Patterning of single-wall carbon nanotubes via a combined technique (chemical anchoring and photolithography) on patterned substrates

Single-walled carbon nanotubes (SWNTs) have been chemically attached with high density onto a patterned substrate. To form the SWNT pattern, the substrate was treated with acid-labile group protected amine, and an amine prepattern was formed using a photolithographic process with a novel polymeric photoacid generator (PAG). The polymeric PAG contains a triphenylsulfonium salt on its backbone and was synthesized to obtain a PAG with enhanced efficiency and ease of spin-coating onto the amine-modified glass substrate. The SWNT monolayer pattern was then formed through the amidation reaction between the carboxylic acid groups of carboxylated SWNTs (ca-SWNTs) and the prepatterned amino groups. A high-density multilayer was fabricated via further repeated reaction between the carboxylic acid groups of the ca-SWNTs and the amino groups of the linker with the aid of a condensation agent. The formation of covalent amide bonding was confirmed by X-ray photoelectron spectroscopy (XPS) analysis. Scanning electron microscopy and UV-vis-near-IR results show that the patterned SWNT films have uniform coverage with high surface density. Unlike previously reported patterned SWNT arrays, this ca-SWNT patterned layer has high surface density and excellent surface adhesion due to its direct chemical bonding to the substrate.     

UV cross-linking of unmodified DNA on glass surfaces

The performance of DNA microarrays strongly depends on their surface properties. Furthermore, the immobilization method of the capture molecules is of importance for the efficiency of the microarray in terms of sensitivity and specificity. This work describes the immobilization of single-stranded capture oligonucleotides by UV cross-linking on silanated (amino and epoxy) glass surfaces. Thereby we used amino (NH₂) and poly thymine/poly cytosine modifications of the capture sequences as well as unmodified capture molecules. The results were compared to UV cross-linking of the same DNA oligonucleotides on unmodified glass surfaces. Immobilization and hybridization efficiency was demonstrated by fluorescence and enzyme-induced deposition of silver nanoparticles. We found out that single-stranded DNA molecules do not require a special modification to immobilize them by UV cross-linking on epoxy- or amino-modified glass surfaces. However, higher binding rates can be achieved when using amino-modified oligonucleotides on an epoxy surface. The limit of detection for the used settings was 5 pM.     

Synthesis and Hybridization Properties of Oligodeoxynucleotides with Long‐Chain Linkers

New oligonucleotides with a long‐chain linker (6,9‐dioxa‐3,12‐diazatetradecane‐1,14‐diyl) in their backbone were synthesized, and their hybridization properties were studied by measurement of their T_m curves and fluorescence spectra. The T_m analyses revealed that these oligonucleotides could bind to their complementary strands despite the presence of the long‐chain linker. We also demonstrated interesting fluorescence properties of oligodeoxynucleotides with an anthracen‐9‐ylmethyl group on one of the two N‐atoms in the long‐chain linker. The fluorescence intensity of these oligonucleotides increased upon their hybridization to the complementary strands and was sensitive to the presence of the mismatch base pairs at a specific position.     

Novel polymeric platform produced by photodegradation-induced rearrangement for a multifunctional negative photoresist

Herein, a series of polymers containing the photosensitive 2-dinitro-benzenemethanol carbonate (DNBC) was developed by click polymerization. Due to the unique photochemical cleavage recombination behavior of DNBC, these polymers were used as negative photoresists to create micropatterns. Furthermore, the photochemical behaviors of DNBC were studied by nuclear magnetic resonance (NMR) and high performance liquid chromatography (HPLC). According the results, we speculated that the photochemical reaction of DNBC involved an initial chemical bond-breaking process and a subsequent recombination process. Importantly, by extending the aldehyde to a branched-chain structure, reactive patterns were developed by film preparation. Clickable amine functional molecules could be grafted upon the substrates by surface modification. Surface modification of reactive patterns with fluorescent amines gave a multifunctional pattern with tunable properties confirmed by scanning electron microscopy (SEM) and confocal fluorescence microscopy.     

