SEM-induced shrinking of solid-state nanopores for single molecule detection

We have investigated the mechanism by which the diameter of solid-state nanopores is reduced by a scanning electron microscope. The process depends on beam parameters such as the accelerating voltage and electron flux and does not involve simple electron-beam-induced deposition of hydrocarbon contaminants. Instead, it is an energy-dependent process that involves material flow along the surface of the nanopore membrane. We also show that pores fabricated in this manner can detect double stranded DNA.     

Chemical, thermal, and electric field induced unfolding of single protein molecules studied using nanopores

Single-molecule experimental techniques have recently shown to be of significant interest for use in numerous applications in both the research laboratory and industrial settings. Although many single-molecule techniques exist, the nanopore platform is perhaps one of the more popular techniques due to its ability to act as a molecular sensor of biological macromolecules. For example, nanopores offer a unique, new method for probing various properties of proteins and can contribute to elucidating key biophysical information in conjunction with existing techniques. In the present study, various forms of bovine serum albumin (BSA) are detected including thermally refolded BSA, urea-denatured BSA, and multiple forms of BSA detected at elevated electric field strengths (with and without urea). We also provide excluded volume measurements for each of these states that normally are difficult to obtain due to unknown and unstable protein conformations.     

Nanoparticle-induced fluorescence lifetime modification as nanoscopic ruler: demonstration at the single molecule level

We combine interferometric detection of single gold nanoparticles, single molecule microscopy, and fluorescence lifetime measurement to study the modification of the fluorescence decay rate of an emitter close to a nanoparticle. In our experiment, gold particles with a diameter of 15 nm were attached to single dye molecules via double-stranded DNA of different lengths. Nanoparticle-induced lifetime modification (NPILM) has promise in serving as a nanoscopic ruler for the distance range well beyond 10 nm, which is the upper limit of fluorescence resonant energy transfer (FRET). Furthermore, the simultaneous detection of single nanoparticles and fluorescent molecules presented in this work provides new opportunities for single molecule biophysical studies.     

Lambda/4 resonance of an optical monopole antenna probed by single molecule fluorescence

We present a resonant optical nanoantenna positioned at the end of a metal-coated glass fiber near-field probe. Antenna resonances, excitation conditions, and field localization are directly probed in the near field by single fluorescent molecules and compared to finite integration technique simulations. It is shown that the antenna is equivalent to its radio frequency analogue, the monopole antenna. For the right antenna length and local excitation conditions, antenna resonances occur that lead to an enhanced localized field near the antenna apex. Direct mapping of this field with single fluorescent molecules reveals a spatial localization of 25 nm, demonstrating the importance of such antennas for nanometer resolution optical microscopy.     

Label-free detection of single protein molecules and protein-protein interactions using synthetic nanopores

Nanofabricated pores in 20 nm-thick silicon nitride membranes were used to probe various protein analytes as well as to perform an antigen-antibody binding assay. A two-compartment electrochemical cell was separated by a single nanopore, 28 nm in diameter. Adding proteins to one compartment caused current perturbations in the ion current flowing through the pore. These perturbations correlated with both the charge and the size of the protein or of a protein-protein complex. The potential of this nanotechnology for studying protein-protein interactions is highlighted with the sensitive detection of beta-human chorionic gonadotropin, a hormone and clinical biomarker of pregnancy, by monitoring in real time and at a molecular level the formation of a complex between hormones and antibodies in solution. In this form, the assay compared advantageously to immunoassays, with the important difference that labels, immobilization, or amplification steps were no longer needed. In conclusion, we present proof-of-principle that properties of proteins and their interactions can be investigated in solution using synthetic nanopores and that these interactions can be exploited to measure protein concentrations accurately.     

