figures at a glance * Figure 1: A single-molecule force spectroscopy experiment reveals the molecular distance between two 5-methylcytosine bases in a DNA strand. , ssDNA is coupled to an aldehyde-bearing glass surface through an amine group at its 3′-end, and the antibody is tethered via a lysine residue or its natural oligosaccharide and a flexible PEG crosslinker to the cantilever tip. The two Fab-arms and the Fc-arm of the antibody are indicated. Panels 1, 2, 3 and 4 correspond to different states that occur upon retracting the cantilever from the surface, including the elongation of the PEG and DNA strands and the sequential breaking of the two methylcytosine antibody bonds. , These molecular changes are reflected in a force–distance curve, with the rupture distance in the curve (points 2 to 3) corresponding to the spacing between two 5-methylcytidines in a DNA strand. * Figure 2: A two-step unbinding event between antibody and methylcytosine-containing ssDNA. , Examples of antibody–DNA ruptures with two unbinding events (indicated by red arrows, 1 and 2). The sketches show the possible binding positions of the antibody on the DNA, with 4, 8, 12 and 16 nucleotides (nt) separation. , Distribution of the distances between two unbinding events. The thick red line represents the experimental probability density function of distances constructed from distance values of 224 force curves. The thin lines are the result of a multiple Gaussian fit. Inset: possible pairs of dual antibody binding. * Figure 3: Two-step unbinding from ssDNA with nine 5-methylcytidines separated by six nucleotides. , Examples of force–distance curves with sketches showing the possible binding positions of the antibody on the DNA. , Distribution of the rupture distance between two unbinding events. The thick red line represents the experimental probability density function of distances constructed from 150 force curves. The thin lines are the result of a multiple Gaussian fit. * Figure 4: Single nucleotide resolution enables 5-methylcytidine sequencing and the detection of single epigenetic changes. , Distance distribution from a DNA containing six 5-methylcytidines separated by 3, 8, 1, 8 and 3 nucleotides. The thick red line represents the experimental probability density function of distances constructed from distance values of 298 force curves. The thin lines are the result of a multiple Gaussian fit. , Three possible sequences can be reconstructed (see text for explanation) from the peaks corresponding to 3, 8, 9, 11, 12, 17, 20 and 23 nucleotides in the distance distribution in . , Removal of a single methyl group from the DNA. The distance distribution shows similar peaks when compared to those in , except for the absence of the peak corresponding to 17 nucleotides. The thick red line represents the experimental probability density function of distances constructed from distance values of 216 force curves. The thin lines are the result of a multiple Gaussian fit. Author information * Abstract * Author information * Supplementary information Affiliations * Institute for Biophysics, Johannes Kepler University of Linz, A-4040 Linz, Austria * Rong Zhu, * Ferry Kienberger, * Johannes Preiner, * Jan Hesse, * Andreas Ebner, * Vassili Ph. Pastushenko, * Hermann J. Gruber & * Peter Hinterdorfer * Christian Doppler Laboratory for Nanoscopic Methods in Biophysics, Johannes Kepler University of Linz, A-4040 Linz, Austria * Rong Zhu & * Peter Hinterdorfer * Center for Advanced Bioanalysis GmbH, 4020 Linz, Austria * Stefan Howorka, * Jan Hesse & * Peter Hinterdorfer * University College London, Department of Chemistry, London WC1H 0AJ, UK * Stefan Howorka * Department of Internal Medicine I, Elisabethinen Hospital, A-4010 Linz, Austria * Johannes Pröll * Present address: Red Cross Transfusion Service of Upper Austria, A-4020 Linz, Austria * Johannes Pröll Contributions R.Z. performed the experiments and data evaluation. S.H. developed the surface chemistry and co-wrote the paper. J.Pröll performed the surface chemistry and selected the DNA sequences. F.K., J.Preiner and A.E. discussed the results. J.H. contributed to the surface chemistry. V.Ph.P. programmed the data evaluation. H.J.G. developed the tip chemistry. P.H. led the experimental design and wrote the paper. Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * Peter Hinterdorfer (peter.hinterdorfer@jku.at) Supplementary information * Abstract * Author information * Supplementary information PDF files * Supplementary information (379 KB) Supplementary information Additional data - Magnetoelectric coupling at metal surfaces
- UNKNOWN 5(11):792-797 (2010)
Nature Nanotechnology | Article Magnetoelectric coupling at metal surfaces * L. Gerhard1 Search for this author in: * NPG journals * PubMed * Google Scholar * T. K. Yamada1, 2 Search for this author in: * NPG journals * PubMed * Google Scholar * T. Balashov1 Search for this author in: * NPG journals * PubMed * Google Scholar * A. F. Takács3 Search for this author in: * NPG journals * PubMed * Google Scholar * R. J. H. Wesselink1 Search for this author in: * NPG journals * PubMed * Google Scholar * M. Däne4, 5 Search for this author in: * NPG journals * PubMed * Google Scholar * M. Fechner4 Search for this author in: * NPG journals * PubMed * Google Scholar * S. Ostanin4 Search for this author in: * NPG journals * PubMed * Google Scholar * A. Ernst4 Search for this author in: * NPG journals * PubMed * Google Scholar * I. Mertig4, 6 Search for this author in: * NPG journals * PubMed * Google Scholar * W. Wulfhekel1wulf.wulfhekel@kit.edu Search for this author in: * NPG journals * PubMed * Google Scholar * Affiliations * Contributions * Corresponding authorJournal name:Nature NanotechnologyVolume: 5 ,Pages:792–797Year published:(2010)DOI:doi:10.1038/nnano.2010.214Received04 June 2010Accepted07 October 2010Published online31 October 2010 Abstract * Abstract * Author information * Supplementary information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Magnetoelectric coupling allows the magnetic state of a material to be changed by an applied electric field. To date, this phenomenon has mainly been observed in insulating materials such as complex multiferroic oxides. Bulk metallic systems do not exhibit magnetoelectric coupling, because applied electric fields are screened by conduction electrons. We