Liquid-liquid extraction of enzymatically synthesized functional RNA oligonucleotides using reverse micelles with a DNA-surfactant

We successfully implemented solvent extraction of short, single-stranded RNA using reverse micelles (water-in-oil microemulsions) with a DNA-surfactant. A thrombin-binding RNA aptamer was enzymatically synthesized and purified by extraction using the reverse micellar system. The extracted RNA aptamer retained thrombin-binding activity after the extraction procedure.

Increasing the stability of DNA nanostructure templates by atomic layer deposition of Al2O3 and its application in imprinting lithography

We present a method to increase the stability of DNA nanostructure templates through conformal coating with a nanometer-thin protective inorganic oxide layer created using atomic layer deposition (ALD). DNA nanotubes and origami triangles were coated with ca. 2 nm to ca. 20 nm of Al₂O₃. Nanoscale features of the DNA nanostructures were preserved after the ALD coating and the patterns are resistive to UV/O₃ oxidation. The ALD-coated DNA templates were used for a direct pattern transfer to poly(L-lactic acid) films.

Strategies and perspectives of assembling multi-enzyme systems

Multi-enzyme complexes have the potential to achieve high catalytic efficiency for sequence reactions due to their advantages in eliminating product inhibition, facilitating intermediate transfer and in situ regenerating cofactors. Constructing functional multi-enzyme systems to mimic natural multi-enzyme complexes is of great interest for multi-enzymatic biosynthesis and cell-free synthetic biotransformation, but with many challenges. Currently, various assembly strategies have been developed based on the interaction of biomacromolecules such as DNA, peptide and scaffolding protein. On the other hand, chemical-induced assembly is based on the affinity of enzymes with small molecules including inhibitors, cofactors and metal ions has the advantage of simplicity, site-to-site oriented structure control and economy. This review summarizes advances and progresses employing these strategies. Furthermore, challenges and perspectives in designing multi-enzyme systems are highlighted.

One-pot bioinspired synthesis of all-inclusive protein-protein nanoflowers for point-of-care bioassay: detection of E. coli O157:H7 from milk

Protein-protein conjugates play a vital role in bioassays with their inherent functions of biological recognition and signal amplification. Herein, a one-pot green method for synthesis of all-inclusive protein-protein nanoflowers has been developed. The protein-protein nanoflowers integrate both essential functions of biological recognition and signal amplification, and they were used as ideal signal labels for the sensitive point-of-care detection of Escherichia coli O157:H7. Especially noteworthy, the prepared Con A-invertase-CaHPO₄ hybrid nanoflowers simultaneously loaded sufficient invertase and enhanced the activity of the immobilized invertase, which fits well with the requirements of signal labels for bioassays. Due to the conversion of sucrose to glucose by invertase, Con A-invertase-CaHPO₄ hybrid nanoflowers were successfully used for the reliable point-of-care detection of food pathogens by a personal glucose meter. The presented approach successfully resolved the bottleneck in preparing protein-protein conjugate-based signal labels for bioassays using enzyme-based signal amplification strategies, which holds great promise to develop on-demand protein-protein conjugates for a variety of applications extending from biosensors and biomedicine to energy, environmental monitoring and remediation.

Direct protein-protein conjugation by genetically introducing bioorthogonal functional groups into proteins

Proteins often function as complex structures in conjunction with other proteins. Because these complex structures are essential for sophisticated functions, developing protein-protein conjugates has gained research interest. In this study, site-specific protein-protein conjugation was performed by genetically incorporating an azide-containing amino acid into one protein and a bicyclononyne (BCN)-containing amino acid into the other. Three to four sites in each of the proteins were tested for conjugation efficiency, and three combinations showed excellent conjugation efficiency. The genetic incorporation of unnatural amino acids (UAAs) is technically simple and produces the mutant protein in high yield. In addition, the conjugation reaction can be conducted by simple mixing, and does not require additional reagents or linker molecules. Therefore, this method may prove very useful for generating protein-protein conjugates and protein complexes of biochemical significance.

The use of a selective saturation pulse to suppress t1 noise in two-dimensional (1)H fast magic angle spinning solid-state NMR spectroscopy

A selective saturation pulse at fast magic angle spinning (MAS) frequencies (60+kHz) suppresses t1 noise in the indirect dimension of two-dimensional (1)H MAS NMR spectra. The method is applied to a synthetic nucleoside with an intense methyl (1)H signal due to triisopropylsilyl (TIPS) protecting groups. Enhanced performance in terms of suppressing the methyl signal while minimising the loss of signal intensity of nearby resonances of interest relies on reducing spin diffusion--this is quantified by comparing two-dimensional (1)H NOESY-like spin diffusion spectra recorded at 30-70 kHz MAS. For a saturation pulse centred at the methyl resonance, the effect of changing the nutation frequency at different MAS frequencies as well as the effect of changing the pulse duration is investigated. By applying a pulse of duration 30 ms and nutation frequency 725 Hz at 70 kHz MAS, a good compromise of significant suppression of the methyl resonance combined with the signal intensity of resonances greater than 5 ppm away from the methyl resonance being largely unaffected is achieved. The effectiveness of using a selective saturation pulse is demonstrated for both homonuclear (1)H-(1)H double quantum (DQ)/single quantum (SQ) MAS and (14)N-(1)H heteronuclear multiple quantum coherence (HMQC) two-dimensional solid-state NMR experiments.

