Dual Optical Response Strategy for the Detection of Cytochrome c Using Highly Luminescent Lanthanide-Based Nanotubular Sensor Arrays

Here, we demonstrate a label-free dual optical response strategy for the detection of cytochrome c (Cyt c) with ultrahigh sensitivity using highly luminescent lanthanides containing inorganic-organic hybrid nanotubular sensor arrays. These sensor arrays are formed by the sequential incorporation of the photosensitizers 2,3-dihydroxynaphthalene (DHN) or 1,10-phenanthroline (Phen), and trivalent lanthanide terbium ions (Tb3+) into sodium lithocholate (NaLC) nanotube templates. Our sensing platform relies on the detection and quantification of Cyt c in solution by providing dual photoluminescence quenching responses from the nanotubular hybrid arrays in the presence of Cyt c. The large quenching of the sensitized Tb3+ emission within the DHN/Phen-Tb3+-NaLC nanotubular sensor arrays caused by the strong binding of the photosensitizers to Cyt c provides an important signal response for the selective detection of Cyt c. This long-lived lanthanide emission response-based sensing strategy can be highly advantageous for the detection of Cyt c in a cellular environment eliminating background fluorescence and scattering signals through time-gated measurements. The DHN containing nanotubular sensor arrays (DHN-NaLC and DHN-Tb3+-NaLC) provide an additional quenching response characterized by a unique spectral valley splitting with quantized quenching dip on the DHN fluorescence emission. This spectral quenching dip resulting from efficient FRET between the protein bound DHN photosensitizer and the heme group of Cyt c serves as an important means for specific detection and quantification of Cyt c in the concentration range of 0-30 μM with a low detection limit of around 20 nM.

Potential utility of bacterial protein nanoreactor for sustainable in-situ biocatalysis in wide range of bioprocess conditions

Bacterial microcompartments (MCPs) are proteinaceous organelles that natively encapsulates the enzymes, substrates, and cofactors within a protein shell. They optimize the reaction rates by enriching the substrate in the vicinity of enzymes to increase the yields of the product and mitigate the outward diffusion of the toxic or volatile intermediates. The shell protein subunits of MCP shell are selectively permeable and have specialized pores for the selective inward diffusion of substrates and products release. Given their attributes, MCPs have been recently explored as potential candidates as subcellular nano-bioreactor for the enhanced production of industrially important molecules by exercising pathway encapsulation. In the current study, MCPs have been shown to sustain enzyme activity for extended periods, emphasizing their durability against a range of physical challenges such as temperature, pH and organic solvents. The significance of an intact shell in conferring maximum protection is highlighted by analyzing the differences in enzyme activities inside the intact and broken shell. Moreover, a minimal synthetic shell was designed with recruitment of a heterologous enzyme cargo to demonstrate the improved durability of the enzyme. The encapsulated enzyme was shown to be more stable than its free counterpart under the aforementioned conditions. Bacterial MCP-mediated encapsulation can serve as a potential strategy to shield the enzymes used under extreme conditions by maintaining the internal microenvironment and enhancing their cycle life, thereby opening new means for stabilizing, and reutilizing the enzymes in several bioprocess industries.

Stimuli-Responsive Transformable Supramolecular Nanotubes

Supramolecular nanotubes produced by self-assembly of organic molecules can have unique structural features such as a one-dimensional morphology with no branching, distinguishable inner and outer surfaces and membrane walls, or a structure that is hollow and has a high aspect ratio. Incorporation of functional groups that respond to external chemical or physical stimuli into the constituent organic molecules of supramolecular nanotubes allows us to drastically change the structure of the nanotubes by applying such stimuli. This ability affords an array of controllable approaches for the encapsulation, storage, and release of guest compounds, which is expected to be useful in the fields of physics, chemistry, biology, and medicine. In this article, I review the supramolecular nanotubes developed by our group that exhibit morphological transformations in response to pH, chemical reaction, light, temperature, or moisture.

Influences of Hydrogen Bonding-Based Stabilization of Bolaamphiphile Layers on Molecular Diffusion within Organic Nanotubes Having Inner Carboxyl Groups