demonstrate strong magnetoelectric coupling at the surface of thin iron films using the electric field from a scanning tunnelling microscope, and are able to write, store and read information to areas with sides of a few nanometres. Our work demonstrates that high-density, non-volatile information storage is possible in metals. View full text Subject terms: * Electronic properties and devices * Nanomagnetism and spintronics * Nanoparticles Figures at a glance * Figure 1: Simulations of surface relaxations under the influence of an electric field in Fe/Cu(111). ,, Normalized electronic charge density in fcc bilayers Fe and two underlying Cu layers under positive () and negative () electric fields. The electric field is modelled by a plate capacitor placed 4 Å above the surface. The electron charge is attracted (repelled) by the positively (negatively) charged electrode, causing the ions to move away from (towards) the surface. The Fe layers were found to be layerwise antiferromagnetic (AFM) in and ferromagnetic (FM) in . ,, Relative total energy per unit cell as a function of the lateral displacement δ of the top Fe layer due to the martensitic phase transition (red for antiferromagnetic and blue for ferromagnetic states). When a positive electric field is applied, the iron atoms adopt fcc stacking, and the layer magnetizations align in an antiparallel arrangement (). When the applied field is negative, bcc stacking of magnetic layers aligned in parallel is energetically preferred (). The ball model illustrates the movement of th! e top Fe atoms from their threefold hollow site position of fcc (111) stacking (blue) to the bcc (110) bridge position (orange). Grey and red balls represent Cu and bottom Fe atoms, respectively. Lattice directions in the fcc (111) plane and respective unit cells are indicated. * Figure 2: Crystallographic and electronic structure of Fe islands. , Topographic STM image showing two crystallographic phases in a bilayer Fe island on Cu(111) (image size, 19 nm × 19 nm). The coexisting phases can be distinguished by a difference in height. , Atomically resolved image showing the fcc configuration on the left and the bcc configuration on the right. The top-layer atoms on the left follow the hexagonal fcc (111) structure of the Cu substrate (red grid). The atomic directions on the right (green line) show a slight misalignment of 5° with the fcc directions (red line) and a shift δ indicating a bcc (110) stacking (image size 3.7 nm × 3.7 nm). , Identification of the two phases as ferromagnetic bcc and antiferromagnetic fcc by their LDOS: typical normalized differential conductance spectrum (continuous lines) on the island rim (orange) and in the island centre (blue), compared to the calculated spin-averaged LDOS of 2 ML Fe/Cu(111) in the ferromagnetic bcc and antiferromagnetic fcc configurations (dashed lines). * Figure 3: Controlled switching with electric fields. –, Switching of antiferromagnetic fcc (blue) and ferromagnetic bcc (orange) areas with electric field pulses. Three STM scans of an island corner were recorded at subcritical electric fields. By applying a positive field pulse after the acquisition of scan , the bcc region is expanded in and reduced again by a negative field pulse in . Image sizes in –, 6 nm × 6 nm. Positions of the pulses are marked in red. , Applied gap voltage (black line) and height (coloured line) recorded as function of time at a fixed tip position. It can be seen that the switching process is deterministic and reproducible. ,, Small Fe islands can be completely switched from an antiferromagnetic fcc () to a ferromagnetic bcc () structure. Image size in and , 11 nm × 9 nm (horizontal × vertical). * Figure 4: Controlling fcc versus bcc structures with the local electric field. , A single line across the fcc–bcc domain boundary was scanned with the STM, decreasing the gap voltage scan line by scan line. At a critical gap voltage (0.16 V) a transition from fcc to bcc occurs. This experiment has been carried out at different tunnelling currents (in a range from 150 pA to 28 nA), that is, with different tip sample separations. , By plotting the critical gap voltage against the corresponding tip–sample separation, the boundary (black triangles) in the phase diagram is obtained. The experimental results can be compared with possible distance dependencies of the critical voltage (coloured lines) resulting from different models (E, constant electric field; I, constant current; U, constant voltage; P, constant power; d, constant distance; for details see main text). The curves are all fitted freely to the experimental data. Author information * Abstract * Author information * Supplementary information Affiliations * Physikalisches Institut, Karlsruher Institut für Technologie (KIT), Wolfgang-Gaede-Straße 1, 76131 Karlsruhe, Germany * L. Gerhard, * T. K. Yamada, * T. Balashov, * R. J. H. Wesselink & * W. Wulfhekel * Graduate School of Advanced Integration Science, Chiba University, Chiba 263-8522, Japan * T. K. Yamada * Faculty of Physics, Babes-Bolyai University, 400084 Cluj-Napoca, Romania * A. F. Takács * Max-Planck-Institut für Mikrostrukturphysik, Weinberg 2, 06120 Halle, Germany * M. Däne, * M. Fechner, * S. Ostanin, * A. Ernst & * I. Mertig * Materials Science and Technology Division, Oak Ridge National Laboratory Oak Ridge, Tennessee 37831, USA * M. Däne * Martin-Luther-Universität Halle-Wittenberg, Institut für Physik, 06099 Halle, Germany * I. Mertig Contributions L.G., T.K.Y. and W.W. conceived and designed the experiments. L.G., T.B., A.F.T. and R.J.H.W. performed the experiments. L.G., R.J.H.W. and T.K.Y. analysed the data. A.E., I.M. and S.O. designed the calculations. A.E., S.O. and M.D. performed the calculations. M.F. and M.D. contributed analysis tools. A.E., L.G., I.M. and W.W. co-wrote the paper. All authors discussed the results and commented on the manuscript. Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * W. Wulfhekel (wulf.wulfhekel@kit.edu) Supplementary information * Abstract * Author information * Supplementary information PDF files * Supplementary information (673 KB) Supplementary information Additional data - Replication of individual DNA molecules under electronic control using a protein nanopore
- UNKNOWN 5(11):798-806 (2010)