Double enzymatic cascade reactions within FeSe-Pt@SiO2 nanospheres: synthesis and application toward colorimetric biosensing of H2O2 and glucose

A facile process was developed for the synthesis of FeSe-Pt@SiO2 nanospheres based on the hydrothermal treatment of FeCl3·6H2O, selenium and NaBH4 in ethanolamine solvent, followed by reducing HPtCl4 with NaBH4 in the presence of FeSe particles to obtain FeSe coated with Pt NPs (FeSe-Pt), ending with a surfactant assembled sol-gel process to obtain FeSe-Pt@SiO2. The morphology and composition of FeSe-Pt@SiO2 were characterized by transmission electron microscopy, high resolution TEM, X-ray diffraction and Fourier transform infrared spectroscopy. Structural analyses revealed that FeSe-Pt@SiO2 nanospheres were of regular spherical shape with smooth surfaces due to the SiO2 shells, compared with FeSe particles with 150 nm lateral diameter. The prepared FeSe-Pt@SiO2 nanospheres possessed both intrinsic glucose oxidase (GOx-) and peroxidase-mimic activities, and we engineered an artificial enzymatic cascade system with high activity and stability based on this nanostructure. The good catalytic performance of the composites could be attributed to the synergy between the functions of FeSe particles and Pt NPs. Significantly, the FeSe-Pt@SiO2 nanospheres as robust nanoreactors can catalyze a self-organized cascade reaction, which includes oxidation of glucose by oxygen to yield gluconic acid and H2O2, and then oxidation of 3,3,5,5-tetramethylbenzidine (TMB) by H2O2 to produce a colour change. Colorimetric detection of H2O2 and glucose using the FeSe-Pt@SiO2 nanospheres was conducted with high detection sensitivities, 0.227 nM and 1.136 nM, respectively, demonstrating the feasibility of practical sensing applications. It is therefore believed that our findings in this study could open up the possibility of utilizing FeSe-Pt@SiO2 nanospheres as enzymatic mimics in diagnostic and biotechnology fields.

Double clicking for site-specific coupling of multiple enzymes

Herein, we report a novel strategy to site-specifically couple multiple enzymes using two compatible click chemistries and site-specific incorporation of a clickable non-natural amino acid.

Cascade biocatalysis by multienzyme-nanoparticle assemblies

Multienzyme complexes are of paramount importance in biosynthesis in cells. Yet, how sequential enzymes of cascade catalytic reactions synergize their activities through spatial organization remains elusive. Recent development of site-specific protein-nanoparticle conjugation techniques enables us to construct multienzyme assemblies using nanoparticles as the template. Sequential enzymes in menaquinone biosynthetic pathway were conjugated to CdSe-ZnS quantum dots (QDs, a nanosized particulate material) through metal-affinity driven self-assembly. The assemblies were characterized by electrophoretic methods, the catalytic activities were monitored by reverse-phase chromatography, and the composition of the multienzyme-QD assemblies was optimized through a progressive approach to achieve highly efficient catalytic conversion. Shorter enzyme-enzyme distance was discovered to facilitate intermediate transfer, and a fine control on the stoichiometric ratio of the assembly was found to be critical for the maximal synergy between the enzymes. Multienzyme-QD assemblies thereby provide an effective model to scrutinize the synergy of cascade enzymes in multienzyme complexes.

Chemical approaches for the construction of multi-enzyme reaction systems

Inspired by nature, researchers aim at bringing together different types of enzymes by the generation of multi-enzymatic structures. Amongst others, chemical methods have been exploited enabling the covalent linkage of a set of enzymes to the same macromolecular scaffold or direct cross-linking. Control over the relative position of enzymes in the system has been realized by sequential immobilization in microchannels and by positional co-localization on DNA nanostructures. So far, site-specific conjugation reactions such as the azide-alkyne cycloaddition, N-terminal transamination and enzyme-mediated cross-linking, have been applied to a limited extent only. These methods are expected to allow for co-immobilization of less robust enzymes, hence, an expansion in the diversity of immobilized biocatalytic cascades. In addition, the combination of multiple bioconjugation methods will provide control over the composition in scaffold-free multi-enzyme complexes.

Oligonucleotide-Based Systems for Input-Controlled and Non-Covalently Regulated Protein-Binding

Supramolecular chemists continuously take inspiration from complex biological systems to develop functional molecules involved in molecular recognition and self-assembly. In this regard, "smart" synthetic molecules that emulate allosteric proteins are both exciting and challenging, since many allosteric proteins can be considered as molecular switches that bind to other protein targets in a non-covalent fashion, and importantly, are capable of having their output activity controlled by prior binding to input molecules. This review discusses the foundations and passage toward the development of non-covalently operated oligonucleotide-based systems with protein-binding capacity that can be precisely regulated in an input-controlled manner.

Protein supramolecular complex formation by site-specific avidin-biotin interactions

The precise accumulation of protein functions on a nanoscale to fabricate advanced biomaterials has become possible by a bottom-up approach based on molecular self-assembly. The avidin-biotin interaction is widely employed in the design of functional protein self-assemblies. Herein we assessed how the spatial arrangement of the avidin-biotin interaction between protein building blocks affects the formation of a protein supramolecular complex (PSC). The enzymatic site-specific internal labeling of a symmetric protein scaffold, bacterial alkaline phosphatase (AP), with specifically designed biotinylation substrates revealed that the precise positioning of the biotinylation sites on AP and the linker flexibility of the substrate are critical factors for the growth of PSCs in the presence of streptavidin (SA). A potential diagnostic application of the PSCs comprised of AP and SA was demonstrated in an enzyme-linked immunosorbent assay.