Photoactivatable Reaction for Covalent Nanoscale Patterning of Multiple Proteins

Conditional Control of Benzylguanine Reaction with the Self-Labeling SNAP-tag Protein

SNAP-tag, a mutant of the O6-alkylguanine-DNA-alkyltransferase, self-labels by reacting with benzylguanine (BG) substrates, thereby forming a thioether bond. SNAP-tag has been genetically fused to a wide range of proteins of interest in order to covalently modify them. In the context of both diagnostic and therapeutic applications, as well as use as a biological recording device, precise control in a spatial and temporal fashion over the covalent bond-forming reaction is desired to direct inputs, readouts, or therapeutic actions to specific locations, at specific time points, in cells and organisms. Here, we introduce a comprehensive suite of six caged BG molecules: one light-triggered and five others that can be activated through various chemical and biochemical stimuli, such as small molecules, transition metal catalysts, reactive oxygen species, and enzymes. These molecules are unable to react with SNAP-tag until the trigger is present, which leads to near complete SNAP-tag conjugation, as illustrated both in biochemical assays and on human cell surfaces. This approach holds promise for targeted therapeutic assembly at disease sites, offering the potential to reduce off-target effects and toxicity through precise trigger titration.

Construction of homologous branched oligomer megamolecules based on linker-directed protein assembly

Utilizing the building blocks of recombinant proteins and synthetic linkers, we have obtained two distinct octameric megamolecules with diverse branched structures. This approach combines principles from both click chemistry and protein engineering technology, enabling the integration of functional domains within highly ordered protein assemblies for biomedical applications.

Kaleidoscope megamolecules synthesis and application using self-assembly technology

The megamolecules with high ordered structures play an important role in chemical biology and biomedical engineering. Self-assembly, a long-discovered but very appealing technique, could induce many reactions between biomacromolecules and organic linking molecules, such as an enzyme domain and its covalent inhibitors. Enzyme and its small-molecule inhibitors have achieved many successes in medical application, which realize the catalysis process and theranostic function. By employing the protein engineering technology, the building blocks of enzyme fusion protein and small molecule linker can be assembled into a novel architecture with the specified organization and conformation. Molecular level recognition of enzyme domain could provide both covalent reaction sites and structural skeleton for the functional fusion protein. In this review, we will discuss the range of tools available to combine functional domains by using the recombinant protein technology, which can assemble them into precisely specified architectures/valences and develop the kaleidoscope megamolecules for catalytic and medical application.

Strategy based on multiplexed brush architectures for regulating the spatiotemporal immobilization of biomolecules

Functional surfaces that enable both spatial and temporal control of biomolecules immobilization have attracted enormous attention for various fields including smart biointerface materials, high-throughput bioarrays, and fundamental research in the biosciences. Here, a flexible and promising method was presented for regulating the spatiotemporal arrangement of multiple biomolecules by constructing the topographically and chemically diverse polymer brushes patterned surfaces. A series of polymer brushes patterned surfaces, including antifouling brushes patterned surface, epoxy-presenting brushes patterned surface without and with antifouling background layer, were fabricated to control the spatial distribution of protein and cell adhesion through specific and nonspecific means. The fluorescence measurements demonstrated the effectiveness of spatially regulating the density of surface-immobilized protein through controlling the areal thickness of the poly (glycidyl methacrylate) (PGMA) brush patterns, leading to various complex patterns featuring well-defined biomolecule concentration gradients. Furthermore, a multiplexed surface bearing epoxy groups and azido groups with various areal densities was fabricated for regulating the spatiotemporal arrangement of different proteins, enabling binary biomolecules patterns with higher degrees of functionality and complexity. The presented strategy for the spatiotemporal control of biomolecules immobilization would boost the development of dynamic and multifunctional biosystems.

UV- and Visible-Light Photopatterning of Molecular Gradients Using the Thiol-yne Click Reaction

The rational design of chemical coatings is used to control surface interactions with small molecules, biomolecules, nanoparticles, and liquids as well as optical and other properties. Specifically, micropatterned surface coatings have been used in a wide variety of applications, including biosensing, cell growth assays, multiplexed biomolecule interaction arrays, and responsive surfaces. Here, a maskless photopatterning process is studied, using the photocatalyzed thiol-yne "click" reaction to create both binary and gradient patterns on thiolated surfaces. Nearly defect-free patterns are produced by first coating glass surfaces with mercaptopropylsilatrane, a silanizing agent that forms smoother self-assembled monolayers than the commonly used 3-mercaptopropyltrimethoxysilane. Photopatterning is then performed using UV (365 nm) or visible (405 nm) light to graft molecules onto the surface in tunable concentrations based on the local exposure. The technique is demonstrated for multiple types of molecular grafts, including fluorescent dyes, poly(ethylene glycol), and biotin, the latter allowing subsequent deposition of biomolecules via biotin-avidin binding. Patterning is demonstrated in water and dimethylformamide, and the process is repeated to combine molecules soluble in different phases. The combination of arbitrary gradient formation, broad applicability, a low defect rate, and fast prototyping thanks to the maskless nature of the process creates a particularly powerful technique for molecular surface patterning that could be used for a wide variety of micropatterned applications.