Nature Nanotechnology | Article Replication of individual DNA molecules under electronic control using a protein nanopore * Felix Olasagasti1 Search for this author in: * NPG journals * PubMed * Google Scholar * Kate R. Lieberman1 Search for this author in: * NPG journals * PubMed * Google Scholar * Seico Benner1 Search for this author in: * NPG journals * PubMed * Google Scholar * Gerald M. Cherf1 Search for this author in: * NPG journals * PubMed * Google Scholar * Joseph M. Dahl1 Search for this author in: * NPG journals * PubMed * Google Scholar * David W. Deamer1 Search for this author in: * NPG journals * PubMed * Google Scholar * Mark Akeson1makeson@soe.ucsc.edu Search for this author in: * NPG journals * PubMed * Google Scholar * Affiliations * Contributions * Corresponding authorJournal name:Nature NanotechnologyVolume: 5 ,Pages:798–806Year published:(2010)DOI:doi:10.1038/nnano.2010.177Received30 March 2010Accepted04 August 2010Published online26 September 2010 Abstract * Abstract * Author information * Supplementary information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Nanopores can be used to analyse DNA by monitoring ion currents as individual strands are captured and driven through the pore in single file by an applied voltage. Here, we show that serial replication of individual DNA templates can be achieved by DNA polymerases held at the α-haemolysin nanopore orifice. Replication is blocked in the bulk phase, and is initiated only after the DNA is captured by the nanopore. We used this method, in concert with active voltage control, to observe DNA replication catalysed by bacteriophage T7 DNA polymerase (T7DNAP) and by the Klenow fragment of DNA polymerase I (KF). T7DNAP advanced on a DNA template against an 80-mV load applied across the nanopore, and single nucleotide additions were measured on the millisecond timescale for hundreds of individual DNA molecules in series. Replication by KF was not observed when this enzyme was held on top of the nanopore orifice at an applied potential of 80 mV. Sequential nucleotide additions by KF w! ere observed upon applying controlled voltage reversals. View full text Subject terms: * Nanobiotechnology * Nanosensors and other devices Figures at a glance * Figure 1: The nanopore device. , A patch-clamp amplifier supplies voltage and measures ionic current through a single α-haemolysin channel inserted in a ~30-μm-diameter lipid bilayer. Current through the nanopore is carried by K+ and Cl− ions. , Characteristic current blockade event structure for A family DNAP–DNA complexes captured in the nanopore. The black current trace corresponds to a KF–DNA complex formed with a substrate composed solely of standard DNA residues; the grey current trace represents a KF–DNA complex formed with a substrate bearing an insert of six consecutive abasic residues in the template strand. Cartoons i–iii illustrate the molecular events that correspond to each current level1, 5, with the abasic residues indicated as red circles. The initial longer blockade (i) is the enzyme bound state (IEBS) observed upon capture of a DNAP–DNA complex, with the duplex DNA held on top of the pore vestibule by the polymerase. The amplitude of this initial segment is increased when ! abasic residues are positioned to reside in the nanopore lumen during the EBS5. The shorter terminal step (IDNA; ii) occurs upon voltage-promoted DNAP dissociation, when the duplex DNA is drawn into the nanopore vestibule. Electrophoresis of the unbound DNA through the nanopore (iii) restores the open channel current (60 ± 2 pA at 180 mV in buffer containing 0.3 M KCl). This event structure is observed for DNAP–DNA binary complexes and for DNAP–DNA–dNTP ternary complexes, with both KF and T7DNAP. Average EBS duration for DNA substrates bearing a 3′-H-terminated primer is increased in the presence of correct dNTP in a concentration-dependent manner3, 5. , Structure of abasic residues. A section of a strand bearing abasic (1′,2′-dideoxy) residues is compared to a section of a DNA strand. * Figure 2: Blocking oligomer inhibition of DNAP-catalysed DNA synthesis. , (i) DNA polymerase substrate consisting of a 79-mer template strand (tan and black) and a 23-mer primer strand (dark blue). The primer/template junction where DNA polymerase binds and initiates replication at the first unpaired base (n = 0) and the single-stranded region of the template just beyond the 3′ end of the primer strand are magnified. This region is the target for a series of oligonucleotides (ii–v) tested for their ability to inhibit DNA synthesis in the bulk phase bathing the nanopore. These oligomers (in red) are (ii) a standard DNA oligonucleotide complementary to 25 template nucleotides, extended on its 3′ end by seven non-complementary cytosine residues; (iii) the oligonucleotide shown in (ii), with a single acridine residue, represented in yellow, at its 5′ terminus (this acridine replaces the nucleobase that participates in the terminal base pair of the fully base-paired segment of ii); (iv) the oligonucleotide shown in (ii), with its 5′ terminu! s extended by a single acridine overhang, represented in orange; and (v) the oligonucleotide shown in (ii), with two acridine residues at its 5′ terminus. In (v), one acridine residue (yellow) replaces the nucleobase that participates in the terminal base pair of the fully base-paired segment of (ii) and a second acridine residue (orange) is an overhang. , Inhibition of T7DNAP-catalysed primer extension. Denaturing gel electrophoresis showing the effect of the blocking oligomers shown in (ii–v) on primer extension catalysed by T7DNAP for 60 min under nanopore buffer conditions. The location of bands corresponding to the 5′-6-FAM primer, the +1 extension product, and the full-length extension product (+56) are indicated. Also indicated are the locations of bands arising from the fluorescence of the acridine moieties of blocking oligomers (iii) and (v). The presence of these bands in lanes for reactions conducted without (lanes 1, 3 and 5) and with (lanes 2, 4 and 6) en! zyme confirms that they are not extension products. , Inhibiti! on of KF-catalysed primer extension. Denaturing gel electrophoresis showing the effect of blocking oligomers (iv) and (v) shown in on primer extension catalysed by KF under nanopore buffer conditions in 60 min (left panel) or 10 and 20 min (right panel). * Figure 3: Blocking oligomer inhibition