Covalent Attachment of Functional Proteins to Microfiber Surfaces via a General Strategy for Site-Selective Tetrazine Ligation

Surface modification of materials with proteins has various biological applications, and hence the methodology for surface modification needs to accommodate a wide range of proteins that differ in structure, size, and function. Presented here is a methodology that uses the Affinity Bioorthogonal Chemistry (ABC) tag, 3-(2-pyridyl)-6-methyltetrazine (PyTz), for the site-selective modification and purification of proteins and subsequent attachment of the protein to trans-cyclooctene (TCO)-functionalized hydrogel microfibers. This method of surface modification is shown to maintain the functionality of the protein after conjugation with proteins of varying size and functionalities, namely, HaloTag, NanoLuc luciferase (NanoLuc), and fibronectin type III domains 9-10 (FNIII 9-10). The method also supports surface modification with multiple proteins, which is shown by the simultaneous conjugation of HaloTag and NanoLuc on the microfiber surface. The ability to control the relative concentrations of multiple proteins presented on the surface is shown with the use of HaloTag and superfolder GFP (sfGFP). This application of the ABC-tagging methodology expands on existing surface modification methods and provides flexibility in the site-selective protein conjugation methods used along with the rapid kinetics of tetrazine ligation.

Surface chemical reactions on self-assembled silane based monolayers

In this review, we aim to update our review "Chemical modification of self-assembled silane-based monolayers by surface reactions" which was published in 2010 and has developed into an important guiding tool for researchers working on the modification of solid substrate surface properties by chemical modification of silane-based self-assembled monolayers. Due to the rapid development of this field of research in the last decade, the utilization of chemical functionalities in self-assembled monolayers has been significantly improved and some new processes were introduced in chemical surface reactions for tailoring the properties of solid substrates. Thus, it is time to update the developments in the surface functionalization of silane-based molecules. Hence, after a short introduction on self-assembled monolayers, this review focuses on a series of chemical reactions, i.e., nucleophilic substitution, click chemistry, supramolecular modification, photochemical reaction, and other reactions, which have been applied for the modification of hydroxyl-terminated substrates, like silicon and glass, which have been reported during the last 10 years.

Understanding the 1,3-Dipolar Cycloadditions of Allenes

We have quantum chemically studied the reactivity, site-, and regioselectivity of the 1,3-dipolar cycloaddition between methyl azide and various allenes, including the archetypal allene propadiene, heteroallenes, and cyclic allenes, by using density functional theory (DFT). The 1,3-dipolar cycloaddition reactivity of linear (hetero)allenes decreases as the number of heteroatoms in the allene increases, and formation of the 1,5-adduct is, in all cases, favored over the 1,4-adduct. Both effects find their origin in the strength of the primary orbital interactions. The cycloaddition reactivity of cyclic allenes was also investigated, and the increased predistortion of allenes, that results upon cyclization, leads to systematically lower activation barriers not due to the expected variations in the strain energy, but instead from the differences in the interaction energy. The geometric predistortion of cyclic allenes enhances the reactivity compared to linear allenes through a unique mechanism that involves a smaller HOMO-LUMO gap, which manifests as more stabilizing orbital interactions.