This paper reports molecular diffusion behavior in two bolaamphiphile-based organic nanotubes having inner carboxyl groups with different inner dimeters (10 and 20 nm) and wall structures, COOH-ONT_10nm and COOH-ONT_20nm, using imaging fluorescence correlation spectroscopy (imaging FCS). The results were compared to those previously obtained in a similar nanotube with inner amine groups (NH₂-ONT_10nm). COOH-ONT_10nm, as with NH₂-ONT_10nm, were formed from a rolled bolaamphiphile layer incorporating triglycine moieties, whereas COOH-ONT_20nm consisted of four stacks of triglycine-free bolaamphiphile layers. Imaging FCS measurements were carried out for anionic sulforhodamine B (SRB), zwitterionic/cationic rhodamine B (RB), and cationic rhodamine-123 (R123) diffusing within ONTs (1-9 μm long) at different pH (3.4-8.4) and ionic strengths (1.6-500 mM). Diffusion coefficients (D) of these dyes in the ONTs were very small (0.01-0.1 μm²/s), reflecting the significant contributions of molecule-nanotube interactions to diffusion. The D of SRB was larger at higher pH and ionic strength, indicating the essential role of electrostatic repulsion that was enhanced by the deprotonation of the inner carboxyl groups. Importantly, the D of SRB was virtually independent of nanotube inner diameter and wall structure, indicating the diffusion of the hydrophilic molecule was controlled by short time scale adsorption/desorption processes onto the inner surface. In contrast, pH effects on D were less clear for relatively hydrophobic R123 and RB, suggesting the significant contributions of non-Coulombic interactions. Interestingly, the diffusion of these molecules in COOH-ONT_20nm was slower than in COOH-ONT_10nm. Slower diffusion in COOH-ONT_20nm was attributable to relatively efficient partitioning of the hydrophobic dyes into the bolaamphiphile layers, which was reduced in COOH-ONT_10nm due to the stabilization of its layer by polyglycine-II-type hydrogen bonding networks. These results show that, by tuning the bolaamphiphile structures and their intermolecular interactions, unique environments can be created within the nanospaces for enhanced molecular separations and reactions.

Removal of Diclofenac, Paracetamol, and Carbamazepine from Model Aqueous Solutions by Magnetic Sol-Gel Encapsulated Horseradish Peroxidase and Lignin Peroxidase Composites

Sustainable and green synthesis of nanocomposites for degradation of pharmaceuticals was developed via immobilization and stabilization of the biological strong oxidizing agents, peroxidase enzymes, on a solid support. Sol–gel encapsulated enzyme composites were characterized using electron microscopy (TEM, SEM), atomic force microscopy, FTIR spectroscopy, and thermogravimetric analysis. Horseradish peroxidase (HRP) and lignin peroxidase (LiP) were adsorbed onto magnetite nanoparticles and sol–gel encapsulated in a surface silica layer. Encapsulation enhanced the stability of the biocatalysts over time and thermal stability. The biocatalysts showed appreciable selectivity in oxidation of the organic drinking water pollutants diclofenac, carbamazepine, and paracetamol with improved activity being pharmaceutical specific for each enzyme. In particular, sol–gel encapsulated LiP- and HRP-based nanocomposites were active over 20 consecutive cycles for 20 days at 55 °C (24 h/cycle). The stability of the sol–gel encapsulated catalysts in acidic medium was also improved compared to native enzymes. Carbamazepine and diclofenac were degraded to 68% and 64% by sol–gel LiP composites respectively at pH 5 under elevated temperature. Total destruction of carbamazepine and diclofenac was achieved at pH 3 (55 °C) within 3 days, in the case of both immobilized HRP and LiP. Using NMR spectroscopy, characterization of the drug decomposition products, and decomposition pathways by the peroxidase enzymes suggested.

Soft-Matter Nanotubes: A Platform for Diverse Functions and Applications

Self-assembled organic nanotubes made of single or multiple molecular components can be classified into soft-matter nanotubes (SMNTs) by contrast with hard-matter nanotubes, such as carbon and other inorganic nanotubes. To date, diverse self-assembly processes and elaborate template procedures using rationally designed organic molecules have produced suitable tubular architectures with definite dimensions, structural complexity, and hierarchy for expected functions and applications. Herein, we comprehensively discuss every functions and possible applications of a wide range of SMNTs as bulk materials or single components. This Review highlights valuable contributions mainly in the past decade. Fifteen different families of SMNTs are discussed from the viewpoints of chemical, physical, biological, and medical applications, as well as action fields (e.g., interior, wall, exterior, whole structure, and ensemble of nanotubes). Chemical applications of the SMNTs are associated with encapsulating materials and sensors. SMNTs also behave, while sometimes undergoing morphological transformation, as a catalyst, template, liquid crystal, hydro-/organogel, superhydrophobic surface, and micron size engine. Physical functions pertain to ferro-/piezoelectricity and energy migration/storage, leading to the applications to electrodes or supercapacitors, and mechanical reinforcement. Biological functions involve artificial chaperone, transmembrane transport, nanochannels, and channel reactors. Finally, medical functions range over drug delivery, nonviral gene transfer vector, and virus trap.