Photochemical modification and patterning of polymer surfaces by surface adsorption of photoactive block copolymers

We report a simple photolithographic approach for the creation and micropatterning of chemical functionality on polymer surfaces by use of surface-active block copolymers that contain protected photoactive functional groups. The block copolymers self-assemble at the substrate-air interface to generate a surface that is initially hydrophobic with low surface tension but that can be rendered hydrophilic and functional by photodeprotection with UV radiation. The block copolymer employed, poly(styrene-b-tert butyl acrylate), segregates preferentially to the surface of a polystyrene substrate because of the low surface tension of the polyacrylate blocks. The strong adsorption of block copolymers causes a bilayer structure to form presenting a photoactive polyacrylate layer at the surface. In the example described, the tert-butyl ester groups on the polyacrylate blocks are deprotected by exposure to UV radiation in the presence of added photoacid generators to form surface carboxylic acid groups. Surface micropatterns of carboxylic acid groups are generated by UV exposure through a contact mask. The success of surface chemical modification and pattern formation is demonstrated by X-ray photoelectron spectroscopy and contact angle measurements along with imaging by optical and fluorescence microscopy methods. The resultant chemically patterned surfaces are then used to template patterns of various biomolecules by means of selective adsorption, covalent bonding and molecular recognition mechanisms. The surface modification/patterning concept can be applied to virtually any polymeric substrate because protected functional groups have intrinsically low surface tensions, rendering properly designed block copolymers surface active in almost all polymeric substrates.     

Novel Method for Preparation of Monoesters of Symmetric Diphenolic Compounds like Curcumin (1,7‐Bis(4‐hydroxy‐3‐methoxy phenyl)‐1,6‐heptadiene‐3,5‐dione) via Solid‐Phase Synthesis

Synthesis of a monoester of symmetrical diphenolic compound curcumin (1,7‐bis(4‐hydroxy‐3‐methoxy phenyl)‐1,6‐heptadiene‐3,5‐dione) with glycine has been carried out by anchoring one of its free phenolic groups to an insoluble polymeric solid‐support resin controlled pore glass‐long chain alkylamine (CPG‐LCAA) via a 2‐carbon linker by solid‐phase synthesis. The other free phenolic was esterified selectively with N‐protected glycinoyl chloride to give the monoester exclusively. Subsequent deprotection of the amino group and deblocking of the monoester from polymer support by treatment with hydriodic acid (HI) gave the desired product. We earlier reported synthesis of a large number of diesters of curcumin, but selective esterification of one phenolic has been accomplished by this novel method, which can be used for preparing monoesters of any symmetric diphenol in quantitative yields.     

Triplet‐Sensitized Photodeprotection of Oligonucleotides in Solution and on Microarray Chips

Conditions and kinetics of triplet sensitization as a method for increasing the light sensitivity of photolabile protecting groups used for the photolithographic synthesis of oligonucleotide microarrays were quantitatively studied with the photolabile 2‐(2‐nitrophenyl)propyl protecting group in homogeneous solutions and on glass substrates by using laser flash photolysis, continuous illumination with HPLC analysis, fluorescence dye labelling, and hybridization. In terms of efficiency and avoidance of chemical side reactions, 9H‐thioxanthen‐9‐one was the most‐suitable sensitizer. Both in solution and on a glass substrate, the photostationary kinetics were quantitatively modelled and the relevant kinetic parameters determined. While the sensitization kinetics was diffusion‐controlled both in solution and on the chip, the photostationary kinetics was essentially of zero order only on the chip because here the triplet‐quenching effect of the released photoproduct 2‐(2‐nitrophenyl)propene was suppressed as a consequence of the inhomogeneous reaction that took place in a narrow diffusion zone above the surface from where the photoproducts could quickly escape. The kinetic simulation allowed quantitative estimate of the density of reactive groups on the surface. It was further demonstrated that, with 9H‐thioxanthen‐9‐one as a sensitizer, high‐density oligonucleotide microarrays of high quality can be produced with one‐third of the normal exposure time.     

Inside/Outside: Post-Synthetic Modification of the Zr-Benzophenonedicarboxylate Metal–Organic Framework

The Zr-based metal–organic framework, Zr-bzpdc-MOF, contains the photoreactive linker molecule benzophenone-4,4′-dicarboxylate (bzpdc) which imparts the possibility for photochemical post-synthetic modification. Upon irradiation with UV light, the keto group of the benzophenone moiety will react with nearly every C−H bond-containing molecule. Within this paper, we further explore the photochemical reactivity of the Zr-bzpdc-MOF, especially with regard to which restrictions govern internal versus external reactions. We show that apart from reactions with C−H bond-containing molecules, the MOF reacts also with water. By studying the reactivity versus linear alcohols we find a clear delineation in that shorter alcohol molecules (up to butanol as a borderline case) react with photoexcited keto groups throughout the whole crystals whereas longer ones react only with surface-standing keto groups. In addition, we show that with the alkanes n-butane to n-octane, the reaction is restricted to the outer surface. We hypothesize that the reactivity of the Zr-bzpdc-MOF versus different reagents depends on the accessibility of the pore system which in turn depends mainly on the size of the reagents and on their polarity. The possibility to direct the post-synthetic modification of the Zr-bzpdc-MOF (selective modification of the whole pore system versus surface modification) gives additional degrees of freedom in the design of this metal–organic framework for shaping and for applications.     

