The use of a detectable,mass-spectrometry-cleavable linker for quality control on an addressable microelectrode array

The synthesis, site-selective placement, and TOF-SIMS cleavage properties of a new, fluorescent linker for attaching molecules to a microelectrode array are reported. The linker was developed to provide a handle for quality control assessment of the microelectrode arrays being used to probe the binding of molecular libraries with biological receptors.     

A Neoglycoprotein-Immobilized Fluorescent Magnetic Bead Suspension Multiplex Array for Galectin-Binding Studies

Carbohydrate-protein conjugates have diverse applications. They have been used clinically as vaccines against bacterial infection and have been developed for high-throughput assays to elucidate the ligand specificities of glycan-binding proteins (GBPs) and antibodies. Here, we report an effective process that combines highly efficient chemoenzymatic synthesis of carbohydrates, production of carbohydrate-bovine serum albumin (glycan-BSA) conjugates using a squarate linker, and convenient immobilization of the resulting neoglycoproteins on carboxylate-coated fluorescent magnetic beads for the development of a suspension multiplex array platform. A glycan-BSA-bead array containing BSA and 50 glycan-BSA conjugates with tuned glycan valency was generated. The binding profiles of six plant lectins with binding preference towards Gal and/or GalNAc, as well as human galectin-3 and galectin-8, were readily obtained. Our results provide useful information to understand the multivalent glycan-binding properties of human galectins. The neoglycoprotein-immobilized fluorescent magnetic bead suspension multiplex array is a robust and flexible platform for rapid analysis of glycan and GBP interactions and will find broad applications.     

A novel heterotrifunctional peptide-based cross-linking reagent for facile access to bioconjugates. Applications to peptide fluorescent labelling and immobilisation

A convenient, versatile and straightforward synthesis of a novel heterotrifunctional peptide-based linker molecule is described. This generic bio-labelling reagent contains an amine-reactive N-hydroxysuccinimidyl carbamate moiety, an aldehyde/ketone-reactive aminooxy group and a thiol group with a propensity to form urea, oxime and thioether linkages respectively. The full chemical orthogonality between the free aminooxy and thiol functionalities was demonstrated through the preparation of a fluorescent reagent suitable for the selective staining of a carboxaldehyde-modified surface by means of oxime ligation. The absence of reactivity of these two functions toward the nucleophile-sensitive active carbamate was obtained by using temporary aminooxy- and thiol-protecting groups removable under mild conditions. The utility of the linker molecule to cross-link three different molecular partners has been illustrated by the preparation of fluorescent tripod-functionalised surfaces which may be useful in developing new peptide microarrays and related immunosensors.     

A streptavidin linker layer that functions after drying

The ability of streptavidin (SA) to simultaneously bind four biotins is often used in linker layers, where a biotinylated molecule is linked to a biotin-functionalized surface via SA. For biosensor and array applications, it is desirable that the SA linker layer be stable to drying and rehydration. In this study it was observed that a significant decrease in binding capacity of a SA layer occurred when that layer was dried. For this study a SA linker layer was constructed by binding SA to a biotin-containing alkylthiolate monolayer (BAT/OEG) self-assembled onto gold. Its stability after drying was investigated using surface plasmon resonance (SPR). Approximately a quarter of the SA layer was removed from the BAT/OEG surface upon drying and rehydration, suggesting disruption of SA-biotin binding when dry. This resulted in the dried SA layer losing approximately 40% of its biotinylated ferritin (BF) binding capacity. Coating the layer with trehalose before drying was found to inhibit the loss of SA from the BAT/OEG surface. SPR showed that the trehalose-protected SA linker layer retained approximately 91% of its original BF binding capacity after drying and rehydration. Atomic force microscopy, which was used to image individual surface-bound SA and BF molecules, qualitatively confirmed these observations.     

Site-selective, cleavable linkers: quality control and the characterization of small molecules on microelectrode arrays

A "safety-catch" linker strategy has been used to release a portion of the products of a Diels-Alder reaction conducted on a microelectrode array for characterization of stereochemistry. The attachment and cleavage of organic compounds from the surface of selected electrodes in the array can be accomplished by site-selective generation of base or acid at the electrode. It was found that the surface of the array had a minor influence on the stereochemistry of the Diels-Alder reaction, leading to slightly more of the exo-product relative to a similar solution-phase reaction.     

