Cytosine-rich mismatched DNA aptamer combined with superparamagnetic photonic crystal sensing material for the specific visual detection of silver ions

DNA aptamer superparamagnetic photonic crystals (DSPCs), enriched with a highly selective cytosine-rich mismatched single-stranded DNA aptamer (CRDA), were successfully employed in a novel visual detection strategy for the detection of silver ions (Ag+). The technologies of superparamagnetic colloidal nanospheres (SCNs), DNA aptamer, and photonic crystals were combined to fabricate DPSCs. The aptamer was immobilized via electrostatic adsorption with amino groups that were chemically introduced on the surface of the SCNs, forming D-NH-SCNs. The detection is achieved by forming an Ag+ complex (C-Ag+-C) between Ag+ and D-NH-SCN. The DSPCs assembled under a magnetic field by D-NH-SCNs effectively detected Ag+ in the range of 1 μg/L to 5 mg/L, corresponding to the critical concentration range for heavy metals in drinking water. During the detection, the DSPC exhibited a wavelength blueshift from 652.8 nm to 626.4 nm (26.4 nm), as well as changes in reflection intensity. Notably, when detecting Ag+, a change in DSPC color from orange to yellow was observed. In summary, the developed visual detection material facilitates direct Ag + sensing. In the future, different DNA aptamers will be modified further to detect various targets in the fields of medicine, environmental monitoring, and food safety.

Label-free discrimination of single nucleotide changes in DNA by reflectometric interference Fourier transform spectroscopy

Phenotypic variation - such as disease susceptibility and differential drug response - has a strong genetic component. Substantial effort has therefore been made to identify causal genomic variants explaining such variation among humans. Point mutations (PMs), which are single nucleotide changes in the genome, have been identified to be the most abundant form of causal genomic variants, making them useful, reliable diagnostic markers. Methods developed to genotype PMs have moved towards solid-phase assays, which not only show greater sensitivity and specificity, but also enable scalability and faster processing time. Most current assays are, however, based on fluorescent probes, which makes them relatively expensive. To develop a more cost-effective label-free genotyping method, we used a porous silicon (PSi) base as an efficient support for DNA biosensing and coupled it with reflectometric interference Fourier transform spectroscopy (RIFTS). To assess the versatility of this approach, we tested both a single nucleotide substitution in VKORC1 (-1639G > A; rs9923231) and a single nucleotide insertion in BRCA1 (5382insC; rs80357906). We demonstrate that the PSi-RIFTS method can efficiently detect both PM types with high sensitivity where hybridization of complementary DNA can be quantifiably differentiated from mismatch and non-complementary hybridization events. In addition, we show that the PSi base with immobilized DNA not only can be re-used to type further samples, but it also remains stable for 14 days, suggesting its potential for high-throughput applications.

Identification of mine water inrush using laser-induced fluorescence spectroscopy combined with one-dimensional convolutional neural network

The application of laser-induced fluorescence (LIF) combined with machine learning methods can make up for the shortcomings of traditional hydrochemical methods in the accurate and rapid identification of mine water inrush in coal mines. However, almost all of these methods require preprocessing such as principal component analysis (PCA) or drawing the spectral map as an essential step. Here, we provide our solution for the classification of mine water inrush, in which a one-dimensional convolutional neural network (1D CNN) is trained to automatically identify mine water inrush according to the LIF spectroscopy without the need for preprocessing. First, the architecture and parameters of the model were optimized and the 1D CNN model containing two convolutional blocks was determined to be the best model for the identification of mine water inrush. Then, we evaluated the performance of the 1D CNN model using the LIF spectral dataset of mine water inrush containing 540 training samples and 135 test samples, and we found that all 675 samples could be accurately identified. Finally, superior classification performance was demonstrated by comparing with a traditional machine learning algorithm (genetic algorithm-support vector machine) and a deep learning algorithm (two-dimensional convolutional neural network). The results show that LIF spectroscopy combined with 1D CNN can be used for the fast and accurate identification of mine water inrush without the need for complex pretreatments.

