Efficient surface patterning of oligonucleotides inside a glass capillary through oxime bond formation

Laser Photodissociation Action Spectroscopy for the Wavelength-Dependent Evaluation of Photoligation Reactions

The nitrile imine-mediated tetrazole-ene cycloaddition is a widely used class of photoligation. Optimizing the reaction outcome requires detailed knowledge of the tetrazole photoactivation profile, which can only partially be ascertained from absorption spectroscopy, or otherwise involves laborious reaction monitoring in solution. Photodissociation action spectroscopy (PDAS) combines the advantages of optical spectroscopy and mass spectrometry in that only absorption events resulting in a mass change are recorded, thus revealing the desired wavelength dependence of product formation. Moreover, the sensitivity and selectivity afforded by the mass spectrometer enable reliable assessment of the photodissociation profile even on small amounts of crude material, thus accelerating the design and synthesis of next-generation substrates. Using this workflow, we demonstrate that the photodissociation onset for nitrile imine formation is red-shifted by ca. 50 nm with a novel N-ethylcarbazole derivative relative to a phenyl-substituted archetype. Benchmarked against solution-phase tunable laser experiments and supported by quantum chemical calculations, these discoveries demonstrate that PDAS is a powerful tool for rapidly screening the efficacy of new substrates in the quest toward efficient visible light-triggered ligation for biological applications.

Imparting sensitivity and selectivity to a gold nanoparticle chemiresistor through thiol monolayer functionalization for sensing acetone

Chemiresistor-based gas sensors for detection of target volatile organic compounds (VOCs) in air face common challenges of poor sensitivity and selectivity as well as suffering from interference by other constituent gases and/or humidity. This work demonstrates that functionalizing gold nanoparticles (AuNPs) with a designed thiol monolayer improves sensitivity and selectivity of the derived AuNPs gas sensor. We report the synthesis and application of a thiol ligand fitted with both a urea motif and a tert-butyl end group for functionalizing AuNPs. The AuNPs sensor prepared using the urea thiol ligand demonstrated significantly increased acetone sensing in comparison with tested commercially available thiol-functionalized AuNPs. The sensor worked under ambient temperature and high humidity conditions, and demonstrated a linear relationship between the sensor response and the common logarithm of analyte concentration.

Bioorthogonal Strategies for Engineering Extracellular Matrices

Hydrogels are commonly used as engineered extracellular matrix (ECM) mimics in applications ranging from tissue engineering to in vitro disease models. Ideal mechanisms used to crosslink ECM-mimicking hydrogels do not interfere with the biology of the system. However, most common hydrogel crosslinking chemistries exhibit some form of cross-reactivity. The field of bio-orthogonal chemistry has arisen to address the need for highly specific and robust reactions in biological contexts. Accordingly, bio-orthogonal crosslinking strategies have been incorporated into hydrogel design, allowing for gentle and efficient encapsulation of cells in various hydrogel materials. Furthermore, the selective nature of bio-orthogonal chemistries can permit dynamic modification of hydrogel materials in the presence of live cells and other biomolecules to alter matrix mechanical properties and biochemistry on demand. In this review, we provide an overview of bio-orthogonal strategies used to prepare cell-encapsulating hydrogels and highlight the potential applications of bio-orthogonal chemistries in the design of dynamic engineered ECMs.

Spatiotemporal hydrogel biomaterials for regenerative medicine

Hydrogels mimic many of the physical properties of soft tissue and are widely used biomaterials for tissue engineering and regenerative medicine. Synthetic hydrogels have been developed to recapitulate many of the healthy and diseased states of native tissues and can be used as a cell scaffold to study the effect of matricellular interactions in vitro. However, these matrices often fail to capture the dynamic and heterogenous nature of the in vivo environment, which varies spatially and during events such as development and disease. To address this deficiency, a variety of manufacturing and processing techniques are being adapted to the biomaterials setting. Among these, photochemistry is particularly well suited because these reactions can be performed in precise three-dimensional space and at specific moments in time. This spatiotemporal control over chemical reactions can also be performed over a range of cell- and tissue-relevant length scales with reactions that proceed efficiently and harmlessly at ambient conditions. This review will focus on the use of photochemical reactions to create dynamic hydrogel environments, and how these dynamic environments are being used to investigate and direct cell behavior.

