Porous silicon optical microcavity biosensor on silicon-on-insulator wafer for sensitive DNA detection

Graphitic carbon @ silver nanoparticle @ porous silicon Bragg mirror composite SERS substrate for gallic acid detection

Graphite carbon (G) @ silver (Ag) @ porous silicon Bragg mirror (PSB) composite SERS substrate was successfully synthesized using electrochemical etching (ec) and hydrothermal carbonization (HTC) techniques with silver nitrate as the source of silver and glucose as the source of carbon. The PSB was used as a functional scaffold for the synthesis of graphite-carbon and silver composite nanoparticles (G@AgNPs) on its surface, thereby combining SERS activity and antioxidant properties. To our knowledge, this is the first time that G@AgNPs has been synthesized on the PSB using glucose as a carbon source. The synthesized G@Ag@PSB was utilized as a SERS platform for the detection of gallic acid (GA). Test results demonstrated that the substrate exhibited a remarkable SERS enhancement capability for GA, with the enhancement factor (EF) reaching 2 × 105. The reproducibility of the SERS spectral signal was excellent, with a relative standard deviation (RSD) of 7.5 %. The sensitivity test results showed that the linear range of GA detection based on G@Ag@PSB composite SERS substrate was 2 × 10-3-2 × 10-12M. The relationship between GA concentration and SERS signal intensity exhibited a strong linear correlation, with a linear correlation coefficient (R2) of 0.97634. Moreover, even with an extended storage period, only a marginal decline in the signal intensity of GA on the substrate was observed. The results of this study demonstrate that the prepared G@Ag@PSB composite SERS substrate had good potential application performance as a low-cost SERS detection platform suitable for commercial use. In addition, this advance facilitates the further exploration of more nanomaterials with ultra-high sensitivity in SERS technology.

Non-invasive detection of systemic lupus erythematosus using SERS serum detection technology and deep learning algorithms

Systemic lupus erythematosus (SLE) is an autoimmune disease with multiple symptoms, and its rapid screening is the research focus of surface-enhanced Raman scattering (SERS) technology. In this study, gold@silver-porous silicon (Au@Ag-PSi) composite substrates were synthesized by electrochemical etching and in-situ reduction methods, which showed excellent sensitivity and accuracy in the detection of rhodamine 6G (R6G) and serum from SLE patients. SERS technology was combined with deep learning algorithms to model serum features using selected CNN, AlexNet, and RF models. 92 % accuracy was achieved in classifying SLE patients by CNN models, and the reliability of these models in accurately identifying sera was verified by ROC curve analysis. This study highlights the great potential of Au@Ag-PSi substrate in SERS detection and introduces a novel deep learning approach for SERS for accurate screening of SLE. The proposed method and composite substrate provide significant value for rapid, accurate, and noninvasive SLE screening and provide insights into SERS-based diagnostic techniques.

SLE diagnosis research based on SERS combined with a multi-modal fusion method

As artificial intelligence technology gains widespread adoption in biomedicine, the exploration of integrating biofluidic Raman spectroscopy for enhanced disease diagnosis opens up new prospects for the practical application of Raman spectroscopy in clinical settings. However, for systemic lupus erythematosus (SLE), origin Raman spectral data (ORS) have relatively weak signals, making it challenging to obtain ideal classification results. Although the surface enhancement technique can enhance the scattering signal of Raman spectroscopic data, the sensitivity of the SERS substrate to airborne impurities and the inhomogeneous distribution of hotspots degrade part of the signal. To fully utilize both kinds of data, this paper proposes a two-branch residual-attention network (DBRAN) fusion technique, which allows the ORS to complement the degraded portion and thus improve the model's classification accuracy. The features are extracted using the residual module, which retains the original features while extracting the deep features. At the same time, the study incorporates the attention module in both the upper and lower branches to handle the weight allocation of the two modal features more efficiently. The experimental results demonstrate that both the low-level fusion method and the intermediate-level fusion method can significantly improve the diagnostic accuracy of SLE disease classification compared with a single modality, in which the intermediate-level fusion of DBRAN achieves 100% classification accuracy, sensitivity, and specificity. The accuracy is improved by 10% and 7% compared with the ORS unimodal and the SERS unimodal modalities, respectively. The experiment, by fusing the multimodal spectral, realized rapid diagnosis of SLE disease by fusing multimodal spectral data, which provides a reference idea in the field of Raman spectroscopy and can be further promoted to clinical practical applications in the future.