AFM Probing of Amyloid-Beta 42 Dimers and Trimers

Elucidating the molecular mechanisms in the development of such a devastating neurodegenerative disorder as Alzheimer's disease (AD) is currently one of the major challenges of molecular medicine. Evidence strongly suggests that the development of AD is due to the accumulation of amyloid β (Aβ) oligomers; therefore, understanding the molecular mechanisms defining the conversion of physiologically important monomers of Aβ proteins into neurotoxic oligomeric species is the key for the development of treatments and preventions of AD. However, these oligomers are unstable and unavailable for structural, physical, and chemical studies. We have recently developed a novel flexible nano array (FNA)-oligomer scaffold approach in which monomers tethered inside a flexible template can assemble spontaneously into oligomers with sizes defined by the number of tethered monomers. The FNA approach was tested on short decamer Aβ(14-23) peptides which were assembled into dimers and trimers. In this paper, we have extended our FNA technique for assembling full-length Aβ42 dimers. The FNA scaffold enabling the self-assembly of Aβ42 dimers from tethered monomeric species has been designed and the assembly of the dimers has been validated by AFM force spectroscopy experiments. Two major parameters of the force spectroscopy probing, the rupture forces and the rupture profiles, were obtained to prove the assembly of Aβ42 dimers. In addition, the FNA-Aβ42 dimers were used to probe Aβ42 trimers in the force spectroscopy experiments with the use of AFM tips functionalized with FNA-Aβ42 dimers and the surface with immobilized Aβ42 monomers. We found that the binding force for the Aβ42 trimer is higher than the dimer (75 ± 7 pN vs. 60 ± 3 pN) and the rupture pattern corresponds to a cooperative dissociation of the trimer. The rupture profiles for the dissociation of the Aβ42 dimers and trimers are proposed. Prospects for further extension of the FNA-based approach for probing of higher order oligomers of Aβ42 proteins are discussed.

Functionalization and Patterning of Self-Assembled Monolayers and Polymer Brushes Using Microcontact Chemistry

Because the surface connects a material to its environment, the functionalization, modification, and patterning of surfaces is key to a wide range of materials applied in microelectronics, displays, sensing, microarrays, photovoltaics, catalysis, and other fields. Self-assembled monolayers (SAMs), which can be deposited on a wide range of inorganic materials, are only a few nanometers thick, yet they can radically change the properties of the resulting interface. Alternatively, thin polymer films composed of polymer brushes grown from the surface provide a more robust molecular modification of inorganic materials. For many applications, patterned SAMs or polymer brushes are desired. Over the past decade, our group has shown that both SAMs as well as polymer brushes can be patterned very efficiently using microcontact printing. In microcontact printing, a molecular "ink" is deposited on a suitable substrate using a microstructured elastomer stamp, which delivers the ink exclusively in the area of contact between stamp and substrate. In contrast to most types of lithography, microcontact printing does not require expensive equipment. Our work has shown that "microcontact chemistry" is a powerful additive surface patterning method, in which molecular inks react with a precursor SAM during printing so that surfaces can be modified with various orthogonal functional groups or molecular recognition sites in microscale patterns. Functional groups include reactive groups for click chemistry or photochemistry and initiators for radical polymerization. Molecular recognition sites include host-guest chemistry as well as biochemical ligands such as carbohydrates and biotin. In this Account, we present an overview of our research in this area including selected examples of work by other groups. In the first part, we review our work on the patterning of SAMs using microcontact chemistry, with a focus on click chemistry and photochemistry. We will show how cycloadditions, thiol-ene reactions, and tetrazole chemistry can be used to obtain versatile surface patterns. In the second part, we demonstrate that microcontact chemistry can be used to pattern polymer brushes. Among others, initiators for surface-induced nitroxide-mediated polymerization and atom transfer polymerization were printed and used to grow patterned polymer brushes with molecular recognition groups suitable for responsive surface adhesion. In the third part, we describe how SAMs and polymer brushes can be printed on microparticles instead of flat substrates so that Janus particles with functional patches can be obtained. Finally, we present a brief outlook on further developments expected in this field.