Photomediated oxime ligation as a bioorthogonal tool for spatiotemporally-controlled hydrogel formation and modification

Click chemistry has proved a valuable tool in biocompatible hydrogel formation for 3D cell culture, owing to its bioorthogonal nature and high efficiency under physiological conditions. While traditional click reactions can be readily employed to create uniform functional materials about living cells, their spontaneity prohibits spatiotemporal control of material properties, thereby limiting their utility in recapitulating the dynamic heterogeneity characteristic of the in vivo microenvironment. Photopolymerization-based techniques gain this desired level of 4D programmability, but often at the expense of introducing propagating free radicals that are prone to non-specific reactions with biological systems. Here we present a strategy for bioorthogonal hydrogel formation and modification that does not rely on propagating free radicals, proceeding through oxime ligation moderated by a photocaged alkoxyamine. Upon mild near UV light exposure, the photocage is cleaved, liberating the alkoxyamine and permitting localized condensation with an aldehyde. Multi-arm crosslinkers, functionalized with either benzaldehydes or photocaged alkoxyamines, formed oxime-based hydrogels within minutes of light exposure in the presence of live cells. Polymerization rates and final mechanical properties of these gels could be systematically tuned by varying crosslinker concentrations, light intensity, aniline catalyst equivalents, and pH. Moreover, hydrogel geometry and final mechanical properties were controlled by the location and extent of UV exposure, respectively. Photomediated oxime ligation was then translated to the biochemical modification of hydrogels, where full-length proteins containing photocaged alkoxyamines were immobilized in user-defined regions exposed to UV light. The programmability afforded by photomediated oxime ligation can recapitulate dynamically anisotropic mechanical and biochemical aspects of the native extracellular matrix. Consequently, photopolymerized oxime-based hydrogels are expected to enable an enhanced understanding of cell-matrix interactions by serving as improved 4D cell culture platforms.

An oxime-based glycocluster microarray

Carbohydrate microarrays represent powerful tools to study and detect carbohydrate-binding proteins, pathogens or cells.

Chemoselective Strategies to Peptide and Protein Bioprobes Immobilization on Microarray Surfaces

Ordered and reproducible bioprobe immobilization onto sensor surfaces is a critical step in the development of reliable analytical devices. A growing awareness of the impact of the immobilization scheme on the consistency of the generated data is driving the demand for chemoselective approaches to immobilize biofunctional ligands, such as peptides, in a predetermined and uniform fashion. Herein, the most intriguing strategies to selective and oriented peptide immobilization are described and discussed. The aim of the current work is to provide the reader a general picture on recent advances made in this field, highlighting the potential associated with each chemoselective strategy. Case studies are described to provide illustrative examples, and cross-references to more topic-focused and exhaustive reviews are proposed throughout the text.

A photoreversible protein-patterning approach for guiding stem cell fate in three-dimensional gels

Although biochemically patterned hydrogels are capable of recapitulating many critical aspects of the heterogeneous cellular niche, exercising spatial and temporal control of the presentation and removal of biomolecular signalling cues in such systems has proved difficult. Here, we demonstrate a synthetic strategy that exploits two bioorthogonal photochemistries to achieve reversible immobilization of bioactive full-length proteins with good spatial and temporal control within synthetic, cell-laden biomimetic scaffolds. A photodeprotection-oxime-ligation sequence permits user-defined quantities of proteins to be anchored within distinct subvolumes of a three-dimensional matrix, and an ortho-nitrobenzyl ester photoscission reaction facilitates subsequent protein removal. By using this approach to pattern the presentation of the extracellular matrix protein vitronectin, we accomplished reversible differentiation of human mesenchymal stem cells to osteoblasts in a spatially defined manner. Our protein-patterning approach should provide further avenues to probe and direct changes in cell physiology in response to dynamic biochemical signalling.