Morphological and Optical Transformation of Gas Assisted Direct Laser Written Porous Silicon Films

Direct laser writing (DLW) of mesoporous porous silicon (PS) films is shown to selectively create spatially separated nitridized and carbonized features on a single film. Nitridized or carbonized features are formed during DLW at 405 nm in an ambient of nitrogen and propane gas, respectively. The range of laser fluence required to create varying feature sizes while avoiding damage to the PS film is identified. At high enough fluence, nitridation using DLW has been shown as an effective method for laterally isolating regions on the PS films. The efficacy in preventing oxidation once passivated is investigated via energy dispersive X-ray spectroscopy. Changes in composition and optical properties of the DL written films are investigated using spectroscopic analysis. Results show carbonized DLW regions have a much higher absorption than as-fabricated PS, attributed to pyrolytic carbon or transpolyacetylene deposits in the pores. Nitridized regions exhibit optical loss similar to previously published thermally nitridized PS films. This work presents methods to engineer PS films for a variety of potential device applications, including the application of carbonized PS to selectively engineer thermal conductivity and electrical resistivity and of nitridized PS to micromachining and selective modification of refractive index for optical applications.

Coupling annealed silver nanoparticles with a porous silicon Bragg mirror SERS substrate and machine learning for rapid non-invasive disease diagnosis

Ag₂O-Ag-porous silicon Bragg mirror (PSB) composite SERS substrates were successfully synthesized by using a combination of electrochemical and thermochemical methods. Test results showed that the SERS signal increased and decreased as the annealing temperature used for the substrate increased, where the most intense SERS signal was obtained using a substrate annealed at 300 °C. Stability test results showed substantial enhancement of the SERS signal intensity of the Ag₂O-Ag-PSB composite one month after preparation compared with that of conventional Ag-PSB. We conclude that Ag₂O nanoshells play an essential role in SERS signal enhancement. Ag₂O prevents natural oxidation of Ag nanoparticles (AgNPs) and has a solid localized surface plasmon resonance (LSPR). SERS signal enhancement was tested using this substrate for serum from patients with Sjögren's syndrome (SS) and Diabetic nephropathy (DN), as well as from healthy controls (HC). SERS feature extraction was performed using principal component analysis (PCA). The extracted features were analyzed by a support vector machine (SVM) algorithm. Finally, a rapid screening model for SS and HC, as well as DN and HC, was developed and used to perform controlled experiments. The results showed that the diagnostic accuracy, sensitivity and selectivity for SERS technology combined with machine learning algorithms reached 90.7%, 93.4% and 86.7% for SS/HC and 89.3%, 95.6% and 80% for DN/HC, respectively. The results of this study show that the composite substrate has excellent potential to be developed into a commercially available SERS chip for medical testing.

Application of serum SERS technology based on thermally annealed silver nanoparticle composite substrate in breast cancer

Liquid biopsy is currently a non-destructive and convenient method of cancer screening, due to human blood containing a variety of cancer-related biomolecules. Therefore, the development of an accurate and rapid breast cancer screening technique combined with breast cancer serum is crucial for the treatment and prognosis of breast cancer patients. In this study, the surface enhanced Raman spectroscopy (SERS) technique is used to enhance the Raman spectroscopy (RS) signal of serum based on a high sensitivity thermally annealed silver nanoparticle/porous silicon bragg mirror (AgNPs/PSB) composite substrate. Compared with RS, SERS reflects more and stronger spectral peak information, which is beneficial to discover new biomarkers of breast cancer. At the same time, to further explore the diagnostic ability of SERS technology for breast cancer. In this study, the raw spectral data are processed by baseline correction, polynomial smoothing, and normalization. Then, the relevant feature information of SERS and RS is extracted by principal component analysis (PCA), and five classification models are established to compare the diagnostic performance of SERS and RS models respectively. The experimental results show that the breast cancer diagnosis model based on the improved SERS substrate combined with the machine learning algorithm can be used to distinguish breast cancer patients from controls. The accuracy, sensitivity, specificity and AUC values of the SVM model are 100%, 100%, 100% and 100%, respectively, as well as the training time of 4ms. The above experimental results show that the SERS technology based on AgNPs/PSB composite substrate, combined with machine learning methods, has great potential in the rapid and accurate identification of breast cancer patients.

Spectral-Free Double Light Detection of DNA Based on a Porous Silicon Bragg Mirror

To improve the detection sensitivity of a porous silicon optical biosensor in the real-time detection of biomolecules, a non-spectral porous silicon optical biosensor technology, based on dual-signal light detection, is proposed. Double-light detection is a combination of refractive index change detection and fluorescence change detection. It uses quantum dots to label probe molecules to detect target molecules. In the double-signal-light detection method, the first detection-signal light is the detection light that is reflected from the surface of the porous silicon Bragg mirror. The wavelength of the detection light is the same as the wavelength of the photonic band gap edge of the porous silicon Bragg mirror. CdSe/ZnS quantum dots are used to label the probe DNA and hybridize it with the target DNA molecules in the pores of porous silicon to improve its effective refractive index and enhance the detection-reflection light. The second detection-signal light is fluorescence, which is generated by the quantum dots in the reactant that are excited by light of a certain wavelength. The Bragg mirror structure further enhances the fluorescence signal. A digital microscope is used to simultaneously receive the digital image of two kinds of signal light superimposed on the surface of porous silicon, and the corresponding algorithm is used to calculate the change in the average grey value before and after the hybridization reaction to calculate the concentration of the DNA molecules. The detection limit of the DNA molecules was 0.42 pM. This method can not only detect target DNA by hybridization, but also detect antigen by immune reaction or parallel biochip detection for a porous silicon biosensor.