of bulk-phase T7DNAP binding and voltage-promoted deprotection of individual DNA substrate molecules. , Characteristic current blockade event structure for T7DNAP–DNA complexes captured in the nanopore. Cartoons (i–iii) illustrate the molecular events that correspond to each current level (see Fig. 1b for a detailed description). , Dwell time versus amplitude plot for an experiment in which hundreds of T7DNAP–DNA–dNTP ternary complexes were captured. In , and , the IEBS segments of the polymerase–DNA events are represented as black dots, the lower-amplitude, terminal portion of the polymerase–DNA events as blue dots, and unbound DNA events as red dots (for a description of how events were identified and quantified, see Methods). , Representative current trace for events observed when the primer/template substrate used in and is pre-annealed with a blocking oligomer bearing a single acridine overhang at its 5′ terminus (Fig. 2a,iv). (i) The blocked DNA substrate is captured. The seven-nucleotide non-complementary 3′ tail is designed to promote blocking oligome! r dissociation upon nanopore capture (ii,iii). In concert with blocking oligomer dissociation, the primer/template junction is drawn into the pore vestibule (iii). Open-channel current is restored (iv) upon electrophoresis of the DNA through the pore. , Dwell time versus amplitude plot for the experiment that produced the current trace in . Numerous unbound IDNA events at 18 pA, but almost no 28-pA IEBS events, were observed. , Voltage-promoted deprotection of individual DNA substrate molecules renders them accessible for T7DNAP binding. Lower-case numerals i–vi in the current trace correspond to the states depicted in the cartoons above. Upon capture (+160 mV) of a protected DNA substrate pre-annealed with the blocking oligomer (i), the 7-dC tail of the blocking oligomer is unzipped as the DNA substrate is driven into the pore, where the primer/template junction is protected from polymerase binding (ii). This state is detected by the FSM, voltage is reduced (+45 mV) and ! the template strand in the trans compartment can anneal to a t! ethering oligomer (iii). The potential is reversed (−20 mV) to drive the newly deprotected DNA primer/template into the cis compartment, where it is exposed to T7DNAP and dGTP and can form a ternary complex (iv). The duration of this fishing exposure can be precisely controlled (100 ms in the experiment shown). After the programmed fishing exposure, voltage is again reversed (to +160 mV in the experiment shown), drawing the DNA substrate back to the nanopore orifice. In this probing step, either unbound DNA (IDNA; v) or a T7DNAP-bound molecule is drawn back to the pore (IEBS; vi). Detection of IEBS indicates the blocking oligomer was removed and the DNA substrate was thus made accessible for polymerase binding. Detection of IDNA in (v), or of IDNA following voltage-promoted dissociation of the enzyme in (vi), prompts voltage reversal to −20 mV to fish again after a 2-ms delay. The fish and probe cycle is iterative until the DNA molecule is ejected, whereupon another can! be captured. , Dwell time versus amplitude plot for hundreds of IEBS events measured in iterative fish and probe cycles for dozens of individual DNA substrate molecules captured and deprotected in series. Note that in this panel, the duration of the terminal portion of enzyme-bound events (after polymerase dissociation), represented by the blue dots, is truncated by the FSM logic, which upon recognition of this lower-amplitude state in which the DNA duplex has dropped into the vestibule, commands a rapid voltage reversal. * Figure 4: Nucleotide addition may occur above the nanopore orifice (before the probing step) or at the nanopore orifice (during the probing step). , Nucleotide addition above the nanopore orifice prior to the probing step. (i) The trans-side oligomer has been annealed following blocking oligomer removal. The trans-side voltage is negative, driving the dsDNA/ssDNA junction into the cis compartment (fishing step). During the fishing step, DNAP (ii) and cognate dNTP (iii) may sequentially bind. (iv) This can lead to catalytic nucleotide addition and translocation of the DNA substrate relative to the DNAP before the probing step (v) when the voltage is reversed (trans-side positive). In this scenario, the product of DNA catalysis is detected by the nanopore, but the catalytic cycle itself is not detected. , Nucleotide addition at the nanopore orifice during the probing step. In this scenario, steps (i) and (ii) are the same as in scenario . However, here, the probing step (iii) precedes and then is sustained during catalytic turnover and translocation (iv,v). In this scenario, catalysis is observed in process. PPi, pyropho! sphate. * Figure 5: T7DNA replication of individual DNA substrate molecules deprotected and tethered in the nanopore. , Primer/template substrate used in T7DNAP replication experiments. The first G residue at position 33 of the template is shown in blue, and the six abasic residues are shown as red Xs. Sequences at the 5′ end of the template, which include the binding site for the tethering oligomer on the trans side of the nanopore, are not shown. , Representative current trace for a captured molecule in which T7DNAP catalysed the addition of 10 nucleotides. Following 55 sequential 10-ms fishing exposures and 80-mV probing steps, a progression through three detectable EBS amplitude levels (8.5, 10 and 10.8 pA ternary complex) occurs (for an expanded illustration of this current trace, see Supplementary Movie 1 and Supplementary Fig. S2). , Position of the six-abasic-residue insert for the template shown in , as T7DNAP on top of the pore catalyses single nucleotide additions that advance the template through the three detectable EBS amplitudes ( and ). Assignment of the 8.5, 10 and 10.8 p! A EBS levels to T7DNAP–DNA complexes in which the primer strand has been extended by eight, nine and ten nucleotides, respectively, was verified using chemically synthesized 3′-H-terminated primers corresponding to these extension products that were hybridized to the template in . The mean EBS amplitudes and standard deviations for these control complexes are indicated below each cartoon and were based on at least 15 events analysed using Clampfit software. By comparison, DNA alone gave a current