5-Axis CNC Micromilling for Rapid, Cheap, and Background-Free NMR Microcoils.

The superior mass sensitivity of microcoil technology in nuclear magnetic resonance (NMR) spectroscopy provides potential for the analysis of extremely small-mass-limited samples such as eggs, cells, and tiny organisms. For optimal performance and efficiency, the size of the microcoil should be tailored to the size of the mass-limited sample of interest, which can be costly as mass-limited samples come in many shapes and sizes. Therefore, rapid and economic microcoil production methods are needed. One method with great potential is 5-axis computer numerical control (CNC) micromilling, commonly used in the jewelry industry. Most CNC milling machines are designed to process larger objects and commonly have a precision of >25 µm (making the machining of common spiral microcoils, for example, impossible). Here, a 5-axis MiRA6 CNC milling machine, specifically designed for the jewelry industry, with a 0.3 µm precision was used to produce working planar microcoils, microstrips, and novel microsensor designs, with some tested on the NMR in less than 24 h after the start of the design process. Sample wells could be built into the microsensor and could be machined at the same time as the sensors themselves, in some cases leaving a sheet of Teflon as thin as 10 µm between the sample and the sensor. This provides the freedom to produce a wide array of designs and demonstrates 5-axis CNC micromilling as a versatile tool for the rapid prototyping of NMR microsensors. This approach allowed the experimental optimization of a prototype microstrip for the analysis of two intact adult Daphnia magna organisms. In addition, a 3D volume slotted-tube resonator was produced that allowed for 2D 1H-13C NMR of D. magna neonates and exhibited 1H sensitivity (nLODω600 = 1.49 nmol s1/2) close to that of double strip lines, which themselves offer the best compromise between concentration and mass sensitivity published to date.

Rapid Characterization of a Mechanically Labile α-Helical Protein Enabled by Efficient Site-Specific Bioconjugation.

Atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) is a powerful yet accessible means to characterize mechanical properties of biomolecules. Historically, accessibility relies upon the nonspecific adhesion of biomolecules to a surface and a cantilever and, for proteins, the integration of the target protein into a polyprotein. However, this assay results in a low yield of high-quality data, defined as the complete unfolding of the polyprotein. Additionally, nonspecific surface adhesion hinders studies of α-helical proteins, which unfold at low forces and low extensions. Here, we overcame these limitations by merging two developments: (i) a polyprotein with versatile, genetically encoded short peptide tags functionalized via a mechanically robust Hydrazino-Pictet-Spengler ligation and (ii) the efficient site-specific conjugation of biomolecules to PEG-coated surfaces. Heterobifunctional anchoring of this polyprotein construct and DNA via copper-free click chemistry to PEG-coated substrates and a strong but reversible streptavidin-biotin linkage to PEG-coated AFM tips enhanced data quality and throughput. For example, we achieved a 75-fold increase in the yield of high-quality data and repeatedly probed the same individual polyprotein to deduce its dynamic force spectrum in just 2 h. The broader utility of this polyprotein was demonstrated by measuring three diverse target proteins: an α-helical protein (calmodulin), a protein with internal cysteines (rubredoxin), and a computationally designed three-helix bundle (α3D). Indeed, at low loading rates, α3D represents the most mechanically labile protein yet characterized by AFM. Such efficient SMFS studies on a commercial AFM enable the rapid characterization of macromolecular folding over a broader range of proteins and a wider array of experimental conditions (pH, temperature, denaturants). Further, by integrating these enhancements with optical traps, we demonstrate how efficient bioconjugation to otherwise nonstick surfaces can benefit diverse single-molecule studies.

Identification of a supramolecular functional architecture of Streptococcus mutans adhesin P1 on the bacterial cell surface.