Spatial control of protein binding on lipid bimembrane using photoeliminative linker

Protein adsorption and dissociation on cell membrane surfaces is a topic of important study to reveal biological processes including signal transduction and protein trafficking. We demonstrated here the establishment of a mimic model system for the spatial control of protein adsorption/elimination on a lipid bimembrane using a photochemical technique. The novel photoeliminative linker that we synthesized here consists of three distinct components: a substrate (biotin), a photoeliminative group (4-(4-(1-hydroxyethyl)-2-methoxy-5-nitrophenoxy)butanoic acid), and a lipid bimembrane-adsorbent group (farnesyl). The photoeliminative linker was inserted on the entire surface of the lipid bimembrane and two-dimensionally eliminated by spatial UV irradiation onto the membrane to create a biotin pattern. A target protein, streptavidin was selectively immobilized on the patterned biotin, although it was almost not attached on the nonirradiated region. The streptavidin array was selectively dissociated by UV irradiation onto the entire membrane.     

Dependence of effective molarity on linker length for an intramolecular protein-ligand system

This paper reports dissociation constants and "effective molarities" (M(eff)) for the intramolecular binding of a ligand covalently attached to the surface of a protein by oligo(ethylene glycol) (EG(n)) linkers of different lengths (n = 0, 2, 5, 10, and 20) and compares these experimental values with theoretical estimates from polymer theory. As expected, the value of M(eff) is lowest when the linker is too short (n = 0) to allow the ligand to bind noncovalently at the active site of the protein without strain, is highest when the linker is the optimal length (n = 2) to allow such binding to occur, and decreases monotonically as the length increases past this optimal value (but only by a factor of approximately 8 from n = 2 to n = 20). These experimental results are not compatible with a model in which the single bonds of the linker are completely restricted when the ligand has bound noncovalently to the active site of the protein, but they are quantitatively compatible with a model that treats the linker as a random-coil polymer. Calorimetry revealed that enthalpic interactions between the linker and the protein are not important in determining the thermodynamics of the system. Taken together, these results suggest that the manifestation of the linker in the thermodynamics of binding is exclusively entropic. The values of M(eff) are, theoretically, intrinsic properties of the EG(n) linkers and can be used to predict the avidities of multivalent ligands with these linkers for multivalent proteins. The weak dependence of M(eff) on linker length suggests that multivalent ligands containing flexible linkers that are longer than the spacing between the binding sites of a multivalent protein will be effective in binding, and that the use of flexible linkers with lengths somewhat greater than the optimal distance between binding sites is a justifiable strategy for the design of multivalent ligands.     

Microarrays of synthetic heparin oligosaccharides

We present the first preparation of microarrays containing synthetic heparin oligosaccharides in order to elucidate the heparin-protein interactions involved in a variety of biological processes. For this purpose, we have developed a novel linker strategy that is compatible with the protecting-group manipulations required for the synthesis of the highly sulfated oligosaccharides and can also be extended to an automated solid phase approach. Strategic placement of the orthogonally protected amine linker was key to the success of the array construction. These heparin chips allow for the high-throughput screening of oligosaccharides by using approximately picomoles of protein. The potential of the new method was demonstrated by probing the carbohydrate affinity of two heparin-binding growth factors, FGF-1 and FGF-2, that are implicated in the development and differentiation of several tumors.     

Carbohydrate analysis prepares to enter the "Omics" era

In this issue, Houseman and Mrksich describe a carbohydrate array preparation method that can be used to analyze protein-carbohydrate interactions and to characterize the substrate specificity of a carbohydrate-modifying enzyme. Carbohydrate chips were prepared by a novel procedure that allows the covalent attachment of carbohydrate-diene conjugates to a specially engineered monolayer surface. The surface presents a precisely controllable ratio of reactive benzoquinone and inert ethylene glycol groups. Nonspecific adsorption of proteins to the surface is extremely low, and the surface is compatible with popular detection techniques. The immobilization technique was demonstrated to be compatible with recently developed automated solid phase carbohydrate synthesis methods, paving the way for the development of highly complex carbohydrate arrays.     

Molecular quantum cellular automata cells. Electric field driven switching of a silicon surface bound array of vertically oriented two-dot molecular quantum cellular automata

The amine functionality of the linker on the dinuclear complex [trans-Ru(dppm)(2)(Ctbd1;CFc)(NCCH(2)CH(2)NH(2))][PF(6)] reacts with Si-Cl bonds of a chlorinated, highly B doped Si (111) surface to yield Si-N surface-complex bonds. The surface bound complex is constrained to a near vertical orientation by the chain length of the linker as confirmed by variable angle XPS. Oxidation of the dinuclear complex with ferrocenium ion or electrochemically generates a stable, biased Fe(III)-Ru(II) mixed-valence complex on the surface. Characterization of the array of surface bound complexes with spectroscopic as well as electrochemical techniques confirms the presence of strongly bound, chemically robust, mixed-valence complexes. Capping the flat array of complexes with a minimally perturbing mercury electrode permits the equalization of the Fe and Ru energy wells by an applied electric field. The differential capacitance of oxidized and unoxidized bound complexes is compared as a function of voltage applied between the Hg gate and the Si. The results show that electron exchange between the Fe and Ru sites of the array of dinuclear mixed-valence complexes at energy equalization generates a fluctuating dipole that produces a maximum in the capacitance versus voltage curve for each complex-counterion combination present. Passage through the capacitance maximum corresponds to switching of the molecular quantum cellular automata (QCA) cell array by the electric field from the Fe(III)-Ru(II) configuration to the Fe(II)-Ru(III) configuration, thereby confirming that molecules possess an essential property necessary for their use as elements of a QCA device.     