of 6.33 ± 0.56 pA for the same conditions at 80 mV. , Enlarged view of the region of the current trace in that comprises the three amplitude levels. The red arrows indicate polymerase-catalysed translocation of the DNA template in the pore as the enzyme advances on the template with each nucleotide addition cycle. Importantly, assignment of these three current values to template positions is rigorously supported by the unique templating G base at position +10 that ensures form! ation of only one ternary complex in this experiment. * Figure 6: KF replication of individual DNA substrate molecules deprotected and tethered in the nanopore. , Primer/template substrate used in KF replication experiments. The first G residue at position 35 of the template is shown in blue, and the six abasic residues are shown as red Xs. Sequences at the 5′ end of the template, which include the binding site for the tethering oligomer on the trans side of the nanopore, are not shown. Note that the distance from position n = 0 to the abasic insert is 19 nt for this template, compared to 23 nt for the template in Fig. 5. Thus the number of base additions needed to bring the abasic insert to the limiting pore constriction (lysine 147 of α-haemolysin6) differs. That is, +8 nt in Fig. 5 places the abasic insert 14 to 19 nt from the catalytic site, giving a current of 8.5 pA; the corresponding position here in Fig. 6 is +4 nt, which places the abasic insert 14 to 19 nt from the catalytic site, giving a current of 8.1 pA. , Cartoons depicting the position of the six-abasic residue insert in the template shown in , as it is drawn in s! ingle-nucleotide (5 Å) increments by the KF molecule on top of the pore during replication of the template. The IEBS values were measured at 80 mV for each of these complexes by capturing ternary complexes formed with a series of synthetic primer/template substrates corresponding to each single-nucleotide addition to the substrate shown in . The mean amplitude and standard deviation from these experiments are indicated below each cartoon. Each of these values was estimated by measuring the mean amplitude of at least 20 events using Clampfit software and then calculating the mean and standard deviation of those measurements. , EBS amplitude map at 80 mV for the KF–DNA–dNTP ternary complexes illustrated in . The dashed line indicates IDNA at 80 mV, which was 6.61 ± 0.64 pA. , Representative current trace for a captured molecule in which KF catalysed the addition of 11 nucleotides (for an expanded illustration of this current trace, see Supplementary Fig. S3). Author information * Abstract * Author information * Supplementary information Affiliations * Department of Biomolecular Engineering, Baskin School of Engineering, MS SOE2, University of California, Santa Cruz, California 95064, USA * Felix Olasagasti, * Kate R. Lieberman, * Seico Benner, * Gerald M. Cherf, * Joseph M. Dahl, * David W. Deamer & * Mark Akeson Contributions F.O. designed experiments and performed data analysis. K.R.L. co-authored the manuscript, and designed and conducted experiments. S.B., G.M.C. and J.M.D. conducted nanopore experiments, including FSM implementation. D.W.D. conceived the idea of coupling polymerases to nanopores and helped design experiments. M.A. co-authored the manuscript, conceived the blocking oligomer strategy, designed experiments and is responsible for the overall quality of the work. Competing financial interests M. Akeson and D. Deamer are consultants to Oxford Nanopore Technologies (Oxford, England). Oxford Nanopore Technologies has licensed rights to some of the inventions detailed in this manuscript and has sponsored some of the research presented here through a grant to the University of California. Corresponding author Correspondence to: * Mark Akeson (makeson@soe.ucsc.edu) Supplementary information * Abstract * Author information * Supplementary information Movies * Supplementary information (5,643 KB) Supplementary movie 1 * Supplementary information (27,246 KB) Supplementary movie 2 PDF files * Supplementary information (803 KB) Supplementary information Additional data - Rapid electronic detection of probe-specific microRNAs using thin nanopore sensors
- UNKNOWN 5(11):807-814 (2010)
Nature Nanotechnology | Article Rapid electronic detection of probe-specific microRNAs using thin nanopore sensors * Meni Wanunu1, 3wanunu@sas.upenn.edu Search for this author in: * NPG journals * PubMed * Google Scholar * Tali Dadosh1, 3 Search for this author in: * NPG journals * PubMed * Google Scholar * Vishva Ray1 Search for this author in: * NPG journals * PubMed * Google Scholar * Jingmin Jin2 Search for this author in: * NPG journals * PubMed * Google Scholar * Larry McReynolds2 Search for this author in: * NPG journals * PubMed * Google Scholar * Marija Drndić1drndic@physics.upenn.edu Search for this author in: * NPG journals * PubMed * Google Scholar * Affiliations * Contributions * Corresponding authorsJournal name:Nature NanotechnologyVolume: 5 ,Pages:807–814Year published:(2010)DOI:doi:10.1038/nnano.2010.202Received28 May 2010Accepted14 September 2010Published online24 October 2010 Abstract * Abstract * Author information * Supplementary information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg 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. View full text Subject terms: * Nanobiotechnology * Nanosensors and other devices Figures at a glance * Figure 1: Solid-state nanopore sensors with a thickness of less than 10 nm. , Scheme of a nanopore sensor showing a DNA molecule translocating through the pore (not to scale). The sensor consists of a 5 × 5 mm2 silicon chip that contains a free-standing SiN membrane (~50 × 50 µm2). After locally thinning the membrane using the process shown in , a nanopore is drilled using a TEM (bottom left, image of a 4-nm-diameter nanopore in 6-nm-thick membrane). Electrolyte solution is added above and below the nanopore, each contacted by a Ag/AgCl electrode, and voltage is applied to drive charged biomolecules through the pore. , The membrane thinning process, involves coating the membrane with a PMMA resist, followed by electron-beam exposure and development, and controlled dry etching using SF6 plasma. , Optical image of the membrane after thinning (before removal of the PMMA). The upper inset shows an AFM topography image of a 3 × 