Photonic crystals: emerging biosensors and their promise for point-of-care applications

Biosensors are extensively employed for diagnosing a broad array of diseases and disorders in clinical settings worldwide. The implementation of biosensors at the point-of-care (POC), such as at primary clinics or the bedside, faces impediments because they may require highly trained personnel, have long assay times, large sizes, and high instrumental cost. Thus, there exists a need to develop inexpensive, reliable, user-friendly, and compact biosensing systems at the POC. Biosensors incorporated with photonic crystal (PC) structures hold promise to address many of the aforementioned challenges facing the development of new POC diagnostics. Currently, PC-based biosensors have been employed for detecting a variety of biotargets, such as cells, pathogens, proteins, antibodies, and nucleic acids, with high efficiency and selectivity. In this review, we provide a broad overview of PCs by explaining their structures, fabrication techniques, and sensing principles. Furthermore, we discuss recent applications of PC-based biosensors incorporated with emerging technologies, including telemedicine, flexible and wearable sensing, smart materials and metamaterials. Finally, we discuss current challenges associated with existing biosensors, and provide an outlook for PC-based biosensors and their promise at the POC.

Preparation, characterization, and protein-resistance of films derived from a series of α-oligo(ethylene glycol)-ω-alkenes on H–Si(111) surfaces

Films on Si(111) were prepared by photo-activated grafting of CH₂&#xe001;CH(CH₂)m(OCH₂CH₂)nOCH₃ (m = 8, 9; n = 3–7) by using different vacuum conditions. High vacuum produced a higher thickness (40 Å) and <0.8% fibrinogen adsorption (C₁₀EG₇). Films were stable even after 28 days.

Optical biosensors for bacteria detection by a peptidomimetic antimicrobial compound

In this work we present a label-free optical biosensor for rapid bacteria detection using a novel peptide-mimetic compound, as the recognition element. The biosensor design is based on an oxidized porous silicon (PSiO2) nanostructure used as the optical transducer, functionalized with the sequence K-[C12K]7 (referred to as K-7α12), which is a synthetic antimicrobial peptide. This compound is a member of a family of oligomers of acylated lysines (OAKs), mimicking the hydrophobicity and charge of natural antimicrobial peptides. The OAK is tethered to the PSiO2 film and the changes in the reflectivity spectrum are monitored upon exposure to Escherichia coli (E. coli) bacterial suspensions and their lysates. We show that capture of bacterial cell fragments induces predictable changes in the reflectivity spectrum, proportional to E. coli concentrations, thereby enabling rapid, sensitive and reproducible detection of E. coli at concentrations as low as 10(3) cells per mL. While for intact bacterial cells, the K-7α12-tethered PSiO2 shows a poor capturing ability, resulting in an insignificant optical response. The biosensor performance is also studied upon exposure to model Gram positive and negative bacterial lysates, suggesting preferential capture of E. coli cell fragments in the presented scheme. These OAK-based biosensors offer significant advantages in comparison with conventional antibody-based assays, in terms of their simple and cost-effective production, while providing numerous possible sequence combinations for designing new detection schemes.

Toward Multiplexing Detection of Wound Healing Biomarkers on Porous Silicon Resonant Microcavities

Bacterial wound infections can cause septicemia and lead to limb amputation or death. Therefore, early detection of bacteria is important in chronic wound management. Here, an optical biosensor based on porous silicon resonant microcavity (pSiRM) structure modified with fluorogenic peptide substrate is demonstrated to detect the presence of Sortase A (SrtA), a bacterial enzyme found in the cell membrane protein of Staphylococcus aureus. The combination of fluorescence enhancement effects of the pSiRM architecture with the incorporation of SrtA fluorogenic peptide substrate within the pSi matrix enables the sensing of SrtA with an outstanding limit of detection of 8 × 10-14 m. Modification of the pSiRM structure with microscale spots of two fluorogenic peptide substrates, one specific for SrtA and the other for matrix metalloproteinases, effectively demonstrates the feasibility to perform multiplexed biomarker analysis. The results in this study highlight the potential of the pSiRM sensing platform as a point-of-care diagnostic tool for biomarkers of bacterial wound infection.