Entropy-driven single molecule tug-of-war of DNA at micro-nanofluidic interfaces

Entropy-driven polymer dynamics at the nanoscale is fundamentally important in biological systems but the dependence of the entropic force on the nanoconfinement remains elusive. Here, we established an entropy-driven single molecule tug-of-war (TOW) at two micro-nanofluidic interfaces bridged by a nanoslit, performed the force analysis from a modified wormlike chain in the TOW scenario and the entropic recoiling process, and determined the associated scalings on the nanoconfinement. Our results provide a direct experimental evidence that the entropic forces in these two regimes, though unequal, are essentially constant at defined slit heights, irrespective of the slit lengths and the DNA segments within. Our findings have the implications to polymer transport at the nanoscale, device design for single molecule analysis, and biotechnological applications.     

Stochastic sensing of proteins with receptor-modified solid-state nanopores

Solid-state nanopores are capable of the label-free analysis of single molecules. It is possible to add biochemical selectivity by anchoring a molecular receptor inside the nanopore, but it is difficult to maintain single-molecule sensitivity in these modified nanopores. Here, we show that metallized silicon nitride nanopores chemically modified with nitrilotriacetic acid receptors can be used for the stochastic sensing of proteins. The reversible binding and unbinding of the proteins to the receptors is observed in real time, and the interaction parameters are statistically analysed from single-molecule binding events. To demonstrate the versatile nature of this approach, we detect His-tagged proteins and discriminate between the subclasses of rodent IgG antibodies.     

Investigation of combined unfolding of neutron spectra using the UMG unfolding codes

An investigation of the simultaneous unfolding of data from neutron spectrometers using the UMG codes MAXED and GRAVEL has been performed. This approach involves combining the data from the spectrometers before unfolding, thereby performing a single combined unfolding of all the data to yield a final combined spectrum. The study used measured data from three proton recoil counters and also Bonner sphere and proton recoil counter responses calculated from their response functions. In each case, the spectrum derived from combined unfolding is compared with either the spectrum obtained from merging the independently unfolded spectra or the spectrum used to calculate the responses. The advantages and disadvantages of this technique are discussed.     

Detection of nucleosomal substructures using solid-state nanopores

Histone proteins assemble onto DNA into nucleosomes that control the structure and function of eukaryotic chromatin. More specifically, the structural integrity of nucleosomes regulates gene expression rates and serves as an important early marker for cell apoptosis. Nucleosomal (sub)structures are however hard to detect and characterize. Here, we show that solid-state nanopores are well suited for fast and label-free detection of nucleosomes and its histone subcomplexes. (Nucleo-)protein complexes are individually driven through the nanopore by an applied electric field, which results in characteristic conductance blockades that provide quantitative information on the molecular size of the translocating complex. We observe a systematic dependence of the conductance blockade and translocation time on the molecular weight of the nucleosomal substructures. This allows discriminating and characterizing these protein and DNA-protein complexes at the single-complex level. Finally, we demonstrate the ability to distinguish nucleosomes and dinucleosomes as a first step toward using the nanopore platform to study chromatin arrays.     

Non-planar nanofluidic devices for single molecule analysis fabricated using nanoglassblowing

A method termed 'nanoglassblowing' is presented for fabricating integrated microfluidic and nanofluidic devices with gradual depth changes and wide, shallow nanochannels. This method was used to construct fused silica channels with out-of-plane curvature of channel covers from over ten micrometers to a few nanometers, nanochannel aspect ratios smaller than 2 × 10(-5):1 (depth:width), and nanochannel depths as shallow as 7?nm. These low aspect ratios and shallow channel depths would be difficult to form otherwise without collapse of the channel cover, and the gradual changes in channel depth eliminate abrupt free energy barriers at the transition from microfluidic to nanofluidic regions. Devices were characterized with atomic force microscopy (AFM), white light interferometry, scanned height measurements, fluorescence intensity traces, and single molecule analysis of double-stranded deoxyribonucleic acid (DNA) velocity and conformation. Nanochannel depths and aspect ratios formed by nanoglassblowing allowed measurements of the radius of gyration, R(g), of single λ?DNA molecules confined to slit-like nanochannels with depths, d, ranging from 11?nm to 507?nm. Measurements of R(g) as a function of d agreed qualitatively with the scaling law R(g)∝d(-0.25) predicted by Brochard for nanochannel depths from 36?nm to 156?nm, while measurements of R(g) in 11?nm and 507?nm deep nanochannels deviated from this prediction.     