Immobilization of Allantoinase for the Development of an Optical Biosensor of Oxidative Stress States

Allantoin, the natural end product of purine catabolism in mammals, is non-enzymatically produced from the scavenging of reactive oxygen species through the degradation of uric acid. Levels of allantoin in biological fluids are sensitively influenced by the presence of free radicals, making this molecule a candidate marker of acute oxidative stress in clinical analyses. With this aim, we exploited allantoinase—the enzyme responsible for allantoin hydrolization in plants and lower organisms—for the development of a biosensor exploiting a fast enzymatic-chemical assay for allantoin quantification. Recombinant allantoinase was entrapped in a wet nanoporous silica gel matrix and its structural properties, function, and stability were characterized through fluorescence spectroscopy and circular dichroism measurements, and compared to the soluble enzyme. Physical immobilization in silica gel minimally influences the structure and the catalytic efficiency of entrapped allantoinase, which can be reused several times and stored for several months with good activity retention. These results, together with the relative ease of the sol-gel preparation and handling, make the encapsulated allantoinase a good candidate for the development of an allantoin biosensor.

Surface modification of cerasomes with AuNPs@poly(ionic liquid)s for an enhanced stereo biomimetic membrane electrochemical platform

A novel liposomal nanocomposite, Au@PIL-cerasome, with biocompatibility and conductivity was fabricated via the self-assembly of cerasomes and gold nanoparticles (AuNPs) stabilized by poly(ionic liquid)s (PILs). The surface charge, morphology and chemical composition of the nanocomposites were characterized by the zeta potential, UV-vis, TEM, SEM and EDS. The nanocomposites exhibited structural stability directly on the surface of solid electrodes, without fusion. Electrochemical impedance experiments demonstrated that the nanocomposites had an enhanced conductivity compared with unmodified cerasomes. Horseradish peroxidase (HRP), as a reporter, was immobilized on the nanocomposites without denaturation or inactivation. The direct electron transfer of HRP was achieved, and the HRP/Au@PIL-cerasome/GCE exhibited an amplified current and improved electrocatalytic activity. Activity towards H₂O₂ displayed a linear range over 10-70 μM and a detection limit of 3.3 μM. Activity towards NO₂^- displayed linear ranges over 1-5 mM and 5-1280 mM, and the limit of detection was 0.11 mM. In addition, the electrode was stable and reproducible, with 6% RSD. Such multi-component liposomal nanocomposites with an enhanced electrical performance pave a better way for building novel and straightforward 3D stereo biomimetic electrochemical platforms and even molecular communication systems to investigate information transduction between cells.

An electrochemical enzymatic nanoreactor based on dendritic mesoporous silica nanoparticles for living cell H2O2 detection

The selective and quantitative detection of cellular H2O2 is essential for understanding its roles in physiology and pathology. A new electrochemical H2O2 biosensor, fabricated by immobilizing horseradish peroxidase onto dendritic mesoporous silica nanoparticles (HRP/DMSNs), is employed for living cell H2O2 detection. Taking advantage of the large pore volume and highly accessible internal surface areas of DMSNs, HRP/DMSNs display higher enzymatic loading, better stability and bioactivity in comparison with HRP on nonporous silica nanoparticles (NSNs). Therefore, a HRP/DMSN modified GCE (HRP/DMSNs/GCE) shows attractive electrochemical performance for sensitive and selective detection of H2O2 in 0.1 M pH 7.0 PBS, with a low Kappm value of 11.48 μM and a low detection limit of 0.11 μM. In addition, HRP/DMSNs/GCE is successfully applied to detect H2O2 released from a PC12 cell triggered by ascorbic acid (AA). The detected H2O2 amount is close to the reported values. The developed biosensor has potential in the dynamic detection of the flux of H2O2 from living cells for further evaluation of oxidative stress in cells.

Supramolecular Nanotube Reactors for Production of Imine Polymers with Controlled Conformation, Size, and Chirality

A series of supramolecular nanotubes with inner diameters of 1, 4, 9, 12, 16, and 29 nm are prepared from amino acid lipids. The hydrophobic channels of the nanotubes act as reactors for the formation of imine polymers by not only effectively encapsulating the benzaldehyde and diacetyleneamine precursors of the imine monomers but also markedly accelerating imine formation. The nanotube inner diameter determines whether the imine monomers self-assemble into nanoparticles, nanotapes, nanocoils, or twisted nanofibers in the channels. UV-induced polymerization of the diacetylene units in the imine nanostructures followed by decomposition of the nanotubes into molecular dispersions of the constituent amino acid lipids results in expulsion of the polymerized imine nanostructures with retained conformation. The isolated nanocoils and twisted nanofibers retain the helicity and circular dichroism induced by the nanotubes, which exhibits supramolecular chirality, even though the components of the imine monomers are achiral. These supramolecular nanotubes with tunable diameters and functionalizable surfaces can be expected to be useful for the production of polymers with controlled conformation, size, and chirality without the need for rational design or chemical modification of the monomers or optimization of the polymerization conditions.