Development of an Enzyme-Inhibitor Reaction Using Cellular Retinoic Acid Binding Protein II for One-Pot Megamolecule Assembly

This paper presents an enzyme building block for the assembly of megamolecules. The system is based on the inhibition of the human-derived cellular retinoic acid binding protein II (CRABP2) domain. We synthesized a synthetic retinoid bearing an arylfluorosulfate group, which uses sulfur fluoride exchange click chemistry to covalently inhibit CRABP2. We conjugated both the inhibitor and a fluorescein tag to an oligo(ethylene glycol) backbone and measured a second-order rate constant for the protein inhibition reaction of approximately 3,600 M^-1 s^-1 . We used this new enzyme-inhibitor pair to assemble multi-protein structures in one-pot reactions using three orthogonal assembly chemistries to demonstrate exact control over the placement of protein domains within a single, homogeneous molecule. This work enables a new dimension of control over specificity, orientation, and stoichiometry of protein domains within atomically precise nanostructures.

Analysis of Actin and Focal Adhesion Organisation in U2OS Cells on Polymer Nanostructures

BACKGROUND

In this work, we explore how U2OS cells are affected by arrays of polymer nanopillars fabricated on flat glass surfaces. We focus on describing changes to the organisation of the actin cytoskeleton and in the location, number and shape of focal adhesions. From our findings we identify that the cells can be categorised into different regimes based on their spreading and adhesion behaviour on nanopillars. A quantitative analysis suggests that cells seeded on dense nanopillar arrays are suspended on top of the pillars with focal adhesions forming closer to the cell periphery compared to flat surfaces or sparse pillar arrays. This change is analogous to similar responses for cells seeded on soft substrates.

RESULTS

In this work, we explore how U2OS cells are affected by arrays of polymer nanopillars fabricated on flat glass surfaces. We focus on describing changes to the organisation of the actin cytoskeleton and in the location, number and shape of focal adhesions. From our findings we identify that the cells can be categorised into different regimes based on their spreading and adhesion behaviour on nanopillars. A quantitative analysis suggests that cells seeded on dense nanopillar arrays are suspended on top of the pillars with focal adhesions forming closer to the cell periphery compared to flat surfaces or sparse pillar arrays. This change is analogous to similar responses for cells seeded on soft substrates.

CONCLUSION

Overall, we show that the combination of high throughput nanofabrication, advanced optical microscopy, molecular biology tools to visualise cellular processes and data analysis can be used to investigate how cells interact with nanostructured surfaces and will in the future help to create culture substrates that induce particular cell function.

Antibody Printing Technologies

Antibody microarrays are routinely employed in the lab and in the clinic for studying protein expression, protein-protein, and protein-drug interactions. The microarray format reduces the size scale at which biological and biochemical interactions occur, leading to large reductions in reagent consumption and handling times while increasing overall experimental throughput. Specifically, antibody microarrays, as a platform, offer a number of different advantages over traditional techniques in the areas of drug discovery and diagnostics. While a number of different techniques and approaches have been developed for creating micro and nanoscale antibody arrays, issues relating to sensitivity, cost, and reproducibility persist. The aim of this review is to highlight current state-of the-art techniques and approaches for creating antibody arrays by providing latest accounts of the field while discussing potential future directions.

Solid-Phase Synthesis of Megamolecules

This paper presents a solid-phase strategy to efficiently assemble multiprotein scaffolds-known as megamolecules-without the need for protecting groups and with precisely defined nanoscale architectures. The megamolecules are assembled through sequential reactions of linkers that present irreversible inhibitors for enzymes and fusion proteins containing the enzyme domains. Here, a fusion protein containing an N-terminal cutinase and a C-terminal SnapTag domain react with an ethyl p-nitrophenyl phosphonate (pNPP) or a chloro-pyrimidine (CP) group, respectively, to give covalent products. By starting with resin beads that are functionalized with benzylguanine, a series of reactions lead to linear, branched, and dendritic structures that are released from the solid support by addition of TEV protease and that have sizes up to approximately 25 nm.