In situ Synthesis of Oligonucleotide Arrays on Surfaces Coated with Crosslinked Polymer Multilayers

Nonaqueous Oxidation in DNA Microarray Synthesis Improves the Oligonucleotide Quality and Preserves Surface Integrity on Gold and Indium Tin Oxide Substrates

Nucleic acids attached to electrically conductive surfaces are very frequently used platforms for sensing and analyte detection as well as for imaging. Synthesizing DNA on these uncommon substrates and preserving the conductive layer is challenging as this coating tends to be damaged by the repeated use of iodine and water, which is the standard oxidizing medium following phosphoramidite coupling. Here, we thoroughly investigate the use of camphorsulfonyl oxaziridine (CSO), a nonaqueous alternative to I2/H2O, for the synthesis of DNA microarrays in situ. We find that CSO performs equally well in producing high hybridization signals on glass microscope slides, and CSO also protects the conductive layer on gold and indium tin oxide (ITO)-coated slides. DNA synthesis on conductive substrates with CSO oxidation yields microarrays of quality approaching that of conventional glass with intact physicochemical properties.

Dipodal Silanes Greatly Stabilize Glass Surface Functionalization for DNA Microarray Synthesis and High-Throughput Biological Assays

Glass is by far the most common substrate for biomolecular arrays, including high-throughput sequencing flow cells and microarrays. The native glass hydroxyl surface is modified by using silane chemistry to provide appropriate functional groups and reactivities for either in situ synthesis or surface immobilization of biologically or chemically synthesized biomolecules. These arrays, typically of oligonucleotides or peptides, are then subjected to long incubation times in warm aqueous buffers prior to fluorescence readout. Under these conditions, the siloxy bonds to the glass are susceptible to hydrolysis, resulting in significant loss of biomolecules and concomitant loss of signal from the assay. Here, we demonstrate that functionalization of glass surfaces with dipodal silanes results in greatly improved stability compared to equivalent functionalization with standard monopodal silanes. Using photolithographic in situ synthesis of DNA, we show that dipodal silanes are compatible with phosphoramidite chemistry and that hybridization performed on the resulting arrays provides greatly improved signal and signal-to-noise ratios compared with surfaces functionalized with monopodal silanes.

The synthesis of a chemically reactive and polymeric luminescent gel

In the past, chemically reactive polymeric interfaces have been considered to be of potential interest for developing functional materials for a wide range of practical applications. Furthermore, the rational incorporation of luminescence properties into such chemically reactive interfaces could provide a basis for extending the horizon of their prospective utility. In this report, a simple catalyst-free chemical approach is introduced to develop a chemically reactive and optically active polymeric gel. Branched-polyethyleneimine (BPEI)-derived, inherently luminescent carbon dots (BPEI-CDs) were covalently crosslinked with pentaacrylate (5Acl) through a 1,4-conjugate addition reaction under ambient conditions. The synthesized polymeric gel was milky white under visible light; however, it displayed fluorescence under UV light. Additionally, the residual acrylate groups in the synthesized fluorescent gel allowed its chemical functionality to be tailored through facile, robust 1,4-conjugate addition reactions with primary-amine-containing small molecules under ambient conditions. The chemical reactivity of the luminescent gel was further employed for a proof-of-concept demonstration of portable and parallel 'ON'/'OFF' toxic chemical sensing (namely, the sensing of nitrite ions as a model analyte). First, the chemically reactive luminescent gel derived from BPEI-CDs was covalently post-modified with aniline for the selective synthesis of a diazo compound in the presence of nitrite ions. During this process, the color of the gel under visible light changed from white to yellow and, thus, the colorimetric mode of the sensor was turned 'ON'. In parallel, the luminescence of the gel under UV light was quenched, which was denoted as the 'OFF' mode of the sensor. This parallel and unambiguous 'ON'/'OFF' sensing of a toxic chemical (nitrite ions, with a detection limit of 3 μM) was also achieved even in presence of other relevant interfering ions and at concentrations well below the permissible limit (65 μM) set by the World Health Organization (WHO). Furthermore, this chemically reactive luminescent gel could be of potential interest in a wide range of basic and applied contexts.