P1 (antigen I/II) is a sucrose-independent adhesin of Streptococcus mutans whose functional architecture on the cell surface is not fully understood. S. mutans cells subjected to mechanical extraction were significantly diminished in adherence to immobilized salivary agglutinin but remained immunoreactive and were readily aggregated by fluid-phase salivary agglutinin. Bacterial adherence was restored by incubation of postextracted cells with P1 fragments that contain each of the two known adhesive domains. In contrast to untreated cells, glutaraldehyde-treated bacteria gained reactivity with anti-C-terminal monoclonal antibodies (mAbs), whereas epitopes recognized by mAbs against other portions of the molecule were masked. Surface plasmon resonance experiments demonstrated the ability of apical and C-terminal fragments of P1 to interact. Binding of several different anti-P1 mAbs to unfixed cells triggered release of a C-terminal fragment from the bacterial surface, suggesting a novel mechanism of action of certain adherence-inhibiting antibodies. We also used atomic force microscopy-based single molecule force spectroscopy with tips bearing various mAbs to elucidate the spatial organization and orientation of P1 on living bacteria. The similar rupture lengths detected using mAbs against the head and C-terminal regions, which are widely separated in the tertiary structure, suggest a higher order architecture in which these domains are in close proximity on the cell surface. Taken together, our results suggest a supramolecular organization in which additional P1 polypeptides, including the C-terminal segment originally identified as antigen II, associate with covalently attached P1 to form the functional adhesive layer.

Atomic force microscopy with sub-picoNewton force stability for biological applications.

Atomic force microscopy (AFM) is widely used in the biological sciences. Despite 25 years of technical developments, two popular modes of bioAFM, imaging and single molecule force spectroscopy, remain hindered by relatively poor force precision and stability. Recently, we achieved both sub-pN force precision and stability under biologically useful conditions (in liquid at room temperature). Importantly, this sub-pN level of performance is routinely accessible using a commercial cantilever on a commercial instrument. The two critical results are that (i) force precision and stability were limited by the gold coating on the cantilevers, and (ii) smaller yet stiffer cantilevers did not lead to better force precision on time scales longer than 25 ms. These new findings complement our previous work that addressed tip-sample stability. In this review, we detail the methods needed to achieve this sub-pN force stability and demonstrate improvements in force spectroscopy and imaging when using uncoated cantilevers. With this improved cantilever performance, the widespread use of nonspecific biomolecular attachments becomes a limiting factor in high-precision studies. Thus, we conclude by briefly reviewing site-specific covalent-immobilization protocols for linking a biomolecule to the substrate and to the AFM tip.

Routine and timely sub-picoNewton force stability and precision for biological applications of atomic force microscopy.

Force drift is a significant, yet unresolved, problem in atomic force microscopy (AFM). We show that the primary source of force drift for a popular class of cantilevers is their gold coating, even though they are coated on both sides to minimize drift. Drift of the zero-force position of the cantilever was reduced from 900 nm for gold-coated cantilevers to 70 nm (N = 10; rms) for uncoated cantilevers over the first 2 h after wetting the tip; a majority of these uncoated cantilevers (60%) showed significantly less drift (12 nm, rms). Removing the gold also led to ∼10-fold reduction in reflected light, yet short-term (0.1-10 s) force precision improved. Moreover, improved force precision did not require extended settling; most of the cantilevers tested (9 out of 15) achieved sub-pN force precision (0.54 ± 0.02 pN) over a broad bandwidth (0.01-10 Hz) just 30 min after loading. Finally, this precision was maintained while stretching DNA. Hence, removing gold enables both routine and timely access to sub-pN force precision in liquid over extended periods (100 s). We expect that many current and future applications of AFM can immediately benefit from these improvements in force stability and precision.

Electrochemical simultaneous determination of hydroquinone, catechol, bisphenol A, and bisphenol S using a novel mesoporous nickel-modified carbon sensor.