Dual signal light detection of beta-lactoglobulin based on a porous silicon bragg mirror

In this work, a new dual signal light detection method based on porous silicon Bragg mirror (PSBM) and biological labelling with quantum dots (QDs) is proposed for the detection of beta-lactoglobulin (β-lg). The first signal light is a probe light emitted by a laser with wavelength of 633 nm, which enters the PSBM and is reflected from the surface. The wavelength of the probe light is located at the edge of the PSBM band gap, where it has the lowest reflectivity. β-lg antibodies is labelled with CdSe/ZnS QDs and reacts with β-lg molecules have been fixed to the inner wall of the porous silicon pores. Due to the specific binding of biomolecules in PSBM, the refractive index of the device increases, resulting in the enhancement of detection reflected light. The QDs play the role of refractive index amplification. The second signal light is the fluorescence of QDs in immune reactants. QDs produce fluorescence at 630 nm when excited by a short-wavelength laser. The fluorescence signal is further enhanced by PSBM. The superimposed images of two kinds of light on the surface of PSBM are obtained by digital microscope at the same time. By calculating the average grey value change of the image before and after biological reaction, β-lg can be detected with high sensitivity. The detection limit of β-lg was 0.12 ng/mL. The experimental results showed that the PSBM-based dual signal light method could be used to detect the content of cow milk adulterated in β-lg free camel milk.

Moderate stability of a scissor double fluorescent triple helix molecular switch for the ultrasensitive biosensing of crop transgene

Schematic of the ultrasensitive biosensing of special genes. (I: traditional molecular beacon detection method; II: scissor DFTHMS; III: three cases of BHQ-1-TFO).

Peptide-Based Capture of Chikungunya Virus E2 Protein Using Porous Silicon Biosensor

The detection of pathogens presents specific challenges in ensuring that biosensors remain operable despite exposure to elevated temperatures or other extreme conditions. The most vulnerable component of a biosensor is typically the bioreceptor. Accordingly, the robustness of peptides as bioreceptors offers improved stability and reliability toward harsh environments compared to monoclonal antibodies that may lose their ability to bind target molecules after such exposures. Here, we demonstrate peptide-based capture of the Chikungunya virus E2 protein in a porous silicon microcavity biosensor at room temperature and after exposure of the peptide-functionalized biosensor to high temperature. Contact angle measurements, attenuated total reflectance-Fourier transform infrared spectra, and optical reflectance measurements confirm peptide functionalization and selective E2 protein capture. This work opens the door for other pathogenic biomarker detection using peptide-based capture agents on porous silicon and other surface-based sensor platforms.

Porous Silicon Optical Devices: Recent Advances in Biosensing Applications

This review summarizes the leading advancements in porous silicon (PSi) optical-biosensors, achieved over the past five years. The cost-effective fabrication process, the high internal surface area, the tunable pore size, and the photonic properties made the PSi an appealing transducing substrate for biosensing purposes, with applications in different research fields. Different optical PSi biosensors are reviewed and classified into four classes, based on the different biorecognition elements immobilized on the surface of the transducing material. The PL signal modulation and the effective refractive index changes of the porous matrix are the main optical transduction mechanisms discussed herein. The approaches that are commonly employed to chemically stabilize and functionalize the PSi surface are described.

Highly sensitive SERS assay of genetically modified organisms in maize via a nanoflower substrate coupled with hybridization chain reaction amplification

A novel biosensor based on a high-density “hot spot” SERS substrate coupled with HCR amplification strategy was developed for the ultrasensitive detection of genetically modified organisms in maize.

Label-Free Optical Resonator-Based Biosensors

The demand for biosensor technology has grown drastically over the last few decades, mainly in disease diagnosis, drug development, and environmental health and safety. Optical resonator-based biosensors have been widely exploited to achieve highly sensitive, rapid, and label-free detection of biological analytes. The advancements in microfluidic and micro/nanofabrication technologies allow them to be miniaturized and simultaneously detect various analytes in a small sample volume. By virtue of these advantages and advancements, the optical resonator-based biosensor is considered a promising platform not only for general medical diagnostics but also for point-of-care applications. This review aims to provide an overview of recent progresses in label-free optical resonator-based biosensors published mostly over the last 5 years. We categorized them into Fabry-Perot interferometer-based and whispering gallery mode-based biosensors. The principles behind each biosensor are concisely introduced, and recent progresses in configurations, materials, test setup, and light confinement methods are described. Finally, the current challenges and future research topics of the optical resonator-based biosensor are discussed.