Dynamics of Salmonella infection of macrophages at the single cell level

Salmonella enterica causes a range of diseases. Salmonellae are intracellular parasites of macrophages, and the control of bacteria within these cells is critical to surviving an infection. The dynamics of the bacteria invading, surviving, proliferating in and killing macrophages are central to disease pathogenesis. Fundamentally important parameters, however, such as the cellular infection rate, have not previously been calculated. We used two independent approaches to calculate the macrophage infection rate: mathematical modelling of Salmonella infection experiments, and analysis of real-time video microscopy of infection events. Cells repeatedly encounter salmonellae, with the bacteria often remain associated with the macrophage for more than ten seconds. Once Salmonella encounters a macrophage, the probability of that bacterium infecting the cell is remarkably low: less than 5%. The macrophage population is heterogeneous in terms of its susceptibility to the first infection event. Once infected, a macrophage can undergo further infection events, but these reinfection events occur at a lower rate than that of the primary infection.     

Thermal unfolding of proteins studied by coupled reversed-phase HPLC-electrospray ionization mass spectrometry techniques based on isotope exchange effects

In this study, a deuterium exchange procedure has been employed to evaluate the thermal stability of globular proteins under conditions that replicate their interactive behavior in reversed-phase high performance chromatographic (RP-HPLC) systems. In particular, this investigation has permitted the conformational stability of two proteins, hen egg white lysozyme (HEWL) and horse heart myoglobin (HMYO) to be examined under different temperature and low-pH solvent regimes. The results confirm that this experimental approach provides an efficient strategy to explore fundamental conformational features of polypeptides or proteins in their folded and partial unfolded states under these interactive conditions. In particular, this analytical procedure permits insight to be readily gained into the processes that occur when polypeptides and globular proteins interact with lipophilic liquid/ solid interfaces in the presence of water-organic solvent mixtures at different temperatures.     

Mechanical mapping of single membrane proteins at submolecular resolution

The capacity of proteins to carry out different functions is related to their ability to undergo conformation changes, which depends on the flexibility of protein structures. In this work, we applied a novel imaging mode based on indentation force spectroscopy to map quantitatively the flexibility of individual membrane proteins in their native, folded state at unprecedented submolecular resolution. Our results enabled us to correlate protein flexibility with crystal structure and showed that α-helices are stiff structures that may contribute importantly to the mechanical stability of membrane proteins, while interhelical loops appeared more flexible, allowing conformational changes related to function.     

Electrophoretic time-of-flight measurements of single DNA molecules with two stacked nanopores

Electrophoretic transport through a solid-state nanodevice comprised of two stacked nanopore sensors is used to determine the free-solution mobility of DNA molecules based on their "time-of-flight" between the two pores. Mobility measurements are possible at very low (100 pM) DNA concentration and for low as well as high salt concentrations (here 30 mM and 1 M KCl). The mechanism of DNA transport through the device is elucidated by statistical analysis, showing the free-draining nature of the translocating DNA polymers and a barrier-dominated escape through the second pore. Furthermore, consecutive threading of single molecules through the two pores can be used to gain more detailed information on the dynamics of the molecules by correlation analysis, which also provides a direct electrical proof for translocation.     

Thermal stability of carbon nanotubes probed by anchored tungsten nanoparticles

Abstract

The thermal stability of multiwalled carbon nanotubes (CNTs) was studied in high vacuum using tungsten nanoparticles as miniaturized thermal probes. The particles were placed on CNTs inside a high-resolution transmission electron microscope equipped with a scanning tunneling microscope unit. The setup allowed manipulating individual nanoparticles and heating individual CNTs by applying current to them. CNTs were found to withstand high temperatures, up to the melting point of 60-nm-diameter W particles (～3400 K). The dynamics of W particles on a hot CNT, including particle crystallization, quasimelting, melting, sublimation and intradiffusion, were observed in real time and recorded as a video. Graphite layers reel off CNTs when melted or premelted W particles revolve along the tube axis.     