Dynamic photochemical silane micropatterning

This protocol describes a method for dynamic patterning cells on a glass coverslip. The glass substrate is first functionalized with photocleavable silane bearing 2-nitrobenzyl group, thereafter a cell-repellent polymer, poly(ethylene glycol) (PEG), is conjugated. Upon absorption of near-UV light, the PEG is cleaved from the surface, changing the surface from non-cell-adhesive to cell-adhesive. The method allows not only for spatially controlling cell attachment on the substrate (conventional patterning), but also inducing cell migration or coculturing heterotypic cells (dynamic patterning). Furthermore, it should be emphasized that the surface is compatible with fluorescence imaging in a high-resolution inverted objective setup as it is composed of a normal glass coverslip functionalized with the thin layers. In this chapter, I describe the procedure for the synthesis of the silane molecule, the preparation of the photoactivatable surface, and its application for dynamic cell patterning.

Functionalized ceramics for biomedical, biotechnological and environmental applications

Surface functionalization has become of paramount importance and is considered a fundamental tool for the development and design of countless devices and engineered systems for key technological areas in biomedical, biotechnological and environmental applications. In this review, surface functionalization strategies for alumina, zirconia, titania, silica, iron oxide and calcium phosphate are presented and discussed. These materials have become particularly important concerning the aforementioned applications, being not only of great academic, but also of steadily increasing human and commercial, interest. In this review, special emphasis is given to their use as biomaterials, biosensors, biological targets, drug delivery systems, implants, chromatographic supports for biomolecule purification and analysis, and adsorbents for toxic substances and pollutants. The objective of this review is to provide a broad picture of the enormous possibilities offered by surface functionalization and to identify particular challenges regarding surface analysis and characterization.

α-Oxo aldehyde or glyoxylyl group chemistry in peptide bioconjugation

Since the 1990s, α-oxo aldehyde or glyoxylic acid chemistry has inspired a vast array of synthetic tools for tailoring peptide or protein structures, for developing peptides endowed with novel physicochemical properties or biological functions, for assembling a large diversity of bioconjugates or hybrid materials, or for designing peptide-based micro or nanosystems. This past decade, important developments have enriched the α-oxo aldehyde synthetic tool box in peptide bioconjugation chemistry and explored novel applications. The aim of this review is to give a large overview of this creative field.

Solid-phase glycan isolation for glycomics analysis

Glycosylation is one of the most significant protein PTMs. The biological activities of proteins are dramatically changed by the glycans associated with them. Thus, structural analysis of the glycans of glycoproteins in complex biological or clinical samples is critical in correlation with the functions of glycans with diseases. Profiling of glycans by HPLC-MS is a commonly used technique in analyzing glycan structures and quantifying their relative abundance in different biological systems. Methods relied on MS require isolation of glycans from negligible salts and other contaminant ions since salts and ions may interfere with the glycans, resulting in poor glycan ionization. To accomplish those objectives, glycan isolation and clean-up methods including SPE, liquid-phase extraction, chromatography, and electrophoresis have been developed. Traditionally, glycans are isolated from proteins or peptides using a combination of hydrophobic and hydrophilic columns: proteins and peptides remain on hydrophobic absorbent while glycans, salts, and other hydrophilic reagents are collected as flowthrough. The glycans in the flowthrough are then purified through graphite-activated carbon column by hydrophilic interaction LC. Yet, the drawback in these affinity-based approaches is nonspecific binding. As a result, chemical methods by hydrazide or oxime have been developed for solid-phase isolation of glycans with high specificity and yield. Combined with high-resolution MS, specific glycan isolation techniques provide tremendous potentials as useful tools for glycomics analysis.