Photochemical functionalization of gallium nitride thin films with molecular and biomolecular layers

We demonstrate that photochemical functionalization can be used to functionalize and photopattern the surface of gallium nitride crystalline thin films with well-defined molecular and biomolecular layers. GaN(0001) surfaces exposed to a hydrogen plasma will react with organic molecules bearing an alkene (C=C) group when illuminated with 254 nm light. Using a bifunctional molecule with an alkene group at one end and a protected amine group at the other, this process can be used to link the alkene group to the surface, leaving the protected amine exposed. Using a simple contact mask, we demonstrate the ability to directly pattern the spatial distribution of these protected amine groups on the surface with a lateral resolution of <12 mum. After deprotection of the amines, single-stranded DNA oligonucleotides were linked to the surface using a bifunctional cross-linker. Measurements using fluorescently labeled complementary and noncomplementary sequences show that the DNA-modified GaN surfaces exhibit excellent selectivity, while repeated cycles of hybridization and denaturation in urea show good stability. These results demonstrate that photochemical functionalization can be used as an attractive starting point for interfacing molecular and biomolecular systems with GaN and other compound semiconductors.     

Stereoselective Photopolymerization of Tetraphenylporphyrin Derivatives on Ag(110) at the Sub‐Monolayer Level

We explore a photochemical approach to achieve an ordered polymeric structure at the sub‐monolayer level on a metal substrate. In particular, a tetraphenylporphyrin derivative carrying para‐amino‐phenyl functional groups is used to obtain extended and highly ordered molecular wires on Ag(110). Scanning tunneling microscopy and density functional theory calculations reveal that porphyrin building blocks are joined through azo bridges, mainly as cis isomers. The observed highly stereoselective growth is the result of adsorbate/surface interactions, as indicated by X‐ray photoelectron spectroscopy. At variance with previous studies, we tailor the formation of long‐range ordered structures by the separate control of the surface molecular diffusion through sample heating, and of the reaction initiation through light absorption. This previously unreported approach shows that the photo‐induced covalent stabilization of self‐assembled molecular monolayers to obtain highly ordered surface covalent organic frameworks is viable by a careful choice of the precursors and reaction conditions.     

Switch‐On Fluorescence of a Perylene‐Dye‐Functionalized Metal–Organic Framework through Postsynthetic Modification

A perylene dye was introduced directly as a linker into a metal–organic framework (MOF) during synthesis. Depending on the dye concentration in the MOF synthesis mixture, different fluorescent materials were generated. The successful incorporation of the dye was proven by using ¹³C and ²⁷Al MAS NMR spectroscopy, by solution NMR spectroscopy after digestion of the MOF sample, and by synthesizing a reference dye without connecting groups, which could coordinate on the metal–oxo cluster inside the MOF. Fluorescence quenching effects of the MOF linker, 2‐aminoterephthalate, were observed and overcome by postsynthetic modification with acetic anhydride. We show here for the first time that amino groups, which can be used as anchoring points for covalent attachment of other molecules, are responsible for fluorescence quenching. Thus, a very promising strategy to implement switchable fluorescence into MOFs is shown here.     

Surface modified microarray chip and laser induced fluorescence microscopy to detect DNA cleavage