The Enhanced Sensitivity of a Porous Silicon Microcavity Biosensor Based on an Angular Spectrum Using CdSe/ZnS Quantum Dots

To improve the detection sensitivity of porous silicon microcavity biosensors, CdSe/ZnS quantum dots are used to label complementary DNA molecules for the refractive index amplification and angular spectrum method for detection. In this method, the TE mode laser is used as the detection light and the light source is changed into a parallel beam by collimating and expanding the beam, which illuminates the PSM surface and receives the reflected light from the PSM surface through the detector. The angle corresponding to the weakest reflected light intensity before and after the biological reaction between probe DNA and complementary DNA of different concentrations labeled by quantum dots was measured by the detector, and the relationship between the angle change before and after the biological reaction and the complementary DNA concentration labeled by quantum dots was obtained. The experimental results show that the angle change increases linearly with increasing complementary DNA concentration. The detection limit of the experiment, as determined by fitting, is approximately 36 pM. The detection limit of this method is approximately 1/300 of that without quantum dot labeling. Our method has a low cost because it does not require the use of a reflectance spectrometer, and it also demonstrates high sensitivity.

Applying Speckle Noise Suppression to Refractive Indices Change Detection in Porous Silicon Microarrays

The gray value method can be used to detect gray value changes of each unit almost parallel to the surface image of PSi (porous silicon) microarrays and indirectly measure the refractive index changes of each unit. However, the speckles of different noise intensities produced by lasers on a porous silicon surface have different effects on the gray value of the measured image. This results in inaccurate results of refractive index changes obtained from the change in gray value. Therefore, it is very important to reduce the influence of speckle noise on measurement results. In this paper, a new algorithm based on the concepts of probability-based nonlocal-means filtering (PNLM), gradient operator, and median filtering is proposed for gray value restoration of porous silicon microarray images. A good linear relationship between gray value change and refractive index change is obtained, which can reduce the influence of speckle noise on the gray value of the PSi microarray image, improving detection accuracy. This means the method based on gray value change detection can be applied to the biological detection of PSi microarray arrays.

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.

Photonic crystal nanobeam biosensors based on porous silicon

Photonic crystal (PhC) nanobeams (NB) patterned on porous silicon (PSi) waveguide substrates are demonstrated for the specific, label-free detection of oligonucleotides. These photonic structures combine the large active sensing area intrinsic to PSi sensors with the high-quality (Q) factor and low-mode volume characteristic of compact resonant silicon-on-insulator (SOI) PhC NB devices. The PSi PhC NB can achieve a Q-factor near 9,000 and has an approximately 40-fold increased active sensing area for molecular attachment, compared to traditional SOI PhC NB sensors. The PSi PhC NB exhibits a resonance shift that is more than one order of magnitude larger than that of a similarly designed SOI PhC NB for the detection of small chemical molecules and 16-base peptide nucleic acids. The design and fabrication of PSi PhC NB sensors are compatible with CMOS processing, sensor arrays, and integration with lab-on-chip systems.

Layer-by-layer biofunctionalization of nanostructured porous silicon for high-sensitivity and high-selectivity label-free affinity biosensing

Nanostructured materials premise to revolutionize the label-free biosensing of analytes for clinical applications, leveraging the deeper interaction between materials and analytes with comparable size. However, when the characteristic dimension of the materials reduces to the nanoscale, the surface functionalization for the binding of bioreceptors becomes a complex issue that can affect the performance of label-free biosensors. Here we report on an effective and robust route for surface biofunctionalization of nanostructured materials based on the layer-by-layer (LbL) electrostatic nano-assembly of oppositely-charged polyelectrolytes, which are engineered with bioreceptors to enable label-free detection of target analytes. LbL biofunctionalization is demonstrated using nanostructured porous silicon (PSi) interferometers for affinity detection of streptavidin in saliva, through LbL nano-assembly of a bi-layer of positively-charged poly(allylamine hydrochloride) (PAH) and negatively-charged biotinylated poly(methacrylic acid) (b-PMAA). High sensitivity in streptavidin detection is achieved, with high selectivity and stability, down to a detection limit of 600 fM.

Ultrasensitive Label- and PCR-Free Genome Detection Based on Cooperative Hybridization of Silicon Nanowires Optical Biosensors

The realization of an innovative label- and PCR-free silicon nanowires (NWs) optical biosensor for direct genome detection is demonstrated. The system is based on the cooperative hybridization to selectively capture DNA and on the optical emission of quantum confined carriers in Si NWs whose quenching is used as detection mechanism. The Si NWs platform was tested with Hepatitis B virus (HBV) complete genome and it was able to reach a Limit of Detection (LoD) of 2 copies/reaction for the synthetic genome and 20 copies/reaction for the genome extracted from human blood. These results are even better than those obtained with the gold standard real-time PCR method in the genome analysis. The Si NWs sensor showed high sensitivity and specificity, easy detection method, and low manufacturing cost fully compatible with standard silicon process technology. All these points are key factors for the future development of a new class of genetic point-of-care devices that are reliable, fast, low cost, and easy to use for self-testing including in the developing countries.

