Probing Heterogeneous Folding Pathways of DNA Origami Self-Assembly at the Molecular Level with Atomic Force Microscopy.

A myriad of DNA origami nanostructures have been demonstrated in various intriguing applications. In pursuit of facile yet high-yield synthesis, the mechanisms underlying DNA origami folding need to be resolved. Here, we visualize the folding processes of several multidomain DNA origami structures under ambient annealing conditions in solution using atomic force microscopy with submolecular resolution. We reveal the coexistence of diverse transitional structures that might result in the same prescribed products. Based on the experimental observations and the simulation of the energy landscapes, we propose the heterogeneity of the folding pathways of multidomain DNA origami structures. Our findings may contribute to understanding the high-yield folding mechanism of DNA origami.

Quantitative SERS sensing mediated by internal standard Raman signal from silica nanoparticles in flexible polymer matrix.

Attributed to poor signal uniformity and external interference, ultrasensitive surface-enhanced Raman spectroscopy (SERS) still faces difficulties in the reliable and quantitative detection of trace molecules. Here, a facile Ag/Si/sodium carboxy methyl cellulose (NaCMC) film with internal standard (IS) was promoted for quantitative determination of thiram. The effects of preparation conditions on SERS activity of the film were systematically investigated and then a flexible SERS substrate with high sensitivity and uniformity was fabricated. The enhancement factor was calculated to be 1.12 × 106 and SERS mapping was recorded with a relative standard deviation value of 19.8% by utilizing 4-mercaptobenzoic acid (4-MBA) as target molecule. Additionally, the dominant contribution of the IS from encapsulated Si nanoparticles (NPs) was confirmed in the quantitative assay of 4-MBA and thiram, facilitating attractive fitting coefficients (R2) as 0.991 and 0.998. Besides that, the proposed flexible film was conducted to scrub trace thiram from the surfaces of apple, orange, and cucumber, resulting in recoveries of 89%, 94%, and 91%. A smart and facile quantitative SERS substrate was developed here for monitoring trace biochemical molecules, verifying its potential utilizations in monitoring pesticide residues.

Bioinspired surface-enhanced Raman scattering substrate with intrinsic Raman signal for the interactive SERS detection of pesticides residues.

Although biomimetic surface enhanced Raman scattering (SERS) substrate which makes use of naturally existing raw materials have been fully utilized, it remains challenging to achieve credible quantitative detection. Herein, nanoimprint technology was exploited to engineer internal standard (IS) enabled quantitative flexible biomimetic SERS substrates, in which polydimethylsiloxane (PDMS) with intrinsic Raman signal was utilized as a tool to reversely duplicate surface structures from different agriculture products and then deposited with Ag nanoparticles. The resultant four kinds of biomimetic SERS substrates with different surface geometries all permit highly sensitive assay with enhancement factors (EFs) of about 106 in both drop-dry and in situ SERS detection modes. Moreover, the quantitative degree in the SERS detection was effectively corrected based on the IS strategy. Finally, an ingenious interactive in situ SERS detection was conducted. Interestingly, the maximum recovery rate was achieved when the template food was used as target surface compared with other foods, indicating the significance of manufacturing the highly conformed SERS-active structure from the surface to be tested. The proposed quantitative biomimetic SERS substrate is expected to be widely used in the field of biochemical supervision.

Investigation of the Dissociation Mechanism of Single-Walled Carbon Nanotube on Mature Amyloid-ß Fibrils at Single Nanotube Level.