3 square array following PMMA removal, as well as a line profile that shows uniform, 17-nm-deep trenches. The lower inset sh! ows that the etch depth, measured by AFM, is a linear function of the etch time and that the etch rate is 1 nm s−1. , Epi-fluorescence image of a 41-nm-thick SiN membrane in which 5-µm squares were thinned to 8 nm (λex = 488 nm, λem = 525 ± 25 nm). The fluorescence intensity histograms show that the fluorescence background is lower in the thinned region. * Figure 2: Characterization of a 4.5-nm-diameter pore in a 7-nm-thick silicon nitride membrane. , BF-STEM image, showing the etched 250 × 250 nm square as a brighter area with uniform intensity. , ADF-STEM image of a zoomed-in portion of the nanopore in . The height profile of a line through the centre of the pore is shown by the red line. Membrane thickness h (y-axis) was measured from the difference of the initial membrane thickness and the etch depth (see text), normalized by assigning a thickness of 0 nm to the signal intensity at the pore (that is, in vacuum). STEM probe size, 0.2 nm. * Figure 3: Increasing the measurement resolution by nanopore thinning. , Concatenated sets of ~200 translocations of 3-kb linear dsDNA through 4-nm-diameter pores fabricated in membranes with different h values; heff is the nanopore effective thickness used in the geometric model discussed in the text. On decreasing h from 60 to 6 nm, the open-pore current increased and the DNA signal amplitude increased. All traces were filtered using the Axopatch 100 kHz filter setting. For h = 60 nm, the data was low-pass filtered at 10 kHz using the Axopatch filter to make events visible. , Magnified view of the traces in , Semi-logarithmic histograms of the blocked current amplitudes normalized by subtracting ΔI, which show increased current amplitudes for thinner nanopores. Although the most probable blocked current ΔIp increased with decreasing h, open-pore noise values were similar. , Dependence of average experimental Io (black circles) and the most probable DNA current amplitude ΔIp (red triangles) on h. The black dashed line is a fit using equatio! n (1) to the average Io data from the combined data of ~20 pores, which yields an effective pore thickness heff = h/(3.04 ± 0.30) (heff scale shown on top x-axis). The fit to ΔIp values (red dashed line) is based on a geometric model described in detail in Supplementary Section SI-4. Inset shows ΔIp/ Io , which did not change appreciably with h. The green dashed line is the ratio of the fits to ΔIp and Io from the main plot. , S/N and mean transport time as a function of h (heff shown on top x-axis). S/N is defined as ΔI/Irms, where Irms at 100 kHz bandwidth is 75 ± 5 pA. Mean transport times were obtained from the dwell-time distributions (see ref. 47 for more details). * Figure 4: Discrimination among small nucleic acids using thin nanopores. , Continuous current versus time traces from a 3-nm-diameter pore in a 7-nm-thick membrane measured at 0 °C, V = 500 mV (TEM image of pore is shown). Traces were median-filtered with rank of 1 to improve the S/N. Based on the conductance, the effective pore thickness heff = 2.3 nm. The analyte chamber contains 25-bp dsDNA (blue), 22-bp dsRNA (red) or phenylalanine tRNA (black), at concentrations of ~80 fmol µl−1. Sample events are shown above the continuous traces, and models based on crystal structures are shown to the right. The all-point current histograms on the bottom right show that the three molecules can be distinguished based on their current amplitudes. The mean transport times for the DNA, RNA and tRNA molecules are 20 µs, 50 µs and 1.04 ms, respectively (Supplementary Section SI-7). , Dependence of the capture rate on the applied voltage for 25-bp DNA and 22-bp RNA. The exponential dependence reveals that capture is voltage-activated. Blue and red lines are! exponential fits to the data. , Log–log plot of capture rate versus DNA concentration. Linearity is observed for three orders of magnitude in DNA concentration, as indicated by a power-law fit exponent of 1.05 ± 0.03. * Figure 5: miRNA detection using solid-state molecular counters. , Scheme of the miRNA-specific detection method. First, RNA is extracted from tissue (not shown), and the extract is hybridized to a miRNA-specific oligonucleotide probe (red). In step (I), the probe:miRNA duplex is enriched by binding to p19-functionalized magnetic beads, followed by thorough washing to remove other RNAs from the mixture. In step (II), the hybridized probe:miRNA duplex is eluted from the magnetic beads. In step (III), the eluted probe:miRNA duplex is electronically detected using a nanopore. , Detection of miR122a from 1 µg of rat liver total RNA using a 3-nm-diameter nanopore in a 7-nm-thick membrane. Representative 30-s current versus time traces are shown for a pore after the addition of the enriched miR122a (), a positive control containing a synthetic miR122a RNA duplex bound to magnetic beads, followed by washing, elution and detection (), and four different negative controls (, see Methods). The negative controls did not produce any signal below the! threshold, which was set to Io − 0.4 nA (see dashed grey lines in Fig. 5b). , Quantification of miR122a from the mean capture rates. A calibration curve of capture rate versus concentration was constructed (dashed black line) using different concentrations of synthetic 22-bp RNA duplex, showing that capture rate scales linearly with concentration over three orders of magnitude. Determination of miR122a amounts (per µl solution) is based on the spike rate for sample (thick red lines) and the positive control (thick blue lines). , Relative error in the determined RNA concentration as a function of the number of molecules counted by the nanopore (see text). To achieve 93% accuracy under our conditions, the time required for determination of 1 fmol RNA sample is 4 min, corresponding to ~250 spikes. Author information * Abstract * Author information * Supplementary information Primary authors * These authors contributed equally to this work * Meni Wanunu & * Tali Dadosh Affiliations * Department of Physics and Astronomy, University of Pennsylvania, Philadelphia Pennsylvania, USA * Meni Wanunu, * Tali Dadosh, * Vishva Ray & * Marija Drndić * New England Biolabs, Ipswich, Massachusetts, USA * Jingmin Jin & * Larry McReynolds Contributions M.W. and L.M. conceived and designed the experiments. T.D., V.R. and M.W. designed, fabricated and characterized the nanopore devices. J.J. and L.M. developed and performed the miRNA enrichment protocols. M.W. performed the nanopore experiments and analysed the data. M.W., T.D., L.M. and M.D. wrote the manuscript, and all other authors commented on it. Competing financial interests J.J. and L.M. are employees of New England BioLabs, a company that sells p19 and other proteins for RNA and DNA research. Corresponding authors Correspondence to: * Marija Drndić (drndic@physics.upenn.edu) or * Meni Wanunu (wanunu@sas.upenn.edu) Supplementary information * Abstract * Author information * Supplementary information PDF files * Supplementary information (1,744 KB) Supplementary information Additional data - Geometrical confinement of gadolinium-based contrast agents in nanoporous particles enhances T1 contrast