Optimization of Porous Silicon Conditions for DNA-based Biosensing via Reflectometric Interference Spectroscopy

Objective

Substantial effort has been put into designing DNA-based biosensors, which are commonly used to detect presence of known sequences including the quantification of gene expression. Porous silicon (PSi), as a nanostructured base, has been commonly used in the fabrication of optimally transducing biosensors. Given that the function of any PSi-based biosensor is highly dependent on its nanomorphology, we systematically optimized a PSi biosensor based on reflectometric interference spectroscopy (RIS) detecting the high penetrance breast cancer susceptibility gene, BRCA1.

Materials and Methods

In this experimental study, PSi pore sizes on the PSi surface were controlled for optimum filling with DNA oligonucleotides and surface roughness was optimized for obtaining higher resolution RIS patterns. In addition, the influence of two different organic electrolyte mixtures on the formation and morphology of the pores, based on various current densities and etching times on doped p-type silicon, were examined. Moreover, we introduce two cleaning processes which can efficiently remove the undesirable outer parasitic layer created during PSi formation. Results of all the optimization steps were observed by field emission scanning electron microscopy (FE-SEM).

Results

DNA sensing reached its optimum when PSi was formed in a two-step process in the ethanol electrolyte accompanied by removal of the parasitic layer in NaOH solution. These optimal conditions, which result in pore sizes of approximately 20 nm as well as a low surface roughness, provide a considerable RIS shift upon complementary sequence hybridization, suggesting efficient detectability.

Conclusion

We demonstrate that the optimal conditions identified here makes PSi an attractive solid-phase DNA-based biosensing method and may be used to not only detect full complementary DNA sequences, but it may also be used for detecting point mutations such as single nucleotide substitutions and indels.

TiO2 Nanolayer-Enhanced Fluorescence for Simultaneous Multiplex Mycotoxin Detection by Aptamer Microarrays on a Porous Silicon Surface

A new aptamer microarray method on the TiO₂-porous silicon (PSi) surface was developed to simultaneously screen multiplex mycotoxins. The TiO₂ nanolayer on the surface of PSi can enhance the fluorescence intensity 14 times than that of the thermally oxidized PSi. The aptamer fluorescence signal recovery principle was performed on the TiO₂-PSi surface by hybridization duplex strand DNA from the mycotoxin aptamer and antiaptamer, respectively, labeled with fluorescence dye and quencher. The aptamer microarray can simultaneously screen for multiplex mycotoxins with a dynamic linear detection range of 0.1-10 ng/mL for ochratoxin A (OTA), 0.01-10 ng/mL for aflatoxins B₁ (AFB₁), and 0.001-10 ng/mL for fumonisin B₁ (FB₁) and limits of detection of 15.4, 1.48, and 0.21 pg/mL for OTA, AFB₁, and FB₁, respectively. The newly developed method shows good specificity and recovery rates. This method can provide a simple, sensitive, and cost-efficient platform for simultaneous screening of multiplex mycotoxins and can be easily expanded to the other aptamer-based protocol.

Enhanced Raman scattering in porous silicon grating

The enhancement of Raman signal on monocrystalline silicon gratings with varying groove depths and on porous silicon grating were studied for a highly sensitive surface enhanced Raman scattering (SERS) response. In the experiment conducted, porous silicon gratings were fabricated. Silver nanoparticles (Ag NPs) were then deposited on the porous silicon grating to enhance the Raman signal of the detective objects. Results show that the enhancement of Raman signal on silicon grating improved when groove depth increased. The enhanced performance of Raman signal on porous silicon grating was also further improved. The Rhodamine SERS response based on Ag NPs/ porous silicon grating substrates was enhanced relative to the SERS response on Ag NPs/ porous silicon substrates. Ag NPs / porous silicon grating SERS substrate system achieved a highly sensitive SERS response due to the coupling of various Raman enhancement factors.