Direct characterization of native chemical ligation of peptides on silicon nanowires

We describe the site-specific and chemoselective immobilization of peptides on hydrogen-terminated silicon nanowires (SiNWs) using native chemical ligation (NCL) (i.e., the reaction of a thioester group with a cysteine moiety to give a stable amide bond). The SiNWs investigated in this work were grown via a vapor-liquid-solid mechanism and functionalized with a thioester moiety. The immobilization of the peptides on the SiNWs was demonstrated by synthesizing peptides with an N-terminal cysteine residue and labeled with tetramethylrhodamine or trifluoromethyl groups that were detected by fluorescence and X-ray photoelectron spectroscopy, respectively. The peptides labeled with tetramethylrhodamine or trifluoromethyl groups for fluorescence or X-ray photoelectron spectroscopy (XPS) detection studies were synthesized with an N-terminal cysteine residue. N-Terminal seryl peptides and carboxy-terminated SiNWs were used as controls to demonstrate the chemoselectivity of the peptide immobilization.

Protein nanopatterns by oxime bond formation

Patterning proteins on the nanoscale is important for applications in biology and medicine. As feature sizes are reduced, it is critical that immobilization strategies provide site-specific attachment of the biomolecules. In this study, oxime chemistry was exploited to conjugate proteins onto nanometer-sized features. Poly(Boc-aminooxy tetra(ethylene glycol) methacrylate) was synthesized by free radical polymerization. The polymer was patterned onto silicon wafers using an electron beam writer. Trifluoroacetic acid removal of the Boc groups provided the desired aminooxy functionality. In this manner, patterns of concentric squares and contiguous bowtie shapes were fabricated with 150-170-nm wide features. Ubiquitin modified at the N-terminus with an α-ketoamide group and N(ε)-levulinyl lysine-modified bovine serum albumin were subsequently conjugated to the polymer nanopatterns. Protein immobilization was confirmed by fluorescence microscopy. Control studies on protected surfaces and using proteins presaturated with O-methoxyamine indicated that attachment occurred via oxime bond formation.

Recent developments in oligonucleotide conjugation

Synthetic oligonucleotides (ONs) are being investigated for various therapeutic and diagnostic applications. The interest in ONs arises because of their capability to cause selective inhibition of gene expression by binding to the target DNA/RNA sequences through mechanisms such as antigene, antisense, and RNA interference. ONs with catalytic activity (ribozymes and DNAzymes) against the target sequences, and ability to bind to the target molecules (aptamers), ranging from small molecules to proteins, are also known. Therefore ONs are considered potentially useful for the treatment of viral diseases and cancer. ONs also find use in the design of DNA microchips (a powerful bio-analytical tool) and novel materials in nanotechnology. However, the clinical success achieved so far with ONs has not been satisfactory, and the major impediments have been recognised as their instability against nucleases, lack of target specificity, and poor uptake and targeted delivery. Tremendous efforts have been made to improve the ON properties by either incorporating chemical modifications in the ON structure or covalently linking (conjugation) reporter groups, with biologically relevant properties, to ONs. Conjugation is of great interest because it can be used not only to improve the existing ON properties but also to impart entirely new properties. This tutorial review focuses on the recent developments in ON conjugation, and describes the key challenges in efficient ON conjugation and major synthetic approaches available for successful ON conjugate syntheses. In addition, an overview on major classes of ON conjugates along with their use in therapeutics, diagnostics and nanotechnology is provided.

Efficient conjugation of oligonucleotides through aromatic oxime formation

The present work reports on the preparation of oligonucleotide conjugates via the formation of aromatic oxime linkage. The conjugation consists in the reaction between the oligonucleotide derivatized at 5'-extremity with a benzaldehyde moiety and an aminooxy reporter group. The conjugation was found highly efficient and was extended for the conjugation of phosphorothioate oligonucleotide. In addition, the stability of the so-formed oxime conjugate was investigated.