Amyloid fibrils originating from the fibrillogenesis of misfolded amyloid proteins are associated with the pathogenesis of many neurodegenerative diseases, such as Alzheimer's, Parkinson's, and Huntington's diseases. Carbon nanotubes have been extensively applied in our life and industry due to their unique chemical and physical properties. Nonetheless, the details between carbon nanotubes and mature amyloid fibrils remain elusive. In this study, we explored the interplay between single-walled carbon nanotubes (SWCNTs) and preformed amyloid-ß (Aß) fibrils by atomic force microscopy at the single SWCNT level, together with ThT fluorescence, cellular viability assays, infrared spectroscopy, and molecular dynamics (MD) simulations. The results demonstrated that SWCNTs could partially destroy the preformed Aß fibrils and form the Aß-surrounded-SWCNTs conjugates, as well as reduce the ß-sheet structures. Peak force quantitative nanomechanical measurements revealed that the conjugates have lower Young's modulus than fibrils. Furthermore, our MD simulation demonstrated that the dissociation ability was dependent on the binding sites of Aß fibrils. Overall, this study provides an insight into the dissociation mechanism between SWCNT and Aß fibrils, which could be beneficial for the study of bionanomaterials and the development of other potential drug candidates for amyloidosis.

His18 promotes reactive oxidative stress production in copper-ion mediated human islet amyloid polypeptide aggregation.

Copper ions play a critical role in human islet amyloid polypeptide (hIAPP) aggregation, which has been found in more than 90% of patients with type-2 diabetes (T2D). The role of Cu(ii) in the cell cytotoxicity with hIAPP has been explored in two aspects: inhibiting the formation of fibrillar structures and stimulating the generation of reactive oxygen species (ROS). In this work, we carried out spectroscopic studies of Cu(ii) interacting with several hIAPP fragments and their variants as well. Electron paramagnetic resonance (EPR) measurements and Amplex Red analysis showed that the amount of H2O2 generated in hIAPP(11-28) solution co-incubated with Cu(ii) was remarkably more than hIAPP(1-11) and hIAPP(28-37). Furthermore, the H2O2 level was seriously reduced when His18 of hIAPP(11-28) was replaced by Arg(R) or Ser(S), indicating that His18 is the key residue of Cu(ii) binding to hIAPP(11-28) to promote H2O2 generation. This is likely because the donation of electrons from the peptide to Cu(ii) ions would result in the formation of the redox-active complexes, which could stimulate the formation of H2O2. Overall, this study provides further insight into the molecular mechanism of Cu(ii) induced ROS generation.

Mechanical Properties of Sub-Microbubbles with a Nanoparticle-Decorated Polymer Shell.

Nanoparticle-decorated polymer-coated sub-microbubbles (NP-P-coated SMBs), as proved, have shown promising application prospects in ultrasound imaging, magnetic resonance imaging, drug delivery, and so forth. However, the quantitative evaluation of the stability and mechanical properties of single NP-P-coated SMB is absent. Here, we first reported the stiffness and Young's modulus of single NP-P-coated SMB obtained by the PeakForce mode of atomic force microscopy. Such NP-P-coated SMBs could maintain perfect spherical shapes and have a thinner shell thickness (about 10 nm), as determined by characterization using a transmission electron microscope. Young's modulus of NP-P-coated SMBs is about 4.6 ± 1.2 GPa, and their stiffness is about 15.0 ± 3.1 N/m. Both modulus and stiffness are obtained from the linear region in the force-deformation curve and are nearly independent of their sizes. These results should be very useful to evaluate their stability, which plays a key role in maintaining the shell drug loading and acoustic capabilities.

Atomic force microscopy-based single-molecule force spectroscopy detects DNA base mismatches.

Atomic force microscopy-based single-molecule-force spectroscopy is limited by low throughput. We introduce addressable DNA origami to study multiple target molecules. Six target DNAs that differed by only a single base-pair mismatch were clearly differentiated a rupture force of only 4 pN.

Measurement of nanomechanical properties of DNA molecules by PeakForce atomic force microscopy based on DNA origami.

Characterization of the stiffness of thin DNA strands remains difficult. By constructing bilayer DNA molecules, we investigated their mechanical properties using AFM. Increased DNA thickness through DNA origami greatly reduced the substrate effect when measuring Young's modulus, thus providing a more accurate picture of the inherent nanomechanical properties of DNA.