This work describes a quantitative method to detect DNA damage in the presence of Pb and Cd ions using a surface modified microarray chip and a laser induced fluorescence microscopy (LIFM). The detection was carried out by the immobilization of a single-stranded DNA oligomer, tagged with a Cy5 fluorophore on a polydimethylsiloxane (PDMS) microarray chip followed by LIFM. Sulfosuccinimidyl-4-(N-maleimidomethyl) cyclohexane-1-carboxylate (Sulfo-SMCC) was attached as a cross-linker via the formation of covalent amide bonds. Then, the single-stranded DNA oligomer containing Cy5 as a fluorophore and thiol functional groups at both terminals, was bonded to the linker by reaction with sulfhydryl group. As the DNA oligomers were reacted with metal ions of Pb and Cd, the un-cleaved DNA oligomers were quantitatively identified by monitoring Cy5 fluorescence. Cadmium showed a quenching constant of 0.84 in the Stern–Volmer plot, whereas lead gave 0.22, indicating that cadmium ions suppress fluorescence more than lead ions. When optimized, fluorescence reductions of 23% (± 2.1) for Pb and 25% (± 1.4) for Cd were observed in air and decreased to almost < 5.0% in a radical scavenger of 5 mM. The cleaved DNA was also confirmed by MALDI-TOF-MS. In result, this experimental method using a microarray chip with surface modification provided quantitative determination of DNA oligomer damage with reproducible results, significantly reduced sample volumes and analysis times.     

Synthesis of Oligonucleotides Carrying Anchoring Groups and Their Use in the Preparation of Oligonucleotide–Gold Conjugates

Oligodeoxynucleotide conjugates 1 – 15 carrying anchoring groups such as amino, thiol, pyrrole, and carboxy groups were prepared. A post‐synthetic modification protocol was developed. In this method 2′‐deoxy‐O⁴‐(p‐nitrophenyl)uridine‐3‐phosphoramidite was prepared and incorporated in oligonucleotides. After assembly, the modified nucleoside was made to react with different amines carrying the anchoring groups. At the same time, protecting groups were removed to yield the desired oligonucleotide conjugates. In a second approach, amino, thiol, and carboxylic groups were introduced into the 3′‐end of the oligonucleotides by preparing solid supports loaded with the appropriate amino acids. Oligonucleotide gold conjugates were prepared and their binding properties were examined.     

Structural characterization of organic multilayers on silicon(111) formed by immobilization of molecular films on functionalized Si-C linked monolayers

Silicon(111)-H surfaces were derivatized with omega-functionalized alkenes in UV-mediated and thermal hydrosilylation reactions to give Si-C linked monolayers. Additional molecular layers of organic compounds were coupled either directly or via linker molecules to the functionalized alkyl monolayers. In the first instance, amino-terminated monolayers were prepared from a tert-butoxycarbonyl-protected omega-aminoalkene followed by removal of the protecting group. Various thiols were coupled to the monolayer using a heterobifunctional linker, which introduced maleimide groups onto the surface. In the second system, N-hydroxysuccinimide (NHS) ester-terminated monolayers were formed by reaction of Si-H with N-succinimidyl undecenoate. The reactivity of the NHS ester groups was confirmed by further modification of the monolayer. The stepwise assembly of these multilayer structures was characterized by X-ray reflectometry and X-ray photoelectron spectroscopy.     

Chimeric RNA Oligonucleotides with Triazole and Phosphate Linkages: Synthesis and RNA Interference

Chimeric RNA oligonucleotides with an artificial triazole linker were synthesized using solution‐phase click chemistry and solid‐phase automated synthesis. Scalable synthesis methods for jointing units for the chimeric structure have been developed, and after click‐coupling of the jointing units with triazole linkers, a series of chimeric oligonucleotides was prepared by utilizing the well‐established phosphoramidite method for the elongation. The series of chimeric 21‐mer oligonucleotides that possessed the triazole linker at different strands and positions allowed for a screening study of the RNA interference to clarify the preference of the triazole modifications in small‐interfering RNA molecules.     

Covalent Assembly of Hierarchical Particles by Efficient Coupling of β‐Diketones and Benzyl Chloride

A coupling reaction is performed between polymeric nanoparticles and microparticles via the nucleophilic substitution of pendent β‐diketone groups with benzyl chloride. The coupling reaction results in the formation of hierarchical particles, through the nanoparticles being covalently linked onto the microparticles. The coupling reaction is tracked by TEM and SEM, and the formation of covalent C–C bonds through the coupling reaction between the polymeric nanoparticles and microparticles is confirmed by solid‐state ¹³C CP‐MAS NMR spectroscopy and XPS. The proposed coupling reaction between the nanoparticles and the microparticles is believed to be a promising strategy in particle‐surface modification.     