Surfaces with Dual Functionality through Specific Coimmobilization of Self-Assembled Polymeric Nanostructures

Coimmobilization of functional, nanosized assemblies broadens the possibility to engineer dually functionalized active surfaces with a nanostructured texture. Surfaces decorated with different nanoassemblies, such as micelles, polymersomes, or nanoparticles are in high demand for various applications ranging from catalysis, biosensing up to antimicrobial surfaces. Here, we present a combination of bio-orthogonal and catalyst-free strain-promoted azide-alkyne click (SPAAC) and thiol-ene reactions to simultaneously coimmobilize various nanoassemblies; we selected polymersome-polymersome and polymersome-micelle assemblies. For the first time, the immobilization method using SPAAC reaction was studied in detail to attach soft, polymeric assemblies on a solid support. Together, the SPAAC and thiol-ene reactions successfully coimmobilized two unique self-assembled structures on the surfaces. Additionally, poly(dimethylsiloxane) (PDMS)-based polymersomes were used as "ink" for direct immobilization from a PDMS-based microstamp onto a surface creating locally defined patterns. Combining immobilization reactions has the advantage to attach any kind of nanoassembly pairs, resulting in surfaces with "desired" interfacial properties. Different nanoassemblies that encapsulate multiple active compounds coimmobilized on a surface will pave the way for the development of multifunctional surfaces with controlled properties and efficiency.

Structural Distortion of Cycloalkynes Influences Cycloaddition Rates both by Strain and Interaction Energies

The reactivities of 2‐butyne, cycloheptyne, cyclooctyne, and cyclononyne in the 1,3‐dipolar cycloaddition reaction with methyl azide were evaluated through DFT calculations at the M06‐2X/6‐311++G(d)//M06‐2X/6‐31+G(d) level of theory. Computed activation free energies for the cycloadditions of cycloalkynes are 16.5–22.0 kcal mol⁻¹ lower in energy than that of the acyclic 2‐butyne. The strained or predistorted nature of cycloalkynes is often solely used to rationalize this significant rate enhancement. Our distortion/interaction–activation strain analysis has been revealed that the degree of geometrical predistortion of the cycloalkyne ground‐state geometries acts to enhance reactivity compared with that of acyclic alkynes through three distinct mechanisms, not only due to (i) a reduced strain or distortion energy, but also to (ii) a smaller HOMO–LUMO gap, and (iii) an enhanced orbital overlap, which both contribute to more stabilizing orbital interactions.

Reversible DNA micro-patterning using the fluorous effect

We describe a new method for the immobilisation of DNA into defined patterns with sub-micron resolution, using the fluorous effect. The method is fully reversible via a simple solvent wash, allowing the patterning, regeneration and re-patterning of surfaces with no degradation in binding efficiency following multiple removal/attachment cycles of different DNA sequences.

On surface O-glycosylation by catalytic microcontact printing

Carbohydrate microarrays are made by microcontact printing of glycosyl donors on hydroxyl terminated substrates.

Efficient and Tunable Three-Dimensional Functionalization of Fully Zwitterionic Antifouling Surface Coatings

To enhance the sensitivity and selectivity of surface-based (bio)sensors, it is of crucial importance to diminish background signals that arise from the nonspecific binding of biomolecules, so-called biofouling. Zwitterionic polymer brushes have been shown to be excellent antifouling materials. However, for sensing purposes, antifouling does not suffice but needs to be combined with the possibility to efficiently modify the brush with recognition units. So far this has been achieved only at the expense of either antifouling properties or binding capacity. Herein we present a conceptually new approach by integrating both characteristics into a single tailor-made monomer: a novel sulfobetaine-based zwitterionic monomer equipped with a clickable azide moiety. Copolymerization of this monomer with a well-established standard sulfobetaine monomer results in highly antifouling surface coatings with a large yet tunable number of clickable groups present throughout the entire brush. Subsequent functionalization of the azido brushes via widely used strain-promoted alkyne azide click reactions yields fully zwitterionic 3D-functionalized coatings with a recognition unit of choice that can be tailored for any specific application. Here we show a proof of principle with biotin-functionalized brushes on Si₃N₄ that combine excellent antifouling properties with specific avidin binding from a protein mixture. The signal-to-noise ratio is significantly improved over that of traditional chain-end modification of sulfobetaine polymer brushes, even if the azide content is lowered to 1%. This therefore offers a viable approach to the development of biosensors with greatly enhanced performance on any surface.

