Silicon nanopillar substrates for enhancing signal intensity in DNA microarrays

Ingeniously designed Silica nanostructures as an exceptional support: Opportunities, potential challenges and future prospects for viable degradation of pesticides

Despite significant advancements in modern agricultural practices, efficient handling of pesticides is a must as they are continuously defiling our terrestrial as well as aquatic life. During the last couple of decades, substantial efforts by various research groups have been devoted to find innovative solutions to remove pesticides from our environment in a greener way. In this regard, functionalized silica nanoparticles (NPs) have gained considerable attention of scientific community due to their notable properties such as amenable design, large surface area as well as fine-tunable and uniform pore structures which make them an ideal material for pesticides removal. The present review aims to proffer current scientific progress attained by silica-based nanostructures as an excellent material for effective removal of noxious agrochemicals. Further, a brief discussion on the synthetic strategies as well as intrinsic benefits associated with different morphologies of silica have also been highlighted in this article. It also summarizes the recent reports on silica assisted degradation of pesticides via enzymatic, chemical as well as advanced oxidation protocols. Additionally, it presents a critical analysis of different support materials for decontamination of our ecosystem. The review concludes with potential challenges, their possible solutions along with key knowledge gaps and future research directions for successful deployment of silica supported materials in degradation of pesticides at commercial scale.

Three-dimensional protein microarrays fabricated on reactive microsphere modified COC substrates

Fabrication of three-dimensional (3D) surface structures for the high density immobilization of biomolecules is an effective way to prepare highly sensitive biochips. In this work, a strategy to attach polymeric microspheres on a cyclic olefin copolymer (COC) substrate for the preparation of a 3D protein chip was developed. The COC surface was firstly functionalized by the photograft technique with epoxy groups, which were subsequently converted to amine groups. Then monodisperse poly(styrene-alt-maleic anhydride) (PSM) copolymer microspheres were prepared by self-stabilized precipitation polymerization and deposited as a single layer on a modified COC surface to form a 3D surface texture. The surface roughness of the COC support undergoes a significant increase from 1.4 nm to 37.1 nm after deposition of PSM microspheres with a size of 460 nm, and the modified COC still maintains a transmittance of more than 63% at the fluorescence excitation wavelengths (555 nm and 647 nm). The immobilization efficiency of immunoglobulin G (IgG) on the 3D surface reached 75.6% and the immobilization density was calculated to be 0.255 μg cm^-2, at a probe protein concentration of 200 μg mL^-1. The 3D protein microarray can be rapidly blocked by gaseous ethylenediamine within 10 minutes due to the high reactivity of anhydride groups in PSM microspheres. Immunoassay results show that the 3D protein microarray achieved specific identification of the target protein with a linear detection range from 6.25 ng mL^-1 to 250 ng mL^-1 (R² > 0.99) and a limit of detection of 8.87 ng mL^-1. This strategy offers a novel way to develop high performance polymer-based 3D protein chips.

Recent Advances in Biomaterial-Based High-Throughput Platforms

High-throughput systems allow screening and analysis of large number of samples simultaneously under same conditions. Over recent years, high-throughput systems have found applications in fields other than drug discovery like bioprocess industries, pollutant detection, material microarrays, etc. With the introduction of materials in such HT platforms, the screening system has been enabled for solid phases apart from conventional solution phase. The use of biomaterials has further facilitated cell-based assays in such platforms. Here, the authors have focused on the recent developments in biomaterial-based platforms including the fabricationusing contact and non-contact methods and utilization of such platforms for discovery of novel biomaterials exploiting interaction of biological entities with surface and bulk properties. Finally, the authors have elaborated on the application of the biomaterial-based high-throughput platforms in tissue engineering and regenerative medicine, cancer and stem cell studies. The studies show encouraging applications of biomaterial microarrays. However, success in clinical applicability still seems to be a far off task majorly due to absence of robust characterization and analysis techniques. Extensive focus is required for developing personalized medicine, analytical tools and storage/shelf-life of cell laden microarrays.