Reconstitution of membrane proteins into polymer-supported membranes for probing diffusion and interactions by single molecule techniques

We have established a robust and versatile analytical platform for probing membrane protein function in a defined lipid environment on solid supports. This approach is based on vesicle capturing onto an ultrathin poly(ethylene glycol) (PEG) polymer brush functionalized with fatty acid moieties and subsequent vesicle fusion into a contiguous membrane. In order to ensure efficient formation of these tethered polymer-supported membranes (PSM), very small unilamellar vesicles (VSUV) containing fluorescent lipids or model transmembrane proteins were generated by detergent depletion with cyclodextrin. Thus, very rapid reconstitution of membrane proteins into PSM was possible in a format compatible with microfluidics. Moreover, surfaces could be regenerated with detergent solution and reused multiple times. Lipid and protein diffusion in these membranes was investigated by fluorescence recovery after photobleaching, single molecule tracking, and fluorescence correlation spectroscopy. Full mobility of lipids and a high degree of protein mobility as well as homogeneous diffusion of both were observed. Quantitative ligand binding studies by solid phase detection techniques confirmed functional integrity of a transmembrane receptor reconstituted into these PSM. Colocomotion of individual ligand-receptor complexes was detected, demonstrating the applicability for single molecule fluorescence techniques.     

High-resolution mapping of redox-immunomarked proteins using electrochemical-atomic force microscopy in molecule touching mode

We explore the possibility of using molecule touching atomic force electrochemical microcopy (Mt/AFM-SECM) for high-resolution mapping of proteins on conducting surfaces. The proposed imaging strategy relies on making surface-immobilized proteins electrochemically "visible" via redox-immunomarking by specific antibodies conjugated to poly(ethylene glycol) (PEG) chains terminated by redox ferrocene (Fc) heads. The flexibility and length of the PEG chains are such that, upon approaching a combined AFM-SECM microelectrode tip toward the surface, the Fc moieties can efficiently shuttle electrons from the surface to the tip. The so-generated SECM positive feedback tip current allows the specific localized detection of the sought protein molecules on the surface. This new electrochemical imaging scheme is validated experimentally on the basis of a model system consisting of mouse IgGs adsorbed onto electrode surfaces and recognized by Fc-PEG-labeled antimouse antibodies. In order to estimate the resolution of Mt/AFM-SECM for protein imaging, regular arrays of submicrometer-sized spots of mouse IgGs are fabricated onto gold electrode surfaces using particle lithography. The Fc-PEG-immunomarked mouse IgG spots are imaged by Mt/AFM-SECM operated in tapping mode. Both an electrochemical image, reflecting the surface distribution of the redox-labeled IgGs, and a topography image are then simultaneously and independently acquired, with a demonstrated resolution in the ~100 nm range. The strength of Mt/AFM-SECM imaging is to combine the nanometric resolution of AFM with the selectivity of the electrochemical detection, potentially allowing individual target proteins to be identified amidst similarly sized "nano objects" present on a conducting surface.     

Imaging the charge distribution within a single molecule

Scanning tunnelling microscopy and atomic force microscopy can be used to study the electronic and structural properties of surfaces, as well as molecules and nanostructures adsorbed on surfaces, with atomic precision, but they cannot directly probe the distribution of charge in these systems. However, another form of scanning probe microscopy, Kelvin probe force microscopy, can be used to measure the local contact potential difference between the scanning probe tip and the surface, a quantity that is closely related to the charge distribution on the surface. Here, we use a combination of scanning tunnelling microscopy, atomic force microscopy and Kelvin probe force microscopy to examine naphthalocyanine molecules (which have been used as molecular switches) on a thin insulating layer of NaCl on Cu(111). We show that Kelvin probe force microscopy can map the local contact potential difference of this system with submolecular resolution, and we use density functional theory calculations to verify that these maps reflect the intramolecular distribution of charge. This approach could help to provide fundamental insights into single-molecule switching and bond formation, processes that are usually accompanied by the redistribution of charge within or between molecules.