Preparation of Polymeric Films of PVDMA-PEI Functionalized with Fatty Acids for Studying the Adherence and Proliferation of Langerhans β-Cells

This study reports the synthesis of thin polymeric films by the layer-by-layer deposition and covalent cross-linking of polyvinyl dimethylazlactone and polyethylene imine, which were functionalized with lauric (12-C), myristic (14-C), and palmitic (16-C) saturated fatty acids, whose high levels in the bloodstream are correlated with insulin resistance and the potential development of type 2 diabetes mellitus. Aiming to assess the effect of the fatty acids on the adhesion and proliferation of Langerhans β-cells, all prepared films (35 and 35.5 bilayers with and without functionalization with the fatty acids) were characterized in terms of their physical, chemical, and biological properties by a battery of experimental techniques including 1H and 13C NMR, mass spectrometry, attenuated total reflectance-Fourier transform infrared spectroscopy, field emission scanning electron microscopy, atomic force microscopy, cell staining, and confocal laser scanning microscopy among others. In general, the developed films were found to be nanometric, transparent, resistant against manipulation, chemically reactive, and highly cytocompatible. On the other hand, in what the effect of the fatty acids is concerned, palmitic acid was found to impair the proliferation of the cultured β-cells, contrary to its homologues which did not alter this biological process. In our opinion, the multidisciplinary study presented here might be of interest for the research community working on the development of cytocompatible 2D model substrates for the safe and reproducible characterization of cell responses.

Covalent layer-by-layer films: chemistry, design, and multidisciplinary applications

Covalent layer-by-layer (LbL) assembly is a powerful method used to construct functional ultrathin films that enables nanoscopic structural precision, componential diversity, and flexible design. Compared with conventional LbL films built using multiple noncovalent interactions, LbL films prepared using covalent crosslinking offer the following distinctive characteristics: (i) enhanced film endurance or rigidity; (ii) improved componential diversity when uncharged species or small molecules are stably built into the films by forming covalent bonds; and (iii) increased structural diversity when covalent crosslinking is employed in componential, spacial, or temporal (labile bonds) selective manners. In this review, we document the chemical methods used to build covalent LbL films as well as the film properties and applications achievable using various film design strategies. We expect to translate the achievement in the discipline of chemistry (film-building methods) into readily available techniques for materials engineers and thus provide diverse functional material design protocols to address the energy, biomedical, and environmental challenges faced by the entire scientific community.

Parallel DNA Synthesis on Poly(ethylene terephthalate)

The fabrication of DNA arrays directly on aminolyzed sheets of poly(ethylene terephthalate) (PET) is described. Array surfaces typically employ bifunctional linkers or layers of covalently attached polymers to provide substrate hydroxy groups as synthesis attachment points. An amine treatment is used here to expose hydroxy groups on films of PET. These hydroxy groups can then be used to couple phosphoramidites and initiate the array synthesis without further functionalization steps. Arrays fabricated on these substrates with a maskless array synthesizer are tolerant of the high number of chemical exposure steps required to synthesize relatively long oligonucleotides. The results might be of the greatest use to the synthetic biology community, for whom a flexible and robust substrate could enable new strategies to enhance the throughput of oligonucleotide synthesis.