A dimethyl ketal-protected benzoin-based linker suitable for photolytic release of unprotected peptides

Photolabile 3',5'-dimethoxybenzoin-based linkers are advantageous for a variety of solid-phase synthetic procedures and manipulations of biomolecules because UV irradiation in aqueous media provides fast and essentially quantitative release of tethered molecules, while generating unreactive side products. Practical applications of previously reported linkers are compromised to some extent by the 1,3-dithiane protection of the benzoin carbonyl group and the lengthy synthesis. We have extended the group of photocleavable 3',5'-dimethoxybenzoin-based linkers by designing and synthesizing a linker in which the carbonyl group is protected as a dimethyl ketal. This protection is compatible with commonly used esterification and amide bond formation techniques, including the Fmoc/tBu strategy for solid phase peptide synthesis, is stable under mild acidic conditions, and can be quantitatively removed in <5 min by 3% TFA in dichloromethane. Irradiation of beads carrying peptides attached to the linker at 350 nm in aqueous or partially aqueous media affords >90% release after 30 min. The linker was synthesized from commercially available starting materials in five steps with an overall yield of 40% and without any column chromatography purification. Additionally, we developed a route to a dithiane-protected linker that requires only two steps and proceeds in 65% yield, a significant improvement over previous synthetic routes.     

Preparation of stable micropatterns of gold oncell-adhesion-resistant hydrogels assisted by ahetero-bifunctional macromonomer linker

Surface patterning is very useful in biomaterial studies, yet it is not easy to prepare a micropattern with cell-adhesion contrast that is stable in a wet environment. Recently, a platform technique of transfer photolithography was invented to fabricate stable metal microarrays on the surface of a cell-adhesion resistant and mechanically biomimetic poly(ethylene glycol) hydrogel; the linker is the key chemical in such a transfer strategy. This article reports the design and synthesis of a hetero-bifunctional macromonomer linker with a thiol group at one end and an acryloyl group at the other end. The bifunctional linker was characterized by GPC and ¹H NMR, and the average number of thiol groups in the bifunctional linker was detected by Ellman’s reagent. The regent stability under wet conditions was also confirmed by the model reactants. The resultant micropatterned surfaces are meaningful for future studies of cell behaviors on mechanically biomimetic matrixes.     

A Self‐Reporting Tetrazole‐Based Linker for the Biofunctionalization of Gold Nanorods

A photochemical approach based on nitrile imine‐mediated tetrazole‐ene cycloaddition is introduced to functionalize gold nanorods with biomolecules. For this purpose, a bifunctional, photoreactive linker containing thioctic acid as the Au anchoring group and a tetrazole moiety for the light‐induced reaction with maleimide‐capped DNA was prepared. The tetrazole‐based reaction on the nanoparticles’ surface results in a fluorescent pyrazoline product allowing for the spectroscopic monitoring of the reaction. This first example of nitrile imine‐mediated tetrazole‐ene cycloaddition (NITEC)‐mediated biofunctionalization of Au nanorods paves the way for the attachment of sensitive biomolecules, such as antibodies and other proteins, under mild conditions and expands the toolbox for the tailoring of nanomaterials.     

Novel Boronlectins Based on Bispyridium Salt with a Flexible Linker: Discriminative Sensing of Lactose and Other Monosaccharides and Disaccharides in Aqueous Solution

N,N‐Di‐2‐picolylamine (DPA)‐derived diboronic acid receptors (NHBAs) with a flexible linker were designed and synthesized in this study, and two‐component sensing ensembles based on cationic NHBAs and an anionic fluorescent indicator 8‐hydroxypyrene‐1,3,6‐trisulfonic acid trisodium salt (HPTS) were successfully developed for both monosaccharides and disaccharides sensing. The dibranched ortho‐substituted receptor NHoBA exhibited unexpected selectivity towards lactose among five disaccharides used. The discrimination of five disaccharides and six monosaccharides was finally achieved by the integrated sensor array through linear discriminant analysis (LDA).     