Development of a photolabile carbonyl-protecting group toolbox

New salicyl alcohol derived photolabile carbonyl protecting groups have been developed, and the effect of substituents on the photochemical properties of photolabile protecting groups (PPGs) has been studied. The 3-(dimethylamino)phenyl groups at the α position prove to be important to the efficiency of the deprotection reactions, as shown in the photo reactions of the acetal 9. On the other hand, expansion of the salicyl alcohol's benzene skeleton to naphthalene does not improve the photochemical properties of PPGs. A neutral protecting protocol has been generalized to new PPGs with α,α-diaryl salicyl alcohol backbone. Thus, installation of PPGs onto aldehydes is readily achieved at 140 °C without using any other chemical reagents. These PPGs are stable under acidic conditions typical for hydrolyzing acetals and constitute orthogonal protecting groups with traditional 1,3-dioxane/1,3-dioxolane for carbonyl compounds. Highly efficient release of carbohydrate molecules is demonstrated, which can be potentially useful in site-specific release and immobilization of carbohydrates for preparation of high-density microarrays. With the enriched PPG toolbox, PPGs are divided into three subgroups based on their UV absorption profiles. PPGs from different subgroups can be sequentially removed by using different UV irradiation wavelengths. For PPGs absorbing UVA (λ >315 nm), photochemical deprotection can be carried out with sunlight in high yields.     

Cation exchange/hydrophobic interaction monolithic chromatography of small molecules and proteins by nano liquid chromatography†

In this study, vinyl phenyl boronic acid modified lauryl methacrylate‐based monolithic column was successfully prepared for cation exchange/hydrophobic interaction monolithic chromatography of small molecules and proteins in nano LC. The polymeric mixture consisted of lauryl methacrylate, vinyl phenyl boronic acid as cation exchanger, ethylene dimethacrylate as cross‐linker, polyethylene glycol and methanol as binary porogenic solvent, and azobisisobutyronitrile as initiator. The resulting monolith showed good permeability and mechanical stability. Different ratios of monomer and porogens were used for optimizing the properties of the column. The monolithic column performance with respect to hydrophobic and cation exchange interactions was assessed by the separation a series of alkyl benzenes and anilines, respectively. cis‐Diol‐containing compounds such as phenols were also utilized to evaluate the retention behaviors of the vinyl phenyl boronic acid modified monolithic column. The monolithic column showed cation exchange interactions in the separation of aniline compounds. Theoretical plate number up to 52 000 plates/m was successfully achieved. The prepared monolith was further applied to the proteins with different acetonitrile content.     

Integrated surface modification of fully polymeric microfluidic devices using living radical photopolymerization chemistry

Surface modification using living radical polymerization (LRP) chemistry is a powerful technique for surface modification of polymeric substrates. This research demonstrates the ability to use LRP as a polymer substrate surface‐modification platform for covalently grafting polymer chains in a spatially and temporally controlled fashion. Specifically, dithiocarbamate functionalities are introduced onto polymer surfaces using tetraethylthiuram disulfide. This technique enables integration of LRP‐based grafting for the development of an integrated, covalent surface‐modification method for microfluidic device construction. The unique photolithographic method enables construction of devices that are not substrate‐limited. To demonstrate the utility of this approach, both controlled fluid flow and cell patterning applications were demonstrated upon modification with various chemical functionalities. Specifically, poly(ethylene glycol) (375) monoacrylate and trifluoroethyl acrylate were grafted to control fluidic flow on a microfluidic device. Before patterning, surface‐functionalized samples were characterized with both goniometric and infrared spectroscopy to ensure that photografting was occurring through pendant dithiocarbamate functionalities. Near‐infrared results demonstrated conversion of grafted monomers when dithiocarbamate‐functionalized surfaces were used, as compared to dormant control surfaces. Furthermore, attenuated total reflectance/infrared spectroscopy results verified the presence of dithiocarbamate functionalities on the substrate surfaces, which were useful in grafting chains of various functionalities whose contact angles ranged from 7 to 86°. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 1404–1413, 2006     

Micropatterning of cell-repellent polymer on a glass substrate for the highly resolved virus microarray

The development of a simple and easily accessible method to control cellular behavior under a spatially controlled surface is critical for fundamental studies in biotechnology. We fabricated a microarray of Spodoptera frugiperda 9 (Sf9) cells on a glass surface by microcontact printing cell-repellent polymeric molecules of poly(ethylene glycol)-branched-poly(methyl methacrylate) as a template for cell micropatterning. The polymer micropatterns enabled the stable confinement of Sf9 cells on the surface, resulting in the formation of a cell microarray. Subsequently, the patterned Sf9 cells were infected with recombinant baculovirus modified with green fluorescent protein (GFP) to form a virus microarray, and GFP expression in the virus microarray was verified with confocal fluorescence microscopy.