The widespread occurrence of endocrine disruptor compounds in wastewater has garnered significant attention owing to their toxicity, even at low concentrations, and their persistence in the water body. Among various analytical techniques, electrochemical sensors become popular for the environmental monitoring of water pollutants due to their low cost, rapid detection, high sensitivity, and selectivity. In this study, the mesoporous Ni (MNi) material was synthesized with an innovative method using Pluronic™ F-127 as a soft template and applied as a modifier for the simultaneous electrochemical sensing of hydroquinone (HQ), catechol (CC), bisphenol A (BPA), and bisphenol S (BPS). MNi with high porosity efficiently enhanced the redox-active surface area and conductivity of the glassy carbon electrode contributing to a significantly improved sensitivity in the detection of target chemicals. The pore size and surface area of MNi were estimated based on atomic force microscopy and Brunauer Emmett and Teller techniques to be ∼14.2 nm and 31.1 m2 g-1, respectively. The limit of detection for HQ, CC, BPA, and BPS was determined to be 5.3, 5.7, 5.6, and 61.5 nM, respectively. The electrochemical sensor presented in this study holds promise as a platform for developing portable and miniaturized tools offering the rapid and sensitive detection of these hazardous phenolic compounds in environmental water samples.

Different drug loading methods and antibiotic structure modulate the efficacy of polydopamine nanoparticles as drug nanocarriers.

The inefficient delivery of antimicrobials to their target is a significant factor contributing to antibiotic resistance. As such, smart nanomaterials that respond to external stimuli are extensively explored for precise drug delivery. Here, we investigate how drug loading methods and the structure of antibiotics impact the effectiveness of photothermally active polydopamine nanoparticles (PDNPs) as a laser-responsive drug delivery system. We examine two loading methods: in-synthesis and post-synthesis, and evaluate how laser irradiation affects drug release. Density functional theory calculations are also performed to gain deeper insights into the drug-PDNP interactions. Our findings point to the critical role of antibiotic structure and drug loading method in the laser-responsive capabilities of PDNPs as drug nanocarriers. Our study offers valuable insights for optimizing the design and efficiency of PDNP-based drug delivery systems.

Laser-responsive sequential delivery of multiple antimicrobials using nanocomposite hydrogels.

Precise control of antimicrobial delivery can prevent the adverse effects of antibiotics. By exploiting the photothermal activity of polydopamine nanoparticles along with the distinct transition temperatures of liposomes, a near-infrared (NIR) laser can be used to control the sequential delivery of an antibiotic and its adjuvant from a nanocomposite hydrogel-preventing bacterial growth.

Atomic force microscopy force mapping in the study of supported lipid bilayers.

Investigating the structural and mechanical properties of lipid bilayer membrane systems is vital in elucidating their biological function. One route to directly correlate the morphology of phase-segregated membranes with their indentation and rupture mechanics is the collection of atomic force microscopy (AFM) force maps. These force maps, while containing rich mechanical information, require lengthy processing time due to the large number of force curves needed to attain a high spatial resolution. A force curve analysis toolset was created to perform data extraction, calculation and reporting specifically in studying lipid membrane morphology and mechanical stability. The procedure was automated to allow for high-throughput processing of force maps with greatly reduced processing time. The resulting program was successfully used in systematically analyzing a number of supported lipid membrane systems in the investigation of their structure and nanomechanics.

Peptide-Polydopamine Nanocomposite Hydrogel for a Laser-Controlled Hydrophobic Drug Delivery.

Smart antibacterial systems, delivering antimicrobials in a highly controlled manner, are one strategy toward fighting the rise of antibiotic-resistant pathogens. Here, we engineer a laser-responsive antimicrobial nanocomposite hydrogel combining a peptide amphiphile and a photothermally active polydopamine nanoparticle (PDNP) to entrap the hydrophobic rifampicin within the hydrophilic hydrogel matrix. We show that the ability of the gelator to interact and retain rifampicin within the gel induced structural changes in its nanofiber network and mechanical properties. Furthermore, PDNP inclusion enabled laser-induced drug release, preventing growth of a Gram-negative E. coli. Overall, our work provides a significant advance in designing smart materials for controlled drug delivery applications.

Size-controlled synthesis of bioinspired polyserotonin nanoparticles with free radical scavenging activity.