Multifunctional Surface Manipulation Using Orthogonal Click Chemistry

Polymer brushes are excellent substrates for the covalent immobilization of a wide variety of molecules due to their unique physicochemical properties and high functional group density. By using reactive microcapillary printing, poly(pentafluorophenyl acrylate) brushes with rapid kinetic rates toward aminolysis can be partially patterned with other click functionalities such as strained cyclooctyne derivatives and sulfonyl fluorides. This trireactive surface can then react locally and selectively in a one pot reaction via three orthogonal chemistries at room temperature: activated ester aminolysis, strain promoted azide-alkyne cycloaddition, and sulfur(VI) fluoride exchange, all of which are tolerant of ambient moisture and oxygen. Furthermore, we demonstrate that these reactions can also be used to create areas of morphologically distinct surface features on the nanoscale, by inducing buckling instabilities in the films and the grafting of nanoparticles. This approach is modular, and allows for the development of highly complex surface motifs patterned with different chemistry and morphology.

Use of Ambient Ionization High-Resolution Mass Spectrometry for the Kinetic Analysis of Organic Surface Reactions

In contrast to homogeneous systems, studying the kinetics of organic reactions on solid surfaces remains a difficult task due to the limited availability of appropriate analysis techniques that are general, high-throughput, and capable of offering quantitative, structural surface information. Here, we demonstrate how direct analysis in real time mass spectrometry (DART-MS) complies with above considerations and can be used for determining interfacial kinetic parameters. The presented approach is based on the use of a MS tag that--in principle--allows application to other reactions. To show the potential of DART-MS, we selected the widely applied strain-promoted alkyne-azide cycloaddition (SPAAC) as a model reaction to elucidate the effects of the nanoenvironment on the interfacial reaction rate.

Simultaneous Dual Encoding of Three-Dimensional Structures by Light-Induced Modular Ligation

A highly efficient strategy for the simultaneous dual surface encoding of 2D and 3D microscaffolds is reported. The combination of an oligo(ethylene glycol)-based network with two novel and readily synthesized monomers with photoreactive side chains yields two new photoresists, which can be used for the fabrication of microstructures (by two-photon polymerization) that exhibit a dual-photoreactive surface. By combining both functional photoresists into one scaffold, a dual functionalization pattern can be obtained by a single irradiation step in the presence of adequate reaction partners based on a self-sorting mechanism. The versatility of the approach is shown by the dual patterning of halogenated and fluorescent markers as well as proteins. Furthermore, we introduce a new ToF-SIMS mode ("delayed extraction") for the characterization of the obtained microstructures that combines high mass resolution with improved lateral resolution.

Strain-promoted azide–alkyne cycloaddition for protein–protein coupling in the formation of a bis-hemoglobin as a copper-free oxygen carrier

Conventional chemical approaches to protein–protein coupling present challenges due to the intrinsic competition between the desired interactions of reagents with groups of the protein as well as reactions with water.

Photocurrent generation in organic photodetectors with tailor-made active layers fabricated by layer-by-layer deposition

Photodetectors supply an electric response when illuminated. The detectors in this study consist of an active layer and a polyvinylidene fluoride (PVDF) blocking layer, which are sandwiched by an aluminum and an indium tin oxide (ITO) electrode. The active layer was prepared of Zn porphyrins and assembled by covalent layer-by-layer (LbL) deposition. Layer growth was monitored by UV-vis absorbance, ellipsometry, and X-ray photoelectron spectroscopy. Upon exposure to chopped light, the detectors show an alternating transient photocurrent, which is limited by the accumulation of space charges at the blocking layer/active layer interface. We could show that the number of photoactive layers has a significant impact on device performance. The fastest response was achieved with fewer layers. The highest photocurrents were measured for detectors with an intermediate number of layers, beyond which, more layers did not lead to an increase in the photocurrent despite containing more active material.