Detection of Ammonia-Oxidizing Bacteria (AOB) Using a Porous Silicon Optical Biosensor Based on a Multilayered Double Bragg Mirror Structure

We successfully demonstrate a porous silicon (PS) double Bragg mirror by electrochemical etching at room temperature as a deoxyribonucleic acid (DNA) label-free biosensor for detecting ammonia-oxidizing bacteria (AOB). Compared to various other one-dimension photonic crystal configurations of PS, the double Bragg mirror structure is quite easy to prepare and exhibits interesting optical properties. The width of high reflectivity stop band of the PS double Bragg mirror is about 761 nm with a sharp and deep resonance peak at 1328 nm in the reflectance spectrum, which gives a high sensitivity and distinguishability for sensing performance. The detection sensitivity of such a double Bragg mirror structure is illustrated through the investigation of AOB DNA hybridization in the PS pores. The redshifts of the reflectance spectra show a good linear relationship with both complete complementary and partial complementary DNA. The lowest detection limit for complete complementary DNA is 27.1 nM and the detection limit of the biosensor for partial complementary DNA is 35.0 nM, which provides the feasibility and effectiveness for the detection of AOB in a real environment. The PS double Bragg mirror structure is attractive for widespread biosensing applications and provides great potential for the development of optical applications.

Experimental study of the sensitivity of a porous silicon ring resonator sensor using continuous in-flow measurements

A highly sensitive photonic sensor based on a porous silicon ring resonator was developed and experimentally characterized. The photonic sensing structure was fabricated by exploiting a porous silicon double layer, where the top layer of a low porosity was used to form photonic elements by e-beam lithography and the bottom layer of a high porosity was used to confine light in the vertical direction. The sensing performance of the ring resonator sensor based on porous silicon was compared for the different resonances within the analyzed wavelength range both for transverse-electric and transverse-magnetic polarizations. We determined that a sensitivity up to 439 nm/RIU for low refractive index changes can be achieved depending on the optical field distribution given by each resonance/polarization.

Real-Time and In-Flow Sensing Using a High Sensitivity Porous Silicon Microcavity-Based Sensor

Porous silicon seems to be an appropriate material platform for the development of high-sensitivity and low-cost optical sensors, as their porous nature increases the interaction with the target substances, and their fabrication process is very simple and inexpensive. In this paper, we present the experimental development of a porous silicon microcavity sensor and its use for real-time in-flow sensing application. A high-sensitivity configuration was designed and then fabricated, by electrochemically etching a silicon wafer. Refractive index sensing experiments were realized by flowing several dilutions with decreasing refractive indices, and measuring the spectral shift in real-time. The porous silicon microcavity sensor showed a very linear response over a wide refractive index range, with a sensitivity around 1000 nm/refractive index unit (RIU), which allowed us to directly detect refractive index variations in the 10⁻⁷ RIU range.

Detection of Echinococcus granulosus antigen by a quantum dot/porous silicon optical biosensor

Highly sensitive labeled detection of Echinococcus granulosus using colloidal quantum dots (QDs) based on a porous silicon Bragg mirror sensor are demonstrated. Rabbit anti-p38 labeled CdSe/ZnS QDs was infiltrated in porous silicon pores immobilized Egp38 antigen. QD-antibodies are specifically bound to antigens linked covalently to the pore walls of PSi after the immune reaction. By the design of the transfer matrix method and the preparation of the electrochemical etching method, the fluorescence peak wavelength of the quantum dots is located in the forbidden band of the Bragg mirror. The fluorescence of QDs are enhanced by PSi Bragg mirror. Egp38 antigen detection limit of 300fg/mL is achievable. Our results exhibit that the biosensor combining PSi Bragg mirror and QDs can potentially be applied to the clinical detection of hydatid disease.

Image Processing of Porous Silicon Microarray in Refractive Index Change Detection

A new method for extracting the dots is proposed by the reflected light image of porous silicon (PSi) microarray utilization in this paper. The method consists of three parts: pretreatment, tilt correction and spot segmentation. First, based on the characteristics of different components in HSV (Hue, Saturation, Value) space, a special pretreatment is proposed for the reflected light image to obtain the contour edges of the array cells in the image. Second, through the geometric relationship of the target object between the initial external rectangle and the minimum bounding rectangle (MBR), a new tilt correction algorithm based on the MBR is proposed to adjust the image. Third, based on the specific requirements of the reflected light image segmentation, the array cells are segmented into dots as large as possible and the distance between the dots is equal in the corrected image. Experimental results show that the pretreatment part of this method can effectively avoid the influence of complex background and complete the binarization processing of the image. The tilt correction algorithm has a shorter computation time, which makes it highly suitable for tilt correction of reflected light images. The segmentation algorithm makes the dots in a regular arrangement, excludes the edges and the bright spots. This method could be utilized in the fast, accurate and automatic dots extraction of the PSi microarray reflected light image.