Advances in click chemistry for silica-based material construction

Click chemistry is undoubtedly the most powerful 1,3-dipolar cycloaddition reaction in organic synthesis.

Soft matter in hard confinement: phase transition thermodynamics, structure, texture, diffusion and flow in nanoporous media

Spatial confinement in nanoporous media affects the structure, thermodynamics and mobility of molecular soft matter often markedly. This article reviews thermodynamic equilibrium phenomena, such as physisorption, capillary condensation, crystallisation, self-diffusion, and structural phase transitions as well as selected aspects of the emerging field of spatially confined, non-equilibrium physics, i.e. the rheology of liquids, capillarity-driven flow phenomena, and imbibition front broadening in nanoporous materials. The observations in the nanoscale systems are related to the corresponding bulk phenomenologies. The complexity of the confined molecular species is varied from simple building blocks, like noble gas atoms, normal alkanes and alcohols to liquid crystals, polymers, ionic liquids, proteins and water. Mostly, experiments with mesoporous solids of alumina, gold, carbon, silica, and silicon with pore diameters ranging from a few up to 50 nm are presented. The observed peculiarities of nanopore-confined condensed matter are also discussed with regard to applications. A particular emphasis is put on texture formation upon crystallisation in nanoporous media, a topic both of high fundamental interest and of increasing nanotechnological importance, e.g. for the synthesis of organic/inorganic hybrid materials by melt infiltration, the usage of nanoporous solids in crystal nucleation or in template-assisted electrochemical deposition of nano structures.

Photonic crystals for chemical sensing and biosensing

This Review covers photonic crystals (PhCs) and their use for sensing mainly chemical and biochemical parameters, with a particular focus on the materials applied. Specific sections are devoted to a) a lead-in into natural and synthetic photonic nanoarchitectures, b) the various kinds of structures of PhCs, c) reflection and diffraction in PhCs, d) aspects of sensing based on mechanical, thermal, optical, electrical, magnetic, and purely chemical stimuli, e) aspects of biosensing based on biomolecules incorporated into PhCs, and f) current trends and limitations of such sensors.

A photonic glucose biosensor for chronic wound prognostics

An optical biosensor based on the switching of poly(4-vinylphenylboronic acid) (PVPBA) grafted to the pores of porous silicon (pSi) films in response to pH and glucose.

Optimising the enzyme response of a porous silicon photonic crystal via the modular design of enzyme sensitive polymers

The incorporation of a versatile and tuneable polymer–peptide network into the pores of porous silicon photonic crystals improves the selectivity of porous silicon optical biosensors to detect certain types of matrix metalloproteinase enzymes.

Photolithographic strategy for patterning preformed, chemically modified, porous silicon photonic crystal using click chemistry

Porous silicon (PSi) is an ideal platform for label-free biosensing, and the development of porous silicon patterning will open a pathway to the development of highly parallel PSi biochips for detecting multiple analytes. The optical response of PSi photonic crystal is determined by the changes in the effective bulk refractive index resulting from reactions/events occurring within the internal pore space. Therefore, introducing precise chemical functionalities in the pores of PSi is essential to ensure device selectivity. Here we describe the fabrication of PSi patterns that possess discrete chemical functionalities that are restricted to precise locations. The key difference to previous patterning protocols for PSi is that the entire porous material is first modified with a self-assembled monolayer of a α,ω-diyne adsorbate prior to patterning using a microfabricated titanium mask. The distal alkyne moieties in the monolayer are then amenable to further selective modification by the archetypal "click" reaction, the copper catalyzed alkyne-azide cycloaddition (CuAAC), using the titanium mask as a resist. This type of patterning is suitable for further immobilization of biological recognition elements, and presents a new platform for highly parallel PSi biosensor for multiple detections.