Molecular recognition of surface-immobilized carbohydrates by a synthetic lectin

The molecular recognition of carbohydrates and proteins mediates a wide range of physiological processes and the development of synthetic carbohydrate receptors (“synthetic lectins”) constitutes a key advance in biomedical technology. In this article we report a synthetic lectin that selectively binds to carbohydrates immobilized in a molecular monolayer. Inspired by our previous work, we prepared a fluorescently labeled synthetic lectin consisting of a cyclic dimer of the tripeptide Cys-His-Cys, which forms spontaneously by air oxidation of the monomer. Amine-tethered derivatives of N-acetylneuraminic acid (NANA), β-D-galactose, β-D-glucose and α-D-mannose were microcontact printed on epoxide-terminated self-assembled monolayers. Successive prints resulted in simple microarrays of two carbohydrates. The selectivity of the synthetic lectin was investigated by incubation on the immobilized carbohydrates. Selective binding of the synthetic lectin to immobilized NANA and β-D-galactose was observed by fluorescence microscopy. The selectivity and affinity of the synthetic lectin was screened in competition experiments. In addition, the carbohydrate binding of the synthetic lectin was compared with the carbohydrate binding of the lectins concanavalin A and peanut agglutinin. It was found that the printed carbohydrates retain their characteristic selectivity towards the synthetic and natural lectins and that the recognition of synthetic and natural lectins is strictly orthogonal.

Sequential "click" - "photo-click" cross-linker for catalyst-free ligation of azide-tagged substrates

Heterobifunctional linker allows for selective catalyst-free ligation of two different azide-tagged substrates via strained-promoted azide-alkyne cycloaddition (SPAAC). The linker contains an azadibenzocyclooctyne (ADIBO) moiety on one end and a cyclopropenone-masked dibenzocyclooctyne (photo-DIBO) group on the other. The first azide-derivatized substrate reacts only at the ADIBO end of the linker as the photo-DIBO moiety is azide-inert. After the completion of the first SPAAC step, photo-DIBO is activated by brief exposure to 350 nm light from a fluorescent UV lamp. The unmasked DIBO group then reacts with the second azide-tagged substrate. Both click reactions are fast (k = 0.4 and 0.07 M(-1) s(-1), respectively) and produce quantitative yield of ligation in organic solvents or aqueous solutions. The utility of the new cross-linker has been demonstrated by conjugation of azide functionalized bovine serum albumin (azido-BSA) with azido-fluorescein and by the immobilization of the latter protein on azide-derivatized silica beads. The BSA-bead linker was designed to incorporate hydrolytically labile fragment, which permits release of protein under the action of dilute acid. UV activation of the second click reaction permits spatiotemporal control of the ligation process.

Finding the right (bioorthogonal) chemistry

Bioorthogonal chemistries can be used to tag diverse classes of biomolecules in cells and other complex environments. With over 20 unique transformations now available, though, selecting an appropriate reaction for a given experiment is challenging. In this article, we compare and contrast the most common classes of bioorthogonal chemistries and provide a framework for matching the reactions with downstream applications. We also discuss ongoing efforts to identify novel biocompatible reactions and methods to control their reactivity. The continued expansion of the bioorthogonal toolkit will provide new insights into biomolecule networks and functions and thus refine our understanding of living systems.

A homologation approach to the synthesis of difluorinated cycloalkynes

Difluorinated cyclooctynes are important reagents for labeling azido-biomolecules through copper-free click chemistry. Here, a safe, scalable synthesis of a difluorinated cyclooctyne is reported, which involves a key homologation/ring-expansion reaction. Sequential ring expansions were also employed to synthesize and study a novel difluorinated cyclononyne.

Surface patterning with natural and synthetic polymers via an inverse electron demand Diels–Alder reaction employing microcontact chemistry

Bioorthogonal ligation methods are the focus of current research due to their versatile applications in biotechnology and materials science for post-functionalization and immobilization of biomolecules.