The effect of aluminum ion on the aggregation of human islet amyloid polypeptide (11-28).

Metal ions play a critical role in human islet amyloid polypeptide (hIAPP) aggregation, which is believed to be closely associated with ß-cell death in type II diabetes. In this work, the effect of Al3+ on the aggregation of hIAPP (11-28) was studied by several different experimental approaches. Atomic force microscopy measurements showed that Al3+ could remarkably inhibit hIAPP(11-28) fibrillogenesis, while Zn2+ had a slight promotion effect on peptide aggregation, which was also confirmed by Thioflavin T fluorescence observation. Furthermore, X-ray photoelectron spectroscopy measurement indicated that Al ions might form chemical bonds with neighboring atoms and destroy the secondary structures of the protein. Our studies could deepen the understanding of the role of metal ions in the aggregation of amyloid peptides.

Stiffness and evolution of interfacial micropancakes revealed by AFM quantitative nanomechanical imaging.

Micropancakes are quasi-two-dimensional micron-sized domains on crystalline substrates (e.g. highly oriented pyrolytic graphite (HOPG)) immersed in water. They are only a few nanometers thick, and are suspected to come from the accumulation of dissolved air at the solid-water interface. However, the exact chemical nature and basic physical properties of micropancakes have been under debate ever since their first observation, primarily due to the lack of a suitable characterization technique. In this study, the stiffness of micropancakes at the interface between HOPG and ethanol-water solutions was investigated by using PeakForce Quantitative NanoMechanics (PF-QNM) mode Atomic Force Microscopy (AFM). Our measurements showed that micropancakes were stiffer than nanobubbles, and for bilayer micropancakes, the bottom layer in contact with the substrate was stiffer than the top one. Interestingly, the micropancakes became smaller and softer with an increase in the ethanol concentration in the solution, and were undetectable by AFM above a critical concentration of ethanol. But they re-appeared after the ethanol concentration in the solution was reduced. Clearly the evolution and stiffness of the micropancakes were dependent on the chemical composition in the solution, which could be attributed to the correlation of the mechanical properties of the micropancakes with the surface tension of the liquid phase. Based on the "go-and-come" behaviors of micropancakes with the ethanol concentration, we found that the micropancakes could actually tolerate the ethanol concentration much higher than 5%, a value reported in the literature. The results from this work may be helpful in alluding the chemical nature of micropancakes.

Interfacial nanobubbles on atomically flat substrates with different hydrophobicities.

The dependence of the morphology of interfacial nanobubbles on atomically flat substrates with different wettability ranges was investigated by using PeakForce quantitative nanomechanics. Interfacial nanobubbles were formed and imaged on silicon nitride (Si3N4), mica, and highly ordered pyrolytic graphite (HOPG) substrates that were partly covered by reduced graphene oxide (rGO). The contact angles and sizes of those nanobubbles were measured under the same conditions. Nanobubbles with the same lateral width exhibited different heights on the different substrates, with the order Si3N4≈mica>rGO>HOPG, which is consistent with the trend of the hydrophobicity of the substrates.

Probing tethered targets of a single biomolecular complex with atomic force microscopy.

DNA origami shows tremendous promise as templates for the assembly of nano-components and detection of molecular recognition events. So far, the method of choice for evaluating these structures has been atomic force microscopy (AFM), a powerful tool for imaging nanoscale objects. In most cases, tethered targets on DNA origami have proven to be highly effective samples for investigation. Still, while maximal assembly of the nanostructures might benefit from the greatest flexibility in the tether, AFM imaging requires a sufficient stability of the adsorbed components. The balance between the tether flexibility and sample stability is a major, poorly understood, concern in such studies. Here, we investigated the dependence of the tethering length on molecular capture events monitored by AFM. In our experiments, single biotin molecules were attached to DNA origami templates with various linker lengths of thymidine nucleotides, and their interaction with streptavidin was observed with AFM. Our results show that the streptavidin-biotin complexes are easily detected with short tethered lengths, and that their morphological features clearly change with the tethering length. We identify the functionally useful tether lengths for these investigations, which are also expected to prove useful in the construction and further application of DNA origami in bio-nanotechnology studies.