Efficient Fluorescence Resonance Energy Transfer between Quantum Dots and Gold Nanoparticles Based on Porous Silicon Photonic Crystal for DNA Detection

A novel assembled biosensor was prepared for detecting 16S rRNA, a small-size persistent specific for Actinobacteria. The mechanism of the porous silicon (PS) photonic crystal biosensor is based on the fluorescence resonance energy transfer (FRET) between quantum dots (QDs) and gold nanoparticles (AuNPs) through DNA hybridization, where QDs act as an emission donor and AuNPs serve as a fluorescence quencher. Results showed that the photoluminescence (PL) intensity of PS photonic crystal was drastically increased when the QDs-conjugated probe DNA was adhered to the PS layer by surface modification using a standard cross-link chemistry method. The PL intensity of QDs was decreased when the addition of AuNPs-conjugated complementary 16S rRNA was dropped onto QDs-conjugated PS. Based on the analysis of different target DNA concentration, it was found that the decrease of the PL intensity showed a good linear relationship with complementary DNA concentration in a range from 0.25 to 10 μM, and the detection limit was 328.7 nM. Such an optical FRET biosensor functions on PS-based photonic crystal for DNA detection that differs from the traditional FRET, which is used only in liquid. This method will benefit the development of a new optical FRET label-free biosensor on Si substrate and has great potential in biochips based on integrated optical devices.

Hydatid detection using the near-infrared transmission angular spectra of porous silicon microcavity biosensors

Hydatid, which is a parasitic disease, occurs today in many regions worldwide. Because it can present a serious threat to people's health, finding a fast, convenient, and economical means of detection is important. This paper proposes a label- and spectrophotometer-free apparatus that uses optical biological detection based on porous silicon microcavities. In this approach, the refractive index change induced by the biological reactions of a sample in a porous silicon microcavity is detected by measuring the change in the incidence angle corresponding to the maximum transmitted intensity of a near-infrared probe laser. This paper reports that the proposed method can achieve the label-free detection of 43 kDa molecular weight hydatid disease antigens with high sensitivity.

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.

High Sensitivity Detection of CdSe/ZnS Quantum Dot-Labeled DNA Based on N-type Porous Silicon Microcavities

N-type macroporous silicon microcavity structures were prepared using electrochemical etching in an HF solution in the absence of light and oxidants. The CdSe/ZnS water-soluble quantum dot-labeled DNA target molecules were detected by monitoring the microcavity reflectance spectrum, which was characterized by the reflectance spectrum defect state position shift resulting from changes to the structures’ refractive index. Quantum dots with a high refractive index and DNA coupling can improve the detection sensitivity by amplifying the optical response signals of the target DNA. The experimental results show that DNA combined with a quantum dot can improve the sensitivity of DNA detection by more than five times.

Guided Bloch surface wave resonance for biosensor designs

A guided Bloch surface wave resonance (GBR) configuration is introduced for label-free biosensing. The GBR is realized by coupling the first-order diffraction of a subwavelength grating with the Bloch surface wave at the interface between a 1D photonic crystal slab and bio-solution. In addition to sustaining the Bloch surface mode, the photonic crystal provides the design freedom of simultaneously increasing the quality and decreasing the sideband transmissions of the resonance spectrum. The low sideband and high-quality features along with the large sensitivity rising from the strong overlap between the Bloch surface mode and the bio-solution make the GBR suitable for the design of biosensors. Biosensors with a high figure of merit are realized by the compact configurations.

Piezometric biosensors for anti-apoptotic protein survivin based on buried positive-potential barrier and immobilized monoclonal antibodies

The anti-apoptotic protein survivin (Sur) plays an important role in the regulation of cell division and inducing the chemotherapeutic drug resistance. The Sur protein and its mRNA have recently been studied as cancer biomarkers and potential targets for cancer therapy. In this work, we have focused on the design of immunosensors for the detection of Sur based on buried positive-potential barrier layer structure and anti-survivin antibody. The modification of solid AuQC piezoelectrodes was monitored by recording the resonance frequency shift and electrochemical measurements during each step of the sensor preparation. Our results indicate that the immunosensor with covalently bound monoclonal anti-survivin antibody can detect Sur with the limit of detection, LOD=1.7nM (S/N=3σ). The immunosensor applicability for the analysis of real samples was assessed by testing samples of cell lysate solutions obtained from human astrocytoma (glioblastoma) U-87MG cell line, with the experiments performed using the standard addition method. The good linearity of the calibration curves for PBS and lysate solutions at low Sur concentrations confirm the high specificity of the proposed biosensor and good discrimination against nonspecific interactions with lysate components. The calculations indicate that there is still room to increase the Sur capture capacity for Sur while miniaturizing the sensor. The important advantage of the sensor is that it can be reused by a simple regeneration procedure.

Spectrometer-free biological detection method using porous silicon microcavity devices

This paper proposes a label-free and spectrometer-free method for biological detection with high detecting resolution. Taking advantage of the optical properties of porous silicon microcavity, the refractive index changes caused by biological reaction can be detected by measuring the incident angle of the minimum reflected light intensity. Based on the above method, label-free eight-base pair DNA detection can be realized with a corresponding detection limit is as low as 87 nM. This method provides high detecting resolution at a low equipment cost, and can be further used to develop an advanced instrument for biological detection.