Immobilization of self-quenched DNA hairpin probe with a heterobifunctional reagent on a glass surface for sensitive detection of oligonucleotides

A new sensitive method for the detection of nucleic acids on a glass surface has been described. The self-quenched DNA hairpin probe is immobilized on a glass surface utilizing heterobifunctional reagent, N-(3-triethoxysilylpropyl)-4-(isothiocyanatomethyl)-cyclohexane-1-carboxamide (TPICC). In the closed state fluorescence intensity was quenched due to the presence of guanosine residues in close vicinity of fluorophore while on hybridization with perfectly matched complementary target strand fluorescence was restored. Efficiency and specificity of immobilization as well as thermal stability at variable temperature and pH conditions have been discussed in detail. The method employed has potential for the detection of single nucleotide variations and other diagnostic studies.

Micrometer- and nanometer-scale photopatterning using 2-nitrophenylpropyloxycarbonyl-protected aminosiloxane monolayers

An approach to nanopatterning is reported in which a scanning near-field optical microscope coupled to a near-UV laser is used to selectively deprotect 2-nitrophenylpropyloxycarbonyl (NPPOC)-protected aminosiloxane monolayers on glass. UV deprotection was studied for unpatterned samples using X-ray photoelectron spectroscopy (XPS) and contact angle measurements. Highly efficient photodeprotection of the NPPOC moiety was observed upon irradiation at both 325 and 364 nm, and complete deprotection was found to occur within minutes. The resulting amine-terminated surfaces were then derivatized using trifluoroacetic anhydride (TFAA) and aldehyde-functionalized polymer nanoparticles. Contact angle and XPS measurements postderivatization indicated that surface functionalization was extensive, with the NPPOC-deprotected surfaces and aminopropylsiloxane control materials exhibiting essentially identical characteristics. Micrometer-scale patterns were fabricated using mask-based exposure, functionalized with polymer nanoparticles, and characterized by atomic force microscopy. Nanometer-scale patterns were fabricated using near-field exposure and characterized by friction force microscopy. The nanopatterns were derivatized with TFAA. The resulting images exhibited a clear contrast inversion that was due to an inversion of surface polarity in the patterned areas and confirmed that high spatial resolution (ca. 100 nm) was readily achievable.

Photoactive branched and linear surface architectures for functional and patterned immobilization of proteins and cells onto surfaces: a comparative study

Molecular architecture affects the properties of surface layers. Photosensitive silanes with branched architectures allow patterning and coupling of proteins and cells on surfaces while maintaining their biofunctional state. Attachment can be directed to the activated regions of irradiated substrates with high selectivity (see image of mouse fibroblasts). Novel photosensitive silanes with a branched molecular architecture combining three end-functionalized oligoethylene glycol (OEG) and alkyl arms are presented. These molecules are synthesized and applied to the modification of silica surfaces. The resulting layers are tested in their ability for the selective, patterned and functional immobilization of proteins and cells. The results demonstrate and accurately quantify the benefits of branched OEG structures against linear analogues for preventing non-specific interactions with the biological material. Linear structures guarantee high selectivity for the attachment of proteins, however, they fail in the case of cells. Branched structures provide good antifouling properties in both cases and allow the formation of protein patterns with higher densities of the target protein, as well as cell patterns. The results demonstrate the careful balance between surface functionality, composition and architecture that is required for maximizing the performance of any surface-based assay in biology.

Surface patterning of (bio)molecules onto the inner wall of fused-silica capillary tubes

An efficient photochemical method for the site-specific immobilization and patterning of (bio)molecules inside glass capillary tubes is reported. The strategy involves the photodeprotection of reactive aminooxy groups on surfaces and subsequent reaction with aldehyde containing (bio)molecules.

