scholarly journals An Advanced, Silicon-Based Substrate for Sensitive Nucleic Acids Detection

Sensors ◽  
2018 ◽  
Vol 18 (9) ◽  
pp. 3138 ◽  
Author(s):  
Salvatore Petralia ◽  
Nunzio Vicario ◽  
Giovanna Calabrese ◽  
Rosalba Parenti ◽  
Sabrina Conoci
Keyword(s):  
Limit Of Detection ◽  
Optical Signal ◽  
Fluorescent Label ◽  
Capture Probe ◽  
Microarray Technology ◽  
Probe Sequence ◽  
B Virus ◽  
Nucleic Acids Detection ◽  
Silicon Based ◽  
Dynamic Linear Range

Surface substrate and chemical functionalization are crucial aspects for the fabrication of the sensitive biosensor based on microarray technology. In this paper, an advanced, silicon-based substrate (A-MA) allowing enhancement of optical signal for microarray application is described. The substrate consists in a multilayer of Si/Al/SiO2 layers. The optical signal enhancement is reached by a combination of the mirror effect of Al film and the SiO2 thickness around 830 nm, which is able to