Advanced liquid biopsy technologies for circulating biomarker detection

Liquid biopsy is a new diagnostic concept that provides important information for monitoring and identifying tumor genomes in body fluid samples. Detection of tumor origin biomolecules like circulating tumor cells (CTCs), circulating tumor specific nucleic acids (circulating tumor DNA (ctDNA), circulating tumor RNA (ctRNA), microRNAs (miRNAs), long non-coding RNAs (lnRNAs)), exosomes, autoantibodies in blood, saliva, stool, urine, etc. enables cancer screening, early stage diagnosis and evaluation of therapy response through minimally invasive means. From reliance on painful and hazardous tissue biopsies or imaging depending on sophisticated equipment, cancer management schemes are witnessing a rapid evolution towards minimally invasive yet highly sensitive liquid biopsy-based tools. Clinical application of liquid biopsy is already paving the way for precision theranostics and personalized medicine. This is achieved especially by enabling repeated sampling, which in turn provides a more comprehensive molecular profile of tumors. On the other hand, integration with novel miniaturized platforms, engineered nanomaterials, as well as electrochemical detection has led to the development of low-cost and simple platforms suited for point-of-care applications. Herein, we provide a comprehensive overview of the biogenesis, significance and potential role of four widely known biomarkers (CTCs, ctDNA, miRNA and exosomes) in cancer diagnostics and therapeutics. Furthermore, we provide a detailed discussion of the inherent biological and technical challenges associated with currently available methods and the possible pathways to overcome these challenges. The recent advances in the application of a wide range of nanomaterials in detecting these biomarkers are also highlighted.

Bioinspired photonic barcodes for multiplexed target cycling and hybridization chain reaction

Multiplexed detection of microRNA (miRNA) is of great value in clinical diagnosis. Here, a new type of polydopamine (PDA) encapsulated photonic crystal (PhC) barcodes are employed for target-triggering cycle amplification and hybridization chain reaction (HCR) to achieve multiplex miRNA quantification. The PDA-decorated PhC barcodes not only exhibit distinctive structural color for different encoding miRNAs, they also can immobilize biomolecules, allowing subsequent reaction with amino-modified hairpin probes (H1). When the PDA-decorated PhC barcodes are used in assays, target miRNAs can be circularly used to initiate HCR for cycle amplification. Therefore, by tuning the structural colors of the PDA-integrated PhC, the multiplexed miRNA quantification could be realized. We demonstrate that our strategy for multiplexed detection of miRNA is reasonably accurate, reliable and repeatable, with a detection limit as low as 8.0 fM. Our results show that PDA encapsulated PhC barcodes as a novel platform offer a pathway toward the multiplex analysis of low-abundance biomarkers for biomedical assays.

Specific detection of stable single nucleobase mismatch using SU-8 coated silicon nanowires platform

Novel microarray platform for single nucleotide polymorphisms (SNPs) detection has been developed using silicon nanowires (SiNWs) as support and two different surface modification methods for attaining the necessary functional groups. Accordingly, we compared the detection specificity and stability over time of the probes printed on SiNWs modified with (3-aminopropyl)triethoxysilane (APTES) and glutaraldehyde (GAD), or coated with a simpler procedure using epoxy-based SU-8 photoresist. Scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDX) were used for comparative characterization of the unmodified and coated SiNWs. The hybridization efficiency was assessed by comprehensive statistical analysis of the acquired data from confocal fluorescence scanning of the manufactured biochips. The high detection specificity between the hybridized probes containing different mismatch types was demonstrated on SU-8 coating by one way ANOVA test (adjusted p value *** < .0001). The stability over time of the probes tethered on SiNWs coated with SU-8 was evaluated after 1, 4, 8 and 21 days of probe incubation, revealing values for coefficient of variation (CV) between 2.4% and 5.6%. The signal-to-both-standard-deviations ratio measured for SU-8 coated SiNWs platform was similar to the commercial support, while the APTES-GAD coated SiNWs exhibited the highest values.