- UNKNOWN 5(11):815-821 (2010)
Nature Nanotechnology | Article Geometrical confinement of gadolinium-based contrast agents in nanoporous particles enhances T1 contrast * Jeyarama S. Ananta1, 10 Search for this author in: * NPG journals * PubMed * Google Scholar * Biana Godin2, 9, 10 Search for this author in: * NPG journals * PubMed * Google Scholar * Richa Sethi1 Search for this author in: * NPG journals * PubMed * Google Scholar * Loick Moriggi3 Search for this author in: * NPG journals * PubMed * Google Scholar * Xuewu Liu2, 9 Search for this author in: * NPG journals * PubMed * Google Scholar * Rita E. Serda2, 9 Search for this author in: * NPG journals * PubMed * Google Scholar * Ramkumar Krishnamurthy4 Search for this author in: * NPG journals * PubMed * Google Scholar * Raja Muthupillai5 Search for this author in: * NPG journals * PubMed * Google Scholar * Robert D. Bolskar6 Search for this author in: * NPG journals * PubMed * Google Scholar * Lothar Helm3 Search for this author in: * NPG journals * PubMed * Google Scholar * Mauro Ferrari2, 4, 7, 9, 11 Search for this author in: * NPG journals * PubMed * Google Scholar * Lon J. Wilson1, 11 Search for this author in: * NPG journals * PubMed * Google Scholar * Paolo Decuzzi2, 8, 9, 11PDecuzzi@tmhs.org Search for this author in: * NPG journals * PubMed * Google Scholar * Affiliations * Contributions * Corresponding authorJournal name:Nature NanotechnologyVolume: 5 ,Pages:815–821Year published:(2010)DOI:doi:10.1038/nnano.2010.203Received08 July 2010Accepted15 September 2010Published online24 October 2010 Abstract * Abstract * Author information * Supplementary information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Magnetic resonance imaging contrast agents are currently designed by modifying their structural and physiochemical properties to improve relaxivity and to enhance image contrast. Here, we show a general method for increasing relaxivity by confining contrast agents inside the nanoporous structure of silicon particles. Magnevist, gadofullerenes and gadonanotubes were loaded inside the pores of quasi-hemispherical and discoidal particles. For all combinations of nanoconstructs, a boost in longitudinal proton relaxivity r1 was observed: Magnevist, r1 ≈ 14 mM−1 s−1/Gd3+ ion (~8.15 × 10+7 mM−1 s−1/construct); gadofullerenes, r1 ≈ 200 mM−1 s−1/Gd3+ ion (~7 × 10+9 mM−1 s−1/construct); gadonanotubes, r1 ≈ 150 mM−1 s−1/Gd3+ ion (~2 × 10+9 mM−1 s−1/construct). These relaxivity values are about 4 to 50 times larger than those of clinically available gadolinium-based agents (~4 mM−1 s−1/Gd3+ ion). The enhancement in contrast is attributed to the geome! trical confinement of the agents, which influences the paramagnetic behaviour of the Gd3+ ions. Thus, nanoscale confinement offers a new and general strategy for enhancing the contrast of gadolinium-based contrast agents. View full text Subject terms: * Nanomaterials * Nanomedicine Figures at a glance * Figure 1: The new MRI nanoconstructs. –, Schematic showing Magnevist (), GFs () and debundled GNTs (). ,, Scanning electron micrographs of quasi-hemispherical (H-SiMP: diameter, 1.6 µm; thickness, ~0.6 µm) () and discoidal (D-SiMP: diameter, 1.0 µm; thickness, 0.4 µm) particles (). , Cartoons showing Magnevist, GFs and GNTs (left to right) entrapped within the porous structure of the SiMPs. The geometrical confinement of the Gd-based CAs within the nanopores enhances the T1 contrast by altering both the inner- and outer-sphere contributions. * Figure 2: Concentration of Gd3+ ions in the SiMP nanoconstruct as determined by ICP-OES analysis. , Graph comparing the single-step (grey bars) and sequential (black bars) loading procedures for two different volumes of the GNT solution exposed to the SiMPs (200 µl and 300 µl). For sequential loading, SiMPs were exposed multiple times (numbers after the slash sign) to 100-µl stock solutions of GNTs. No statistically significant differences were observed between the two procedures. , Graph showing the amount of Gd3+ ions within H-SiMPs as a function of the volume of GNT solution exposed. * Figure 3: MRI characterization of the nanoconstruct by a benchtop relaxometer. The longitudinal relaxivity, r1, of the six new MRI nanoconstructs is compared with the corresponding Gd-based CAs (1.41 T and 37 °C). See Supplementary Fig. S3 for the tabular form of the data. Data are presented as mean ± s.d. (n ≥ 4). Student's t-test is used to estimate the P-values between the two groups. * Figure 4: MRI characterization of the H-SiMP/GNT nanoconstruct in a clinical scanner. , Inversion recovery fits for SiMPs (black squares) and SiMP/GNT (black circles) nanoconstructs were acquired using an inversion recovery pulse sequence and plotted as a function of their inversion time Tinv (time at which the signal is completely suppressed). , Inversion recovery phantoms for SiMP and SiMP/GNT nanoconstruct, clearly showing faster recovery for the nanoconstruct. Data were obtained using a 1.5 T commercial clinical scanner with TR = 7,500 ms and TE = 20 ms. * Figure 5: Calculated longitudinal relaxivity for the SiMP/MAG and SiMP/GF nanoconstructs. The experimental NMRD profile for MAG (dots)6 is compared with three curves (solid lines) derived from SBM Theory for different values of the parameter τR (54, 270 and 540 ps) () and τD (40, 180 and 400 ps) (). , Calculated maximum longitudinal relaxivity r1 of the SiMP/MAG nanoconstructs as a function