Molecular threading and tunable molecular recognition on DNA origami nanostructures.

The DNA origami technology holds great promise for the assembly of nanoscopic technological devices and studies of biochemical reactions at the single-molecule level. For these, it is essential to establish well controlled attachment of functional materials to predefined sites on the DNA origami nanostructures for reliable measurements and versatile applications. However, the two-sided nature of the origami scaffold has shown limitations in this regard. We hypothesized that holes of the commonly used two-dimensional DNA origami designs are large enough for the passage of single-stranded (ss)-DNA. Sufficiently long ssDNA initially located on one side of the origami should thus be able to "thread" to the other side through the holes in the origami sheet. By using an origami sheet attached with patterned biotinylated ssDNA spacers and monitoring streptavidin binding with atomic force microscopic (AFM) imaging, we provide unambiguous evidence that the biotin ligands positioned on one side have indeed threaded through to the other side. Our finding reveals a previously overlooked critical design feature that should provide new interpretations to previous experiments and new opportunities for the construction of origami structures with new functional capabilities.

Hierarchical ordering of amyloid fibrils on the mica surface.

The aggregation of amyloid peptides into ordered fibrils is closely associated with many neurodegenerative diseases. The surfaces of cell membranes and biomolecules are believed to play important roles in modulation of peptide aggregation under physiological conditions. Experimental studies of fibrillogenesis at the molecular level in vivo, however, are inherently challenging, and the molecular mechanisms of how surface affects the structure and ordering of amyloid fibrils still remain elusive. Herein we have investigated the aggregation behavior of insulin peptides within water films adsorbed on the mica surface. AFM measurements revealed that the structure and orientation of fibrils were significantly affected by the mica lattice and the peptide concentration. At low peptide concentration (~0.05 mg mL(-1)), there appeared a single layer of short and well oriented fibrils with a mean height of 1.6 nm. With an increase of concentration to a range of 0.2-2.0 mg mL(-1), a different type of fibrils with a mean height of 3.8 nm was present. Interestingly, when the concentration was above 2.0 mg mL(-1), the thicker fibrils exhibited two-dimensional liquid-crystal-like ordering probably caused by the combination of entropic and electrostatic forces. These results could help us gain better insight into the effects of the substrate on amyloid fibrillation.

Assembly of glucagon (proto)fibrils by longitudinal addition of oligomers.

The process of glucagon peptide aggregation was studied with high resolution atomic force microscopy (AFM). The statistical analysis of ex situ AFM images in combination with in situ AFM observation suggests that it is more likely that (proto)fibrils are formed via direct longitudinal growth of oligomers, instead of the lateral association of two or more filaments.

In situ monitoring of single molecule binding reactions with time-lapse atomic force microscopy on functionalized DNA origami.

Individual biomolecular binding events were recorded in situ by combining time-lapse atomic force microscopy and DNA origami. Single streptavidin molecules bound to specifically biotinyated DNA origami were simply counted as a function of time to obtain a direct measure of the binding rate.

Immobilisation of living bacteria for AFM imaging under physiological conditions.