Wafer Scale Fabrication of Dense and High Aspect Ratio Sub-50 nm Nanopillars from Phase Separation of Cross-Linkable Polysiloxane/Polystyrene Blend

We demonstrated a simple and effective approach to fabricate dense and high aspect ratio sub-50 nm pillars based on phase separation of a polymer blend composed of a cross-linkable polysiloxane and polystyrene (PS). In order to obtain the phase-separated domains with nanoscale size, a liquid prepolymer of cross-linkable polysiloxane was employed as one moiety for increasing the miscibility of the polymer blend. After phase separation via spin-coating, the dispersed domains of liquid polysiloxane with sub-50 nm size could be solidified by UV exposure. The solidified polysiloxane domains took the role of etching mask for formation of high aspect ratio nanopillars by O₂ reactive ion etching (RIE). The aspect ratio of the nanopillars could be further amplified by introduction of a polymer transfer layer underneath the polymer blend film. The effects of spin speeds, the weight ratio of the polysiloxane/PS blend, and the concentration of polysiloxane/PS blend in toluene on the characters of the nanopillars were investigated. The gold-coated nanopillar arrays exhibited a high Raman scattering enhancement factor in the range of 10⁸-10⁹ with high uniformity across over the wafer scale sample. A superhydrophobic surface could be realized by coating a self-assembled monolayers (SAM) of fluoroalkyltrichlorosilane on the nanopillar arrays. Sub-50 nm silicon nanowires (SiNWs) with high aspect ratio of about 1000 were achieved by using the nanopillars as etching mask through a metal-assisted chemical etching process. They showed an ultralow reflectance of approximately 0.1% for wavelengths ranging from 200 to 800 nm.

Silicon nanonets for biological sensing applications with enhanced optical detection ability

Optical sensors based on fluorescence methods are used in numerous areas of society, ranging from healthcare to environmental monitoring. But the race to elaborate portable and highly sensitive detection systems leads to the huge development of nanomaterial-based sensors. Here, we have fabricated a silicon nanonet, or silicon nanowire (SiNW) network, -based biosensor for DNA hybridization detection by fluorescence microscopy. We demonstrate that by leveraging the properties of the SiNWs such as their large specific surface and the high aspect ratio, these nanonet sensors have significantly enhanced sensitivity and better selectivity compared to plane substrates. The fluorescence signal shows an intensity increasing with the SiNW density on the nanonet and for the denser nanonets, the detection limit for DNA hybridization is 1 nM. The elaborated Si nanonet-based DNA sensors present more than 50% change in fluorescence intensity between complementary DNA and 1 base mismatch DNA which shows their high selectivity. Finally, we have integrated the Si nanonet-based sensor into a DNA chip and we have shown that this selective sensor can be reproduced on a large scale area.

DNA hybridization on silicon nanowire platform prepared by glancing angle deposition and metal assisted chemical etching process

Porous nanowire surface provides high capacity for oligonucleotide hybridization.

Shrink-induced silica multiscale structures for enhanced fluorescence from DNA microarrays

We describe a manufacturable and scalable method for fabrication of multiscale wrinkled silica (SiO2) structures on shrink-wrap film to enhance fluorescence signals in DNA fluorescence microarrays. We are able to enhance the fluorescence signal of hybridized DNA by more than 120 fold relative to a planar glass slide. Notably, our substrate has improved detection sensitivity (280 pM) relative to planar glass slide (11 nM). Furthermore, this is accompanied by a 30-45 times improvement in the signal-to-noise ratio (SNR). Unlike metal enhanced fluorescence (MEF) based enhancements, this is a far-field and uniform effect based on surface concentration and photophysical effects from the nano- to microscale SiO2 structures. Notably, the photophysical effects contribute an almost 2.5 fold enhancement over the concentration effects alone. Therefore, this simple and robust method offers an efficient technique to enhance the detection capabilities of fluorescence based DNA microarrays.

Nanostructured Si-nanowire microarrays for enhanced-performance bio-analytics

We demonstrate the fabrication of a novel platform based on Si nanowire arrays integrated with a programmable DNA-directed homogeneous-phase analyte-capture strategy for robust detection of bio-analytes. The nanofabrication process used, based on a combination of glancing-angle-deposition and metal-assisted-catalytic-etching, is capable of producing thousands of testing sites per chip, and the sites can be fabricated over entire wafers, with precise control of size and positioning, using conventional microelectronics technology. The analyte-capture strategy used eliminates the well-known interference of the heterogeneous-phase (substrate) with the capturing of analytes. We examine the effects of the nanoscale features of the substrates (nanowire porosity and clumping) on the coupling efficiency of analytes and show that the fabricated microarrays are robust, have high efficiency and capacity, and provide significantly enhanced signal-to-noise ratio detection.