Polyserotonin-based nanoparticles are a new class of bioinspired nanomaterial with recently demonstrated therapeutic potential for future clinical applications. It is therefore important to establish a robust and rapid method of synthesizing polyserotonin nanoparticles (PSeNP) in the size range ideal for in vivo utilization. Since the formation of PSeNP is base-catalyzed, here we report the influence of solution pH, in the presence of different base systems, on the kinetics of PSeNP formation and physico-chemical properties of the resulting nanoparticles. We show that the rate of formation and the size of PSeNP depend on both the nature of the base and the initial pH of the reaction. We have also improved the kinetics of particle formation by performing the synthesis at an elevated temperature (60 °C), leading to a dramatic reduction in synthesis time from days to hours. This presents a significant advance in the efficiency of PSeNP synthesis and provides a facile approach in tuning the size of nanoparticles to suit various applications. Furthermore, we show that similar to serotonin, PSeNP also exhibits free radical scavenging property. Our results demonstrate that PSeNP has the potential to become a key player in the advancement of nanotechnology-mediated antioxidative therapy.

Polyacrylamide hydrogels doped with different shapes of silver nanoparticles: Antibacterial and mechanical properties.

The incorporation of nanoparticles into a hydrogel matrix enables the development of innovative smart materials with enhanced biophysical properties. In this proof-of-concept study, we encapsulated different shapes (spherical, triangular and rod) of silver nanoparticles (AgNPs) within a hydrogel matrix of polyacrylamide (PAA) and N-methylenebisacrylamide (MBA) (PAA-MBA) to investigate whether these hydrogels exhibited shape-dependent antimicrobial and mechanical properties. We examined the mechanism of adsorption of different shapes of AgNPs using time-of-flight secondary ion mass spectrometry (ToF-SIMS). Results showed that the adsorption of AgNPs was primarily occurring on the surface/outer pores of the PAA-MBA hydrogel and that rod AgNPs demonstrated a relatively slower adsorption within the hydrogel matrix. The mechanical properties of AgNP-doped hydrogels were evaluated using rheology and atomic force microscopy (AFM) quantitative imaging. We observed a higher storage and Young's modulus which proved that the incorporation of the various shapes of AgNPs increased the mechanical properties of the hydrogels with no significant differences between the different shapes. While both spherical and triangular AgNP-doped hydrogels showed strong antimicrobial activity, the hydrogel with the rod AgNPs had a relatively lower antimicrobial activity. Overall, our preliminary results demonstrated that nanocomposite hydrogels were promising materials for applications in the future development of wound dressings.

Cholesterol-dependent nanomechanical stability of phase-segregated multicomponent lipid bilayers.

Cholesterol is involved in endocytosis, exocytosis, and the assembly of sphingolipid/cholesterol-enriched domains, as has been demonstrated in both model membranes and living cells. In this work, we explored the influence of different cholesterol levels (5-40 mol%) on the morphology and nanomechanical stability of phase-segregated lipid bilayers consisting of dioleoylphosphatidylcholine/sphingomyelin/cholesterol (DOPC/SM/Chol) by means of atomic force microscopy (AFM) imaging and force mapping. Breakthrough forces were consistently higher in the SM/Chol-enriched liquid-ordered domains (Lo) than in the DOPC-enriched fluid-disordered phase (Ld) at a series of loading rates. We also report the activation energies (DeltaEa) for the formation of an AFM-tip-induced fracture, calculated by a model for the rupture of molecular thin films. The obtained DeltaEa values agree remarkably well with reported values for fusion-related processes using other techniques. Furthermore, we observed that within the Chol range studied, the lateral organization of bilayers can be categorized into three distinct groups. The results are rationalized by fracture nanomechanics of a ternary phospholipid/sphingolipid/cholesterol mixture using correlated AFM-based imaging and force mapping, which demonstrates the influence of a wide range of cholesterol content on the morphology and nanomechanical stability of model bilayers. This provides fundamental insights into the role of cholesterol in the formation and stability of sphingolipid/cholesterol-enriched domains, as well as in membrane fusion.