of the governing parameters τR and τD. All other parameters are listed in ,, The experimental NMRD profile for GF (dots)23 is compared with four curves (solid lines) derived from SBM Theory for different values of the parameter τR (3, 5, 10 and 100 ns) () and τD (200, 550 and 2,000 ps) (). , Calculated maximum longitudinal relaxivity r1 of the SiMP/GF nanoconstructs as a function of the governing parameters τR and τD. All other parameters are listed in . The magnetic properties in and are derived from the best fitting of the experimental NMRD profiles. * Figure 6: NMRD profiles for the GNT and SiMP/GNT constructs. –, Graph showing comparisons of experimental (dotted line)9 NMRD profiles and best fitting curves (solid lines) derived from SBM Theory for q = 1 and 3, τm = 0.9 and 6 ns (), q = 2, 4 and 6, and τm = 1.5 (), q = 2, τm = 1, 1.5 and 2.9 ns (). , All other parameters as derived from the best fitting of the experimental NMRD. Author information * Abstract * Author information * Supplementary information Primary authors * These authors contributed equally to this work * Jeyarama S. Ananta & * Biana Godin Affiliations * Department of Chemistry, Smalley Institute for Nanoscale Science and Technology, Center for Biological and Environmental Nanotechnology, Rice University, Houston, Texas 77251-1892, USA * Jeyarama S. Ananta, * Richa Sethi & * Lon J. Wilson * Department of Nanomedicine and Biomedical Engineering, University of Texas Health Sciences Center at Houston, Houston, Texas, USA * Biana Godin, * Xuewu Liu, * Rita E. Serda, * Mauro Ferrari & * Paolo Decuzzi * Laboratoire de Chimie Inorganique et Bioinorganique, Ecole Polytechnique Federale de Lausanne, EPFL-BCH, CH-1015 Lausanne, Switzerland * Loick Moriggi & * Lothar Helm * Department of Bioengineering, Rice University, Houston, Texas 77251-1892, USA * Ramkumar Krishnamurthy & * Mauro Ferrari * Department of Radiology, St. Luke's Episcopal Hospital, Houston, Texas, USA * Raja Muthupillai * TDA Research Inc. Wheat Ridge, Colorado 80033, USA * Robert D. Bolskar * Department of Experimental Therapeutics, the University of Texas M. D. Anderson Cancer Center, Houston, Texas, USA * Mauro Ferrari * BioNEM—Center of Bio-Nanotechnology and Engineering for Medicine, University of Magna Graecia, Catanzaro, Italy * Paolo Decuzzi * Present address: The Methodist Hospital Research Institute, 6565 Fannin St., Houston, Texas 77030, USA (B.G., X.L., R.E.S., M.F. and P.D.) * Biana Godin, * Xuewu Liu, * Rita E. Serda, * Mauro Ferrari & * Paolo Decuzzi * These authors shared senior authorship * Mauro Ferrari, * Lon J. Wilson & * Paolo Decuzzi Contributions J.S.A. designed the experimental plan, performed all the experiments and helped in writing the manuscript. B.G. designed the experimental plan, developed the protocols for loading, and helped in the loading experiments and in writing the manuscript. R.S. helped in performing the loading experiments and the ICP analysis. L.M. performed MRI characterization. X.L coordinated the microfabrication of the SiMPs and performed their surface modification. R.E.S. performed the SEM analysis. R.K. and R.M. performed the MRI characterization in clinical scanners. R.D.B. manufactured the GFs. L.H. helped in performing the MRI characterization of the GNT, provided input on the original draft and revisions. M.F. provided input on the original draft and revisions. L.J.W. conceived the idea, designed the experimental plan and helped in writing the manuscript. P.D. conceived the idea, designed the experimental plan, wrote the manuscript and performed all the numerical calculations. All the aut! hors discussed the results and commented on the manuscript. Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * Paolo Decuzzi (PDecuzzi@tmhs.org) Supplementary information * Abstract * Author information * Supplementary information PDF files * Supplementary information (1,871 KB) Supplementary information Additional data - Early detection of aging cartilage and osteoarthritis in mice and patient samples using atomic force microscopy
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Nature Nanotechnology | Corrigendum Early detection of aging cartilage and osteoarthritis in mice and patient samples using atomic force microscopy * Martin Stolz Search for this author in: * NPG journals * PubMed * Google Scholar * Riccardo Gottardi Search for this author in: * NPG journals * PubMed * Google Scholar * Roberto Raiteri Search for this author in: * NPG journals * PubMed * Google Scholar * Sylvie Miot Search for this author in: * NPG journals * PubMed * Google Scholar * Ivan Martin Search for this author in: * NPG journals * PubMed * Google Scholar * Raphaël Imer Search for this author in: * NPG journals * PubMed * Google Scholar * Urs Staufer Search for this author in: * NPG journals * PubMed * Google Scholar * Aurelia Raducanu Search for this author in: * NPG journals * PubMed * Google Scholar * Marcel Düggelin Search for this author in: * NPG journals * PubMed * Google Scholar * Werner Baschong Search for this author in: * NPG journals * PubMed * Google Scholar * A. U. Daniels Search for this author in: * NPG journals * PubMed * Google Scholar * Niklaus F. Friederich Search for this author in: * NPG journals * PubMed * Google Scholar * Attila Aszodi Search for this author in: * NPG journals * PubMed * Google Scholar * Ueli Aebi Search for this author in: * NPG journals * PubMed * Google ScholarJournal name:Nature NanotechnologyVolume: 5 ,Page:821Year published:(2010)DOI:doi:10.1038/nnano.2010.219Published online04 November 2010 Article tools * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Nature Nanotechnology4, 186–192 (2009); published online: 1 February 2009; corrected after print: 4 November 2010. In the version of this Article originally published, a systematic error affected all the values of microstiffness presented in the paper (including in the figures and figure captions). This error resulted in all the values of microstiffness being too high by a factor of √π. The values for nanostiffness are not affected and this error does not affect the conclusions of the paper. This error has now been corrected in the HTML and PDF versions of the text. The Supplementary Information and corresponding e-mail address have also been updated. Additional data
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