Vertical etching with isolated catalysts in metal-assisted chemical etching of silicon

Metal assisted chemical etching with interconnected catalyst structures has been used to create a wide array of organized nanostructures. However, when patterned catalysts are not interconnected, but are isolated instead, vertical etching to form controlled features is difficult. A systematic study of the mechanism and catalyst stability of metal assisted chemical etching (MACE) of Si in HF and H(2)O(2) using Au catalysts has been carried out. The effects of the etchants on the stability of Au catalysts were examined in detail. The role of excess electronic holes as a result of MACE was investigated via pit formation as a function of catalyst proximity and H(2)O(2) concentration. We show that a suppression of excess holes can be achieved by either adding NaCl to or increasing the HF concentration of the etching solution. We demonstrate that an electric field can direct most of the excess holes to the back of the Si wafer and thus reduce pit formation at the surface of Si between the Au catalysts. The effect of hydrogen bubbles, generated as a consequence of MACE, on the stability of Au catalysts has also been investigated. We define a regime of etch chemistry and catalyst spacing for which catalyst stability and vertical etching can be achieved.

Creation of nanostructures by interference lithography for modulation of cell behavior

Emerging evidence of the striking differences that can be induced in the behavior of biological cells through topographical modulation of physically and chemically patterned nanostructured surfaces provides a great impetus for developing novel cellular-scale and sub-cellular-scale nanopatterned substrates and for employing them for exciting new applications in life and medical sciences and biotechnology. However, the lack of availability of cost-effective, large-surface-area nanofabricated substrates of appropriate dimensions and features has proved to be a major impediment for research in this area. Here, we demonstrate a simple and cost-effective method based on interference lithography to produce spatially precise and wide-surface-coverage silicon- and polymer-based nanostructures to study how cells react to nanoscale structures or surfaces.

Enhancing the fluorescence intensity of DNA microarrays by using cationic surfactants

DNA microarrays have been used as powerful tools in genomics studies and single nucleotide polymorphisms analysis. However, the fluorescence detection used in most conventional DNA microarrays is still limited by its sensitivity. The aim of this study is to use a cationic surfactant, cetyl trimethylammonium bromide (CTAB), to enhance the fluorescence intensity of 6-carboxy-fluorescene (FAM)-labeled DNA probes immobilized on a DNA microarray. We show that in the presence of CTAB the immobilized FAM-labeled DNA probes is 11-fold brighter than that without exposure to CTAB. Similarly, when we hybridize FAM-labeled DNA targets to a DNA microarray and treat the surface with CTAB solution, the fluorescence intensity shows a 26-fold increase for perfect-match DNA targets. More importantly, the contrast between perfect-match and 1-mismatch DNA is also increased from 1.3-fold to 15-fold. This method offers a simple and efficient technique to enhance the detection limit of DNA microarrays.

Nanoscale control of silica particle formation via silk-silica fusion proteins for bone regeneration

The biomimetic design of silk/silica fusion proteins was carried out, combining the self assembling domains of spider dragline silk (Nephila clavipes) and silaffin derived R5 peptide of Cylindrotheca fusiformis that is responsible for silica mineralization. Genetic engineering was used to generate the protein-based biomaterials incorporating the physical properties of both components. With genetic control over the nanodomain sizes and chemistry, as well as modification of synthetic conditions for silica formation, controlled mineralized silk films with different silica morphologies and distributions were successfully generated; generating 3D porous networks, clustered silica nanoparticles (SNPs), or single SNPs. Silk serves as the organic scaffolding to control the material stability and multiprocessing makes silk/silica biomaterials suitable for different tissue regenerative applications. The influence of these new silk-silica composite systems on osteogenesis was evaluated with human mesenchymal stem cells (hMSCs) subjected to osteogenic differentiation. hMSCs adhered, proliferated, and differentiated towards osteogenic lineages on the silk/silica films. The presence of the silica in the silk films influenced osteogenic gene expression, with the upregulation of alkaline phosphatase (ALP), bone sialoprotein (BSP), and collagen type 1 (Col 1) markers. Evidence for early bone formation as calcium deposits was observed on silk films with silica. These results indicate the potential utility of these new silk/silica systems towards bone regeneration.