Photoresponsive surfaces with two independent wavelength-selective functional levels

Two photoremovable protecting groups, namely, nitroveratryloxycarbonyl (NVo) and diethylamino-coumarin-4-yl (DEACM), have been tested for wavelength-selective, independent removal. The chromophores were attached to the amine group of aminopropyltriethoxysilane and used for the modification of silica surfaces. A photolytic experiment on the photosensitive layers allowed us to identify the irradiation conditions for the selective cleavage of the chromophores. UV measurements revealed that the photolabile DEACM group can be cleaved off with UV light at 412 nm without damaging the NVo group. The NVo group could then be removed at 365 nm. Masked irradiation of substrates modified with a 1:1 molar mixture of both silanes allowed the generation of bifunctional patterns after the selective cleavage of DEACM and NVo in a sequential irradiation process. The deprotection reaction was confirmed by coupling two different fluorescent dyes to the liberated amine groups. The expected two-color pattern could be observed by fluorescence microscopy.

Use of gamma-aminopropyl-coated glass surface for the patterning of oligonucleotides through oxime bond formation

The present work reports on the preparation of glass surfaces coated with NPPOC-protected aminooxy groups and their use for the patterning of oligonucleotides on glass slides and in capillary tubes. The method involves the use of surfaces coated with amino groups using (gamma-aminopropyl)triethoxy silane and subsequent grafting of the aminooxy groups by using the activated ester 1. The NPPOC-protected aminooxy groups on the surfaces can be cleaved upon irradiation. The free aminooxy groups so obtained are subsequently reacted with aldehyde-containing oligonucleotides to achieve efficient surface patterning.

Photopatterned surfaces for site-specific and functional immobilization of proteins

Photosensitive silanes containing nitroveratryl (Nvoc)-caged amine groups and protein repellent tetraethylene glycol units were synthesized and used for modification of silica surfaces. Functional surface layers containing different densities of caged amine groups were prepared and activated by UV-irradiation of the surface. The performance of these layers for functional and site-selective immobilization of proteins was tested. For this purpose, biotin and tris-nitrilotriacetic acid (tris-NTA) were fist coupled to the activated surface, and the interaction of streptavidin and His-tagged proteins with the functionalized surfaces was monitored by real-time label-free detection. After optimizing the coupling protocols, highly selective functionalization of the deprotected amine groups was possible. Furthermore, the degree of functionalization (and therefore the amount of immobilized protein) was controlled by diluting the surface concentration of the amine-functionalized silane with a nonreactive (OMe-terminated) tetraethylene glycol silane. Immobilized proteins were highly functional on these surfaces, as demonstrated by protein-protein interaction assays with the type I interferon receptor. Protein micropatterns were successfully generated after masked irradiation and functionalization of the caged surface following the optimized coupling protocols.

Immobilization of oligonucleotides on glass surface using an efficient heterobifunctional reagent through maleimide-thiol combination chemistry

An efficient heterobifunctional reagent, N-(3-triethoxysilylpropyl)-4-(N'-maleimidylmethyl) cyclohexanamide (TPMC), was developed for the immobilization of thiol-modified oligonucleotides on an unmodified glass surface. The heterobifunctionality of the reagent was used for the construction of a DNA microarray in which the triethoxysilyl functionality has specificity toward a glass surface, whereas the maleimide functionality has thiol-modified oligonucleotides via a stable thioether linkage. Immobilization of DNA was achieved by two alternative approaches. In the first approach, the reagent TPMC was treated with oligonucleotides to get triethoxysilyl-oligonucleotide conjugate, which was then covalently attached via specific triethoxysilyl functionality to an unmodified glass surface. In the second approach, the reagent was first covalently linked with an unmodified glass surface to get maleimide functionality on a glass surface, which was then used for the immobilization of oligonucleotides via a stable thioether linkage. The applicability of the reagent was explored by hybridization studies with the fluorescein-labeled complementary DNA strand and in mismatch discrimination.