Insights into the composition, morphology, and formation of the calcareous shell of the serpulid Hydroides dianthus.

To date, the calcareous tubes of serpulid marine worms have not been studied extensively in a biomineralization context. The structure and composition of the tube shell and adhesive cement of the marine tubeworm Hydroides dianthus were studied using a variety of characterization techniques, including powder XRD, FTIR, SEM, EDX, and AFM. The tube and cement were determined to be inorganic-organic composite materials, consisting of inorganic aragonite (CaCO(3)) and Mg-calcite ((Ca(0.8)Mg(0.2))CO(3)) crystals, and both soluble and insoluble organic matrices (SOM and IOM). SEM imaging revealed a variety of crystal morphologies. AFM nanoindentation of the inorganic components yielded Young's moduli of approximately 20GPa in the wet state, and approximately 50GPa in the dry state. Amino acid analysis of the SOM indicated substantial amounts of acidic and non-polar neutral amino acids. Part of the insoluble organic tube lining was identified as being composed of collagen-containing fibres aligned in a criss-crossed structure. The SOM and organic tube lining were found to contain carboxylated and sulphated polysaccharides. In an artificial seawater solution, the SOM and the organic tube lining mediated CaCO(3) mineralization in vitro.

Interfacial nanomechanical heterogeneity of the E. coli biofilm matrix.

The interface between bacterial biofilms and their environment plays a vital role in the recalcitrance of biofilms to biological, chemical, and mechanical threats. Nonetheless, we know little about the physical parameters that dictate the interfacial morphology and nanomechanics of biofilms. Here, we present a robust, reproducible, and quantitative platform based on atomic force microscopy (AFM) that allows for correlated high-resolution imaging of the morphology and nanomechanical properties of an intact E. coli biofilm-under physiological conditions. We developed analysis algorithms based on linearized Hertzian contact mechanics to discriminate, at the nanoscale, the elasticity of the extracellular polymeric substances (EPS) from bacteria within the biofilm. We were able to identify two distinct EPS populations with approximately 10-fold difference in their elastic properties. A correlation between EPS' elasticity and morphology points to different functions of the EPS populations within a mature E. coli biofilm. Thus, beyond high-resolution nanomechanical maps of a complex biological sample, we provide direct evidence of nanoscale heterogeneities at the biofilm interface. As interactions between biofilms and various antimicrobial agents occur at the nanoscale, understanding the physico-mechanical properties at the interface-with nanometer resolution-is imperative in devising targeted strategies against bacterial biofilms. We anticipate that in conjunction with other existing approaches, our quantitative imaging platform will provide mechanistic insights into the action and effectiveness of antimicrobials and antibiofilm agents.

Multi-component peptide hydrogels - a systematic study incorporating biomolecules for the exploration of diverse, tuneable biomaterials.

Peptide-based supramolecular gels can be designed to be functional "smart" materials that have applications in drug delivery, tissue engineering, and supramolecular chemistry. Although many multi-component gel systems have been designed and reported, many of these applications still rely solely on single-component gel systems which limits the functionalities of the materials. Multi-component self-assembly leads to the formation of highly ordered and complex architectures while offering the possibility to generate hydrogels with interesting properties including functional complexity and diverse morphologies. Being able to incorporate various classes of biomolecules can allow for tailoring the materials' functionalities to specific application needs. Here, a novel peptide amphiphile, myristyl-Phe-Phe (C14-FF), was synthesized and explored for hydrogel formation. The hydrogel possesses a nanofiber matrix morphology, composed of ß-sheet aggregates, a record-low gelation concentration for this class of compounds, and a unique solvent-dependent helical switch. The C14-FF hydrogel was then explored with various classes of biomolecules (carbohydrates, vitamins, proteins, building blocks of HA) to generate a multi-component library of gels that have potential to represent the complex natural extracellular matrix. Selected multi-component gels exhibit an excellent compatibility with mesenchymal stem cells showing high cell viability percentages, which holds great promise for applications in regenerative therapy.