Shrinkable Nanotubes for Duplex Formation of Short Nucleotides

Molecular monolayer nanotubes produced by self-assembly of an amphiphile modified with a 2-nitrobenzyl group as a photoresponsive unit are able to encapsulate dinucleotides via electrostatic attraction. Upon photoirradiation, the 18 nm inner diameter of the nanotubes shrinks to less than 2 nm as a result of photochemical cleavage of the 2-nitrobenzyl group in the amphiphile. This shrinking of the nanotube channels leads to a propulsive release of the dinucleotides into the bulk solution and simultaneously accelerates formation of the dinucleotide duplexes. The larger nanotube channels without photoirradiation merely release each dinucleotide into the bulk solution, indicating that the squeezing via transportation in the narrow nanotube channels is necessary for duplex formation. In addition to the size effect, water with a lower polarity confined within the narrow nanotube channels helps to stabilize the energetically unfavorable hydrogen-bonded base pair between the dinucleotides. This system should enable researchers to perform biological reactions that occur only in specific environments and conditions in living organisms.

Soft Nanotubes Derivatized with Short PEG Chains for Thermally Controllable Extraction and Separation of Peptides

By means of a two-step self-assembly process involving three components, including short poly(ethylene glycol) (PEG) chains, we produced two different types of molecular monolayer nanotubes: nanotubes densely functionalized with PEG chains on the outer surface and nanotubes densely functionalized with PEG chains in the nanochannel. Turbidity measurements and fluorescence spectroscopy with an environmentally responsive probe suggested that the PEG chains underwent dehydration when the nanotubes were heated above 44-57 °C and rehydration when they were cooled back to 25 °C. Dehydration of the exterior or interior PEG chains rendered them hydrophobic and thus able to effectively extract hydrophobic amino acids from the bulk solution. Rehydration of the PEG chains restored their hydrophilicity, thus allowing the extracted amino acids to be squeezed out into the bulk solutions. The nanotubes with exterior PEG chains exhibited selectivity for all of the hydrophobic amino acids, whereas the interior PEG chains were selective for hydrophobic amino acids with an aliphatic side chain over hydrophobic amino acids with an aromatic side chain. The higher selectivity of the latter system is attributable that the extraction and back-extraction processes involve encapsulation and transportation of the amino acids in the nanotube channel. As the result, the latter system was useful for separation of peptides that differed by only a single amino acid, whereas the former system showed no such separation ability.

Synthetic CO2-fixation enzyme cascades immobilized on self-assembled nanostructures that enhance CO2/O2 selectivity of RubisCO

BACKGROUND

With increasing concerns over global warming and depletion of fossil-fuel reserves, it is attractive to develop innovative strategies to assimilate CO₂, a greenhouse gas, into usable organic carbon. Cell-free systems can be designed to operate as catalytic platforms with enzymes that offer exceptional selectivity and efficiency, without the need to support ancillary reactions of metabolic pathways operating in intact cells. Such systems are yet to be exploited for applications involving CO₂ utilization and subsequent conversion to valuable products, including biofuels. The Calvin-Benson-Bassham (CBB) cycle and the enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) play a pivotal role in global CO₂ fixation.

RESULTS

We hereby demonstrate the co-assembly of two RubisCO-associated multienzyme cascades with self-assembled synthetic amphiphilic peptide nanostructures. The immobilized enzyme cascades sequentially convert either ribose-5-phosphate (R-5-P) or glucose, a simpler substrate, to ribulose 1,5-bisphosphate (RuBP), the acceptor for incoming CO₂ in the carboxylation reaction catalyzed by RubisCO. Protection from proteolytic degradation was observed in nanostructures associated with the small dimeric form of RubisCO and ancillary enzymes. Furthermore, nanostructures associated with a larger variant of RubisCO resulted in a significant enhancement of the enzyme's selectivity towards CO₂, without adversely affecting the catalytic activity.

CONCLUSIONS

The ability to assemble a cascade of enzymes for CO₂ capture using self-assembling nanostructure scaffolds with functional enhancements show promise for potentially engineering entire pathways (with RubisCO or other CO₂-fixing enzymes) to redirect carbon from industrial effluents into useful bioproducts.