Matrix Metalloproteinase Biosensor Based on a Porous Silicon Reflector

Matrix metalloproteinases (MMP) are proteolytic enzymes important to wound healing. In non-healing wounds, it has been suggested that MMP levels become dysfunctional, hence it is of great interest to develop sensors to detect MMP biomarkers. This study presents the development of a label-free optical MMP biosensor based on a functionalised porous silicon (pSi) thin film. The biosensor is fabricated by immobilising a peptidomimetic MMP inhibitor in the porous layer using hydrosilylation followed by amide coupling. The binding of MMP to the immobilised inhibitor translates into a change of effective optical thickness over time. We investigated the effect of surface functionalisation on the stability of the pSi surface and evaluated sensing performance. We successfully demonstrated MMP detection in buffer solution and human wound fluid at physiologically relevant concentrations. This biosensor may find application as a point-of-care device that is prognostic of the healing trajectory of chronic wounds.

1-D and 2-D photonic crystals as optical methods for amplifying biomolecular recognition

Label-free sensing strategies are an intensely studied and increasingly used alternative to signal amplification via fluorescent labels and enzymatic methods. This article discusses one class of optical sensors, termed "photonic crystals", that effectively amplify binding events (such as analyte capture) via strong light-matter interactions.

Controlling interferometric properties of nanoporous anodic aluminium oxide

A study of reflective interference spectroscopy [RIfS] properties of nanoporous anodic aluminium oxide [AAO] with the aim to develop a reliable substrate for label-free optical biosensing is presented. The influence of structural parameters of AAO including pore diameters, inter-pore distance, pore length, and surface modification by deposition of Au, Ag, Cr, Pt, Ni, and TiO2 on the RIfS signal (Fabry-Perot fringe) was explored. AAO with controlled pore dimensions was prepared by electrochemical anodization of aluminium using 0.3 M oxalic acid at different voltages (30 to 70 V) and anodization times (10 to 60 min). Results show the strong influence of pore structures and surface modifications on the interference signal and indicate the importance of optimisation of AAO pore structures for RIfS sensing. The pore length/pore diameter aspect ratio of AAO was identified as a suitable parameter to tune interferometric properties of AAO. Finally, the application of AAO with optimised pore structures for sensing of a surface binding reaction of alkanethiols (mercaptoundecanoic acid) on gold surface is demonstrated.

Tandem "click" reactions at acetylene-terminated Si(100) monolayers

We demonstrate a simple method for coupling alkynes to alkynes. The method involves tandem azide-alkyne cycloaddition reactions ("click" chemistry) for the immobilization of 1-alkyne species onto an alkyne modified surface in a one-pot procedure. In the case presented, these reactions take place on a nonoxidized Si(100) surface although the approach is general for linking alkynes to alkynes. The applicability of the method in the preparation of electrically well-behaved functionalized surfaces is demonstrated by coupling an alkyne-tagged ferrocene species onto alkyne-terminated Si(100) surfaces. The utility of the approach in biotechnology is shown by constructing a DNA sensing interface by derivatization of the acetylenyl surface with commercially available alkyne-tagged oligonucleotides. Cyclic voltametry, electrochemical impedance spectroscopy, X-ray photoelectron spectroscopy, and X-ray reflectometry are used to characterize the coupling reactions and performance of the final modified surfaces. These data show that this synthetic protocol gives chemically well-defined, electronically well-behaved, and robust (bio)functionalized monolayers on silicon semiconducting surfaces.

Low power, biologically benign NIR light triggers polymer disassembly

Near infrared (NIR) irradiation can penetrate up to 10 cm deep into tissues and be remotely applied with high spatial and temporal precision. Despite its potential for various medical and biological applications, there is a dearth of biomaterials that are responsive at this wavelength region. Herein we report a polymeric material that is able to disassemble in response to biologically benign levels of NIR irradiation upon two-photon absorption. The design relies on the photolysis of the multiple pendant 4-bromo7-hydroxycoumarin protecting groups to trigger a cascade of cyclization and rearrangement reactions leading to the degradation of the polymer backbone. The new material undergoes a 50% Mw loss after 25 sec of ultraviolet (UV) irradiation by single photon absorption and 21 min of NIR irradiation via two-photon absorption. Most importantly, even NIR irradiation at biologically benign laser power is sufficient to cause significant polymer disassembly. Furthermore, this material is well tolerated by cells both before and after degradation. These results demonstrate for the first time a NIR sensitive material with potential to be used for in vivo applications.