Quantification of the nanomechanical stability of ceramide-enriched domains.

The quantification of the mechanical stability of lipid bilayers is important in establishing composition-structure-property relations and sheds light on our understanding of the functions of biological membranes. Here, we designed an experiment to directly probe and quantify the nanomechanical stability and rigidity of the ceramide-enriched platforms that play a distinctive role in a variety of cellular processes. Our force mapping results have demonstrated that the ceramide-enriched domains require both methyl beta-cyclodextrin (MbCD) and chloroform treatments to weaken their highly ordered organization, suggesting a lipid packing that is different from that in typical gel states. Our results also show the expulsion of cholesterol from the sphingolipid/cholesterol-enriched domains as a result of ceramide incorporation. This work provides quantitative information on the nanomechanical stability and rigidity of coexisting phase-segregated lipid bilayers with the presence of ceramide-enriched platforms, indicating that that generation of ceramide in cells drastically alters the structural organization and the mechanical property of biological membranes.

Nanoscale structures and mechanics of barnacle cement.

Polymerized barnacle glue was studied by atomic force microscopy (AFM), scanning electron microscopy (SEM), Fourier transform infrared (FTIR) spectroscopy and chemical staining. Nanoscale structures exhibiting rod-shaped, globular and irregularly-shaped morphologies were observed in the bulk cement of the barnacle Amphibalanus amphitrite (=Balanus amphitrite) by AFM. SEM coupled with energy dispersive X-ray (EDX) provided chemical composition information, making evident the organic nature of the rod-shaped nanoscale structures. FTIR spectroscopy gave signatures of beta-sheet and random coil conformations. The mechanical properties of these nanoscale structures were also probed using force spectroscopy and indentation with AFM. Indentation data yielded higher elastic moduli for the rod-shaped structures when compared with the other structures in the bulk cement. Single molecule AFM force-extension curves on the matrix of the bulk cement often exhibited a periodic sawtooth-like profile, observed in both the extend and retract portions of the force curve. Rod-shaped structures stained with amyloid protein-selective dyes (Congo red and thioflavin-T) revealed that about 5% of the bulk cement were amyloids. A dominant 100 kDa cement protein was found to be mechanically agile, using repeating hydrophobic structures that apparently associate within the same protein or with neighbors, creating toughness on the 1-100 nm length scale.

Molecular mechanics of coiled coils loaded in the shear geometry.

Coiled coils are important nanomechanical building blocks in biological and biomimetic materials. A mechanistic molecular understanding of their structural response to mechanical load is essential for elucidating their role in tissues and for utilizing and tuning these building blocks in materials applications. Using a combination of single-molecule force spectroscopy (SMFS) and steered molecular dynamics (SMD) simulations, we have investigated the mechanics of synthetic heterodimeric coiled coils of different length (3-4 heptads) when loaded in shear geometry. Upon shearing, we observe an initial rise in the force, which is followed by a constant force plateau and ultimately strand separation. The force required for strand separation depends on the coiled coil length and the applied loading rate, suggesting that coiled coil shearing occurs out of equilibrium. This out-of-equilibrium behaviour is determined by a complex structural response which involves helix uncoiling, uncoiling-assisted sliding of the helices relative to each other in the direction of the applied force as well as uncoiling-assisted dissociation perpendicular to the force axis. These processes follow a hierarchy of timescales with helix uncoiling being faster than sliding and sliding being faster than dissociation. In SMFS experiments, strand separation is dominated by uncoiling-assisted dissociation and occurs at forces between 25-45 pN for the shortest 3-heptad coiled coil and between 35-50 pN for the longest 4-heptad coiled coil. These values are highly similar to the forces required for shearing apart short double-stranded DNA oligonucleotides, reinforcing the potential role of coiled coils as nanomechanical building blocks in applications where protein-based structures are desired.