Controlled Interfacial Permeation, Nanostructure Formation, Catalytic Efficiency, Signal Enhancement Capability, and Cell Spreading by Adjusting Photochemical Cross-Linking Degrees of Layer-by-Layer Films

Interfacial properties including permeation, catalytic efficiency, Raman signal enhancement capabilities, and cell spreading efficiencies are important features that determine material functionality and applications. Here, we propose a facile method to adjust the above-mentioned properties by controlling the cross-linking degrees of multilayer using a photoactive molecule. After treating the cross-linked films in basic solutions, films with different cross-linking degrees presented varying residue thicknesses and film morphologies. As a result, these different films possessed distinct molecular loading and release characteristics. In addition, gold nanoparticles (AuNPs) of different morphological traits were generated by redox reactions coupled with diffusion within these films. The AuNP-polyelectrolyte obtained from the polyelectrolyte films of the medium cross-linking degrees displayed the highest catalytic efficiency and signal enhancement capabilities. Furthermore, cells responded to the variation of film cross-linking degrees, and on the films with the highest cross-linking degree, cells adhered with the highest speed. We expect this report to provide a general interfacial material engineering strategy for material designs.

Photolithographic Synthesis of High-Density DNA and RNA Arrays on Flexible, Transparent, and Easily Subdivided Plastic Substrates

The photolithographic fabrication of high-density DNA and RNA arrays on flexible and transparent plastic substrates is reported. The substrates are thin sheets of poly(ethylene terephthalate) (PET) coated with cross-linked polymer multilayers that present hydroxyl groups suitable for conventional phosphoramidite-based nucleic acid synthesis. We demonstrate that by modifying array synthesis procedures to accommodate the physical and chemical properties of these materials, it is possible to synthesize plastic-backed oligonucleotide arrays with feature sizes as small as 14 μm × 14 μm and feature densities in excess of 125 000/cm(2), similar to specifications attainable using rigid substrates such as glass or glassy carbon. These plastic-backed arrays are tolerant to a wide range of hybridization temperatures, and improved synthetic procedures are described that enable the fabrication of arrays with sequences up to 50 nucleotides in length. These arrays hybridize with S/N ratios comparable to those fabricated on otherwise identical arrays prepared on glass or glassy carbon. This platform supports the enzymatic synthesis of RNA arrays and proof-of-concept experiments are presented showing that the arrays can be readily subdivided into smaller arrays (or "millichips") using common laboratory-scale laser cutting tools. These results expand the utility of oligonucleotide arrays fabricated on plastic substrates and open the door to new applications for these important bioanalytical tools.

Fabrication of oligonucleotide and protein arrays on rigid and flexible substrates coated with reactive polymer multilayers

We report a top-down approach to the fabrication of oligonucleotide and protein arrays on surfaces coated with ultrathin, amine-reactive polymer multilayers fabricated by the covalent "layer-by-layer" (LbL) assembly of polyethyleneimine (PEI) and the amine-reactive, azlactone-functionalized polymer poly(2-vinyl-4,4-dimethylazlactone) (PVDMA). Manual spotting of amine-terminated oligonucleotide probe sequences on planar glass slides coated with PEI/PVDMA multilayers (~35 nm thick) yielded arrays of immobilized probes that hybridized fluorescently labeled complementary sequences with high signal intensities, high signal-to-noise ratios, and high sequence specificity. Treatment of residual azlactone functionality with the nonfouling small-molecule amine d-glucamine resulted in regions between the features of these arrays that resisted adsorption of protein and permitted hybridization in complex media containing up to 10 mg/mL protein. The residual azlactone groups in these films were also exploited to immobilize proteins on film-coated surfaces and fabricate functional arrays of proteins and enzymes. The ability to deposit PEI/PVDMA multilayers on substrates of arbitrary size, shape, and composition permitted the fabrication of arrays of oligonucleotides on the surfaces of multilayer-coated sheets of poly(ethylene terephthalate) and heat-shrinkable polymer film. Arrays fabricated on these flexible plastic substrates can be bent, cut, resized, and manipulated physically in ways that are difficult using more conventional rigid substrates. This approach could thus contribute to the development of new assay formats and new applications of biomolecule arrays. The methods described here are straightforward to implement, do not require access to specialized equipment, and should also be compatible with automated liquid-handling methods used to fabricate higher-density arrays of oligonucleotides and proteins on more traditional surfaces.