Kinetic studies of microfabricated biosensors using local adsorption strategy

Micro/nano scale biosensors integrated with the local adsorption mask have been demonstrated to have a better limit of detection (LOD) and less sample consumptions. However, the molecular diffusions and binding kinetics in such confined droplet have been less studied which limited further development and application of the local adsorption method and imposed restrictions on discovery of new signal amplification strategies. In this work, we studied the kinetic issues via experimental investigations and theoretical analysis on microfabricated biosensors. Mass sensitive film bulk acoustic resonator (FBAR) sensors with hydrophobic Teflon film covering the non-sensing area as the mask were introduced. The fabricated masking sensors were characterized with physical adsorption of bovine serum albumin (BSA) and specific binding of antibody and antigen. Over an order of magnitude improvement on LOD was experimentally monitored. An analytical model was introduced to discuss the target molecule diffusion and binding kinetics in droplet environment, especially the crucial effects of incubation time, which has been less covered in previous local adsorption related literatures. An incubation time accumulated signal amplification effect was theoretically predicted, experimentally monitored and carefully explained. In addition, device optimization was explored based on the analytical model to fully utilize the merits of local adsorption. The discussions on the kinetic issues are believed to have wide implications for other types of micro/nano fabricated biosensors with potentially improved LOD.

Terahertz volatile gas sensing by using polymer microporous membranes

A compact, inexpensive, low loss, highly sensitive gas sensor is important for various biomedical and industrial applications. However, current gas sensors still have an inadequate study in terahertz (THz) frequency range. In this study, simple multilayer-stacked microporous polymer membranes are experimentally validated in the THz regime for organic vapor sensing under ambient atmosphere and room temperature. The hydrophilic porous polymer structure provides a large surface area to adsorb polar vapors, and exhibits excellent discrimination in different types of organic vapors based on distinct dipole moments. Various concentrations of volatile vapors can also be successfully distinguished by detecting the limits of low ppm concentrations. Furthermore, the microporous structural gas sensor has a reasonable response time in repeat usage. This study would provide new perspectives on toxic gas sensing and exhaled breath detection applications in the THz spectral frequency.

Study on Corrosion of Macroporous Silicon in Sodium Hydroxide Solution by Electrochemical Methods and Scanning Electron Microscopy

The fabricated macroporous silicon with a porosity of 26.33% corrosion in NaOH solution was systemically investigated by open circuit potential measurements, linear polarization measurements, potentiodynamic polarization measurements, and scanning electron microscopy, respectively. Results show that the potential open circuit and linear polarization resistance decreases with the NaOH concentration increasing. The corrosion potential shifts significantly to more negative potentials and corrosion current density increases with NaOH concentration increasing. Adding ethanol to 1.0 M NaOH can lead to the linear polarization resistance decrease, corrosion potentials shift in the positive direction, and corrosion current density increase. In addition, the scanning electron microscopy images demonstrate that the macroporous silicon samples are seriously damaged by 1.0 M NaOH and 1.0 M NaOH/EtOH (30%).

Investigation of non-specific signals in nanoporous flow-through and flow-over based sensors

Porous materials are ideal hosts to fabricate high sensitivity devices. Their large specific area and the possibility to modify the type and the strength of the matrix-analyte interactions allow the realization of sensors with finely tailored characteristics. In this article, we investigate how mass transport across the nanoporous structure influences the response due to the non-specific signal by comparing flow-through versus flow-over geometries. We observed a systematic overestimation of the sensitivity for porous substrate devices made of closed-ended pores compared with open-ended pore ones. Our analysis shows that such an effect is due to (unbound) analytes or contaminants that remain trapped within the pores and are not removed by rinsing of the sample. This result was verified by measuring similar samples in both flow through and flow over configurations, as well as their residual response after blockage of all their active sites. We also notice that sensors based on free-standing membranes show similar results independent of the fact that mass transport is induced by either an external pressure source or simply by Brownian motions.

Porous silicon integrated Mach-Zehnder interferometer waveguide for biological and chemical sensing

Optical waveguides comprised of nanoporous materials are uniquely suited for on-chip sensing applications, because they allow for a target chemical or analyte to directly infiltrate the optical material that comprises the core of the waveguide. We describe here the fabrication and characterization of nanoporous waveguides, and demonstrate their usefulness in measuring small changes in refractive index when exposed to a test analyte. We use a process of electrochemical etching and laser oxidation to produce channel waveguides and integrated on-chip Mach-Zehnder structures, and we compare the responsivity and interferometric stability of the integrated sensor to that of a fiber-based interferometer. We quantify the detection capability by selectively applying isopropanol to a 200 μm length waveguide segment in one arm of the interferometer, which produces a phase shift of 9.7 π. The integrated interferometer is shown to provide a more stable response in comparison to a comparable fiber-based implementation.