Nanoscopic Visualization of Cross‐Linking Density in Polymer Networks with Diarylethene Photoswitches

The in situ nanoscopic imaging of soft matter polymer structures is of importance to gain knowledge of the relationship between structure, properties, and functionality on the nanoscopic scale. Cross‐linking of polymer chains effects the viscoelastic properties of gels. The correlation of mechanical properties with the distribution and amount of cross‐linkers is relevant for applications and for a detailed understanding of polymers on the molecular scale. We introduce a super‐resolution fluorescence‐microscopy‐based method for visualizing and quantifying cross‐linker points in polymer systems. A novel diarylethene‐based photoswitch with a highly fluorescent closed and a non‐fluorescent open form is used as a photoswitchable cross‐linker in a polymer network. As an example for its capability to nanoscopically visualize cross‐linking, we investigate pNIPAM microgels as a system known with variations in internal cross‐linking density.     

Array biosensor for detection of toxins

The array biosensor is capable of detecting multiple targets rapidly and simultaneously on the surface of a single waveguide. Sandwich and competitive fluoroimmunoassays have been developed to detect high and low molecular weight toxins, respectively, in complex samples. Recognition molecules (usually antibodies) were first immobilized in specific locations on the waveguide and the resultant patterned array was used to interrogate up to 12 different samples for the presence of multiple different analytes. Upon binding of a fluorescent analyte or fluorescent immunocomplex, the pattern of fluorescent spots was detected using a CCD camera. Automated image analysis was used to determine a mean fluorescence value for each assay spot and to subtract the local background signal. The location of the spot and its mean fluorescence value were used to determine the toxin identity and concentration. Toxins were measured in clinical fluids, environmental samples and foods, with minimal sample preparation. Results are shown for rapid analyses of staphylococcal enterotoxin B, ricin, cholera toxin, botulinum toxoids, trinitrotoluene, and the mycotoxin fumonisin. Toxins were detected at levels as low as 0.5 ng mL^–1.     

Design of a peptide linker group to increase the surface enhanced Raman spectroscopy signal intensity of a rhodamine-nanoparticle system

The surface enhanced resonance Raman spectra of three modified carboxy-x-rhodamine dyes were recorded using Au nanoparticles and an excitation laser operating at 670 nm. The dyes were modified with a linker group designed both to increase the surface enhanced Raman spectroscopy signal and to couple the dye to the Au nanoparticles surface. The maximum signal intensity was recorded for a Cys-Gly linker with Cys thiol group acting as the coupling point to the Au surface and Gly-NH₂ group used to attach the carboxy-x-rhodamine dye. This gave a signal intensity in the 1503 cm⁻¹ Raman peak that was more than 20 times greater than for the unmodified dye. The Au nanoparticles used had a diameter of 49.8 ± 1.2 nm and were synthesised by the citrate reduction method.     

可控异质不对称微粒的制备与组装

以聚合物薄膜作为掩模层来掩蔽有序的单层二氧化硅微粒阵列, 通过等离子体刻蚀控制二氧化硅微粒暴露面积, 并在其上进行可控的化学修饰或可控气相沉积, 利用异质区域选择性组装碲化镉荧光量子点, 得到了具有稳定荧光功能的异质不对称微粒. 利用此方法, 还可以通过引入官能团或粒子进一步得到更高级的多功能不对称微粒.     

Interaction of cyanine dyes with nucleic acids. XXV. Influence of affinity-modifying groups in the structure of benzothiazol-4-[2,6-dimethylpyridinium] dyes on the spectral properties of the dyes in the presence of nucleic acids.

Novel monomethine pyridinium cyanine dyes of similar structure and containing 'affinity-modifying' groups of different chemical nature were studied by spectral-luminescent methods as possible fluorescent probes for the nucleic acids detection. It was shown that the nature of the functional groups in the dye linker influences the fluorescent properties of the dye-nucleic acids complexes. Incorporation of a hydroxyl group into the linker structure leads to a significant increase in the fluorescence intensity of the dye--double-stranded DNA complexes relative to the parent dye Cyan 40.     

Versatile solid-phase synthesis of secondary amines from alcohols. Development of an N-Boc-(o-nitrobenzene)sulfonamide linker

The development of a versatile amine releasing linker based on the modified o-nitrobenzene sulfonamide protective group is described. This new N-Boc-o-nitrobenzenesulfonamide (Boc-ONBS) linker enables the elaboration on resin of primary and secondary amines by sequential substitution of the sulfonamide moiety using the Mitsunobu reaction. A 16-member array of secondary and Boc protected primary amines was then prepared using this linker.