Atomic force microscopy (AFM) holds great potential for studying the nanoscale surface structures of living cells, and to measure their interactions with abiotic surfaces, other cells, or specific biomolecules. However, the application of AFM in microbiology is challenging due to the difficulty of immobilising bacterial cells to a flat surface without changing the cell surface properties or cell viability. We have performed an extensive and thorough study of how to functionalise surfaces in order to immobilise living bacteria for AFM studies in liquid environments. Our aim was to develop a scheme which allows bacterial cells to be immobilised to a flat surface with sufficient strength to avoid detachment during the AFM scanning, and without affecting cell surface chemistry, structure, and viability. We compare and evaluate published methods, and present a new, reproducible, and generally applicable scheme for immobilising bacteria cells for an AFM imaging. Bacterial cells were immobilised to modified glass surfaces by physical confinement of cells in microwells, physisorption to positively charged surfaces, covalent binding to amine- or carboxyl-terminated surfaces, and adsorption to surfaces coated with highly adhesive polyphenolic proteins originating from the mussel Mytilus edulis. Living cells could be immobilised with all of these approaches, but many cells detached when immobilised by electrostatic interactions and imaged in buffers like PBS or MOPS. Cells were more firmly attached when immobilised by covalent binding, although some cells still detached during AFM imaging. The most successful method revealed was immobilisation by polyphenolic proteins, which facilitated firm immobilisation of the cells. Furthermore, the cell viability was not affected by this immobilisation scheme, and adhesive proteins thus provide a fast, reproducible, and generally applicable scheme for immobilising living bacteria for an AFM imaging.

Transport and its enhancement caused by coupling.

Using the Weiss mean-field approximation theory and the particles' transport theory for the spatially periodic stochastic systems, we derive an exact analytical expression for the stationary probability current of a coupled lattice system driven by dichotomous noise. It is shown that, for this coupled lattice system, the spatial asymmetry of the system, the asymmetry of the dichotomous noise, and the coupling among nearest neighbors are the ingredients for the stationary probability current. By applying our theory to two special models, we find that (1) the coupling can lead to the directional transport of the particles (even when the potential and the dichotomous noise are symmetric) and (2) the coupling among nearest neighbors can enhance the transport of the particles in some circumstances. Our results are applied to a device of two-dimensional Josephson-junction arrays and a large protein motors cluster.

Evaluation of the radial deformability of poly(dG)-poly(dC) DNA and G4-DNA using vibrating scanning polarization force microscopy.

Poly(dG)-poly(dC) DNA and G4-DNA are two types of synthetic molecules that are regarded as promising candidates for molecular nanodevices. In this work, vibrating scanning polarization force microscopy (VSPFM) was employed to study the radial deformability of these two molecules coadsorbed on a Ni(2+)-modified mica surface. The values of the radial compressive elastic modulus of these two types of molecules were found to be similar (approximately 5-10 MPa) when the external loading force was between approximately 0.04 and approximately 0.12 nN. However, G4-DNA molecules possessed higher stiffness than poly(dG)-poly(dC) DNA (approximately 20-40 vs approximately 10-20 MPa) when the loading force was larger than approximately 0.12 nN. The results will aid us in understanding these molecule's mechanical performances.

Curvature of synthetic and natural surfaces is an important target feature in classical pathway complement activation.

The binding of Abs to microbial surfaces followed by complement activation constitutes an important line of defense against infections. In this study, we have investigated the relationship between complement activation and the binding of human IgM Abs to surfaces with different curvatures. IgM Abs to dextran were shown to activate complement potently on dextran-coated particles having a diameter around 250 nm, whereas larger (600 nm) particles were less potent activators. This selectivity regarding particle dimension was also found for complement activation by colloidal substances of microbial origin. Peptidoglycan (PGN) is the major chemical component in the cell wall of Gram-positive bacteria. Fragments of purified PGN with sizes of approximately 100 nm promoted complement activation effectively through the classical pathway. By contrast, larger or smaller fragments of PGN did not activate complement strongly. A careful analysis of PGN fragments released during planctonic growth of Staphylococcus aureus showed that these include curvatures that would permit strong IgM-mediated complement activation, whereas the curvature of intact cells would be less effective for such activation. Consistently, we found that the suspended PGN fragments were strong activators of complement through the classical pathway. We suggest that these fragments act as decoy targets for complement activation, providing protection for S. aureus against the host immune response to infection.