Protein recording material: photorecord/erasable protein array using a UV-eliminative linker

Protein patterning on solid surfaces is a topic of significant importance in the fields of biosensors, diagnostic assays, cell adhesion technologies, and biochip microarrays. In this letter, we have established a novel, rapid method for the fabrication of a "protein recording material", which enables us to spatiotemporally regulate the recording, reading, and erasing of a fluorescent protein array as information by a photochemical technique. A photolinker that we synthesized here was used to control the protein array spatiotemporally. The recording process was almost completed after 1 min of photoirradiation to read a clear pattern consisting of a specific protein-ligand complex with high spatiotemporal resolution. The erasing of the protein array was then achieved by photoirradiation onto the entire patterned surface.     

Micro patterning of active proteins with perforated PDMS sheets (PDMS sieve)

We propose a novel technique for patterning active proteins on a glass substrate using a perforated polydimethylsiloxane (PDMS) sheet-sieve. The sieve, which has tapering holes, is fabricated by spin-coating PDMS on a pyramidal-shaped mold. By means of this sieve, FITC (fluorescent isothiocyanate, bovine)-albumin was successfully spotted in a 5 x 5 microm(2) area in an array. The patterned spots were perfectly isolated, which eliminates the problem of non-specific binding of proteins to undesired areas. To show that proteins maintained their activity after the patterning, we used F(1)-ATPase biomolecular motors; their activity can easily be verified by observing their rotary motion after patterning. Selective patterning with three kinds of fluorescent micro beads indicated the possibility of patterning of different proteins on the same substrate by using the sieve.     

New reactions, functional compounds, and materials in the series of coumarin and its analogs

Data on the development of new functional compounds and materials based on the study of the reactions of coumarin and its analogs are generalized. Since coumarin derivatives are characterized by enhanced photochemically activity, special attention is given to the synthesis of photosensitive compounds and materials with intense fluorescence, including the structures capable of changing fluorescence under the action of various factors: solvent, pH of the medium, and interaction with bioorganic substrates. Pathways for design of fluorescent polymethine dyes, fluorescent labels for proteins, fluorescent photochromes, and photoacids for optical data storage with fluorescence read-out are reviewed. The role of isomerization transformations of the new compounds in their sensorial effects is established.     

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.     

Optical technologies for the read out and quality control of DNA and protein microarrays

Microarray formats have become an important tool for parallel (or multiplexed) monitoring of biomolecular interactions. Surface-immobilized probes like oligonucleotides, cDNA, proteins, or antibodies can be used for the screening of their complementary targets, covering different applications like gene or protein expression profiling, analysis of point mutations, or immunodiagnostics. Numerous reviews have appeared on this topic in recent years, documenting the intriguing progress of these miniaturized assay formats. Most of them highlight all aspects of microarray preparation, surface chemistry, and patterning, and try to give a systematic survey of the different kinds of applications of this new technique. This review places the emphasis on optical technologies for microarray analysis. As the fluorescent read out of microarrays is dominating the field, this topic will be the focus of the review. Basic principles of labeling and signal amplification techniques will be introduced. Recent developments in total internal reflection fluorescence, resonance energy transfer assays, and time-resolved imaging are addressed, as well as non-fluorescent imaging methods. Finally, some label-free detection modes are discussed, such as surface plasmon microscopy or ellipsometry, since these are particularly interesting for microarray development and quality control purposes.     

Conversion of the monomeric red fluorescent protein into a photoactivatable probe

Photoactivatable fluorescent proteins bring new dimension to the analysis of protein dynamics in the cell. Protein tagged with a photoactivatable label can be visualized and tracked in a spatially and temporally defined manner. Here, we describe a basic rational design strategy to develop monomeric photoactivatable proteins using site-specific mutagenesis of common monomeric red-shifted fluorescent proteins. This strategy was applied to mRFP1, which was converted into probes that are photoactivated by either green or violet light. The latter photoactivatable variants, named PA-mRFP1s, exhibited a 70-fold increase of fluorescence intensity resulting from the photoconversion of a violet-light-absorbing precursor. Detailed characterization of PA-mRFP1s was performed with the purified proteins and the proteins expressed in mammalian cells where the photoactivatable properties were preserved. PA-mRFP1s were used as protein tags to study the intracellular dynamics of GTPase Rab5.     

Background-free, high sensitivity staining of proteins in one- and two-dimensional sodium dodecyl sulfate-polyacrylamide gels using a luminescent ruthenium complex

SYPRO Ruby dye is a permanent stain comprised of ruthenium as part of an organic complex that interacts noncovalently with proteins. SYPRO Ruby Protein Gel Stain provides a sensitive, gentle, fluorescence-based method for detecting proteins in one-dimensional and two-dimensional sodium dodecyl sulfate-polyacrylamide gels. Proteins are fixed, stained from 3h to overnight and then rinsed in deionized water or dilute methanol/acetic acid solution for 30 min. The stain can be visualized using a wide range of excitation sources commonly used in image analysis systems including a 302 nm UV-B transilluminator, 473 nm second harmonic generation (SHG) laser, 488 nm argon-ion laser, 532 nm yttrium-aluminum-garnet (YAG) laser, xenon arc lamp, blue fluorescent light bulb or blue light-emitting diode (LED). The sensitivity of SYPRO Ruby Protein Gel Stain is superior to colloidal Coomassie Brilliant Blue (CBB) stain or monobromobimane labeling and comparable with the highest sensitivity silver or zinc-imidazole staining procedures available. The linear dynamic range of SYPRO Ruby Protein Gel stain extends over three orders of magnitude, which is vastly superior to silver, zinc-imidazole, monobromobimane and CBB stain. The fluorescent stain does not contain superfluous chemicals (formaldehyde, glutaraldehyde, Tween-20) that frequently interfere with peptide identification in mass spectrometry. While peptide mass profiles are severely altered in protein samples prelabeled with monobromobimane, successful identification of proteins by peptide mass profiling using matrix-assisted laser desorption/ionization mass spectrometry was easily performed after protein detection with SYPRO Ruby Protein Gel stain.     

Designing Silicates as Deep‐UV Nonlinear Optical (NLO) Materials using Edge‐Sharing Tetrahedra

Discovering new deep‐ultraviolet (DUV) nonlinear optical (NLO) materials is currently a great challenge. The reported DUV NLO materials are almost exclusively borates or phosphates. Silicates—the largest constituent of the earth's crust—are excluded owing to their weak second harmonic generation (SHG) response. We report a silicate, Li₂BaSiO₄, with edge‐sharing LiO₄–SiO₄ tetrahedra that achieves the balance between a short UV absorption edge, below 190 nm, and a large SHG response, 2.8×KDP. The SHG intensity is the largest for silicates without second‐order Jahn–Teller cations, and exceeds that of non‐isomorphic Li₂SrSiO₄ by more than an order of magnitude. As such Li₂BaSiO₄ may be seen as a promising DUV‐UV NLO material. This research indicates that edge‐sharing tetrahedra is a new design parameter for discovering new DUV NLO materials.     

Patterned surface derivatization using Diels-Alder photoclick reaction

The utility of photochemically induced hetero-Diels-Alder reaction for the light-directed surface derivatization and patterning was demonstrated. Glass slides functionalized with vinyl ether moieties are covered with aqueous solution of substrates conjugated to 3-(hydroxymethyl)-2-naphthol (NQMP). Subsequent irradiation via shadow mask results in an efficient conversion of the latter functionality into reactive 2-napthoquinone-3-methide (oNQM) in the exposed areas. oNQM undergoes very facile hetero Diels-Alder addition (k(D-A) ≈ 4 × 10(4) M(-1)s(-1)) to immobilized vinyl ether molecules resulting in a photochemically stable covalent link between a substrate and a surface. Unreacted oNQM groups are rapidly hydrated to regenerate NQMP. The click chemistry based on the addition of photochemically generated oNQM to vinyl ether works well in aqueous solution, proceeds at high rate under ambient conditions, and does not require catalyst or additional reagents. This photoclick strategy represents an unusual paradigm in photopatterning: the surface itself is photochemically inert, while photoreactive component is present in the solution. The short lifetime (τ ≈ 7 ms in H(2)O) of the active form of a photoclick reagent in aqueous solution prevents its migration from the site of irradiation, thus allowing for the spatial control of surface derivatization. Both o-napthoquinone methide precursors and vinyl ethers are stable in dark and the reaction is orthogonal to other derivatization techniques, such as acetylene-azide click reaction.     

Designing Silicates as Deep-UV Nonlinear Optical (NLO) Materials using Edge-Sharing Tetrahedra

Discovering new deep-ultraviolet (DUV) nonlinear optical (NLO) materials is currently a great challenge. The reported DUV NLO materials are almost exclusively borates or phosphates. Silicates—the largest constituent of the earth's crust—are excluded owing to their weak second harmonic generation (SHG) response. We report a silicate, Li₂BaSiO₄, with edge-sharing LiO₄–SiO₄ tetrahedra that achieves the balance between a short UV absorption edge, below 190 nm, and a large SHG response, 2.8×KDP. The SHG intensity is the largest for silicates without second-order Jahn–Teller cations, and exceeds that of non-isomorphic Li₂SrSiO₄ by more than an order of magnitude. As such Li₂BaSiO₄ may be seen as a promising DUV-UV NLO material. This research indicates that edge-sharing tetrahedra is a new design parameter for discovering new DUV NLO materials.     

NH4Be2BO3F2 and γ‐Be2BO3F: Overcoming the Layering Habit in KBe2BO3F2 for the Next‐Generation Deep‐Ultraviolet Nonlinear Optical Materials

KBe₂BO₃F₂ (KBBF) is still the only practically usable crystal that can generate deep‐ultraviolet (DUV) coherent light by direct second harmonic generation (SHG). However, applications are hindered by layering, leading to difficulty in the growth of thick crystals and compromised mechanical integrity. Despite efforts, it is still a great challenge to discover new nonlinear optical (NLO) materials that overcome the layering while keeping the DUV SHG available. Now, two new DUV NLO beryllium borates have been successfully designed and synthesized, NH₄Be₂BO₃F₂ (ABBF) and γ‐Be₂BO₃F (γ‐BBF), which not only overcome the layering but also can be used as next‐generation DUV NLO materials with the shortest type I phase‐matching second‐harmonic wavelength down to 173.9 nm and 146 nm, respectively. Significantly, γ‐BBF is superior to KBBF in all metrics and would be the most outstanding DUV NLO crystal.     

Surface patterning by microcontact chemistry

In this Feature Article we describe recent progress in covalent surface patterning by microcontact chemistry. Microcontact chemistry is a variation of microcontact printing based on the transfer of reactive "ink" molecules from a microstructured, elastomeric stamp onto surfaces modified with complementary reactive groups, leading to a chemical reaction in the area of contact. In comparison with other lithographic methods, microcontact chemistry has a number of advantageous properties including very short patterning times, low consumption of ink molecules, high resolution and large area patterning. During the past 5 years we and many others have investigated a set of different reactions that allow the modification of flat and also spherical surfaces in an effective way. Especially click-type reactions were found to be versatile for substrate patterning by microcontact chemistry and were applied for chemical modification of reactive self-assembled monolayers and polymer surfaces. Microcontact chemistry has already found broad application for the production of functional surfaces and was also used for the preparation of DNA, RNA, and carbohydrate microarrays, for the immobilization of proteins and cells and for the development of sensors.     

Protein microarrays: prospects and problems

Protein microarrays are potentially powerful tools in biochemistry and molecular biology. Two types of protein microarrays are defined. One, termed a protein function array, will consist of thousands of native proteins immobilized in a defined pattern. Such arrays can be utilized for massively parallel testing of protein function, hence the name. The other type is termed a protein-detecting array. This will consist of large numbers of arrayed protein-binding agents. These arrays will allow for expression profiling to be done at the protein level. In this article, some of the major technological challenges to the development of protein arrays are discussed, along with potential solutions.     

A robust small-molecule microarray platform for screening cell lysates

Herein we report the expanded functional group compatibility of small-molecule microarrays to include immobilization of primary alcohols, secondary alcohols, phenols, carboxylic acids, hydroxamic acids, thiols, and amines on a single slide surface. Small-molecule "diversity microarrays" containing nearly 10,000 known bioactive small molecules, natural products, and small molecules originating from several diversity-oriented syntheses were produced by using an isocyanate-mediated covalent capture strategy. Selected printed bioactive compounds were detected with antibodies against compounds of interest. The new surface of the diversity microarrays is highly compatible with approaches involving cellular lysates. This feature has enabled a robust, optimized screening methodology using cellular lysates, allowing the detection of specific interactions with a broad range of binding affinity by using epitope-tagged or chimeric fluorescent proteins without prior purification. We believe that this expanded research capability has considerable promise in biology and medicine.     

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.     

Facile preparation of carbohydrate microarrays by site-specific, covalent immobilization of unmodified carbohydrates on hydrazide-coated glass slides

[reaction: see text] A new, simple and efficient immobilization method to attach mono-, di-, oligo-, and polysaccharides to hydrazide-coated glass slides was developed. Protein and cell-binding experiments show that the carbohydrate microarrays prepared by this method are applicable for the rapid analysis of protein-carbohydrate interactions and fast detection of pathogens.     

New photoactivators for multiphoton excited three-dimensional submicron cross-linking of proteins: bovine serum albumin and type 1 collagen

We report the synthesis and optical characterization of two new photoactivators and demonstrate their use for multiphoton excited three-dimensional free-form fabrication with proteins. These reagents were developed with the goal of cross-linking Type 1 collagen. This cross-linking process produces structures on the micron and submicron size scales. A rose bengal diisopropyl amine derivative combines the classic photoactivator and co-initiator system into one molecule, reducing the reaction kinetics and increasing cross-linking efficiency. This derivative was successful at producing stable structures from collagen, whereas rose bengal alone was not effective. A benzophenone dimer connected by a flexible diamine tether was also synthesized. This activator has two photochemically reactive groups and is highly efficient in cross-linking bovine serum albumin and Type 1 collagen to form stable, robust structures. This approach is more flexible in terms of cross-linking a variety of proteins than by traditional benzophenone photochemistry. The photophysical properties vary greatly from that of benzophenone, with the appearance of a new, lower energy absorption band (lambda max approximately 370 nm in water) and broad, visible emission band (approximately 500 nm maximum). This absorption band is highly solvatochromic, suggesting it arises, at least in part, from a charge transfer interaction. Collagens are typically difficult to cross-link photochemically, and the results here suggest that these two new activators will be suitable for cross-linking other forms of collagen and additional proteins for biomedical applications such as the de novo assembly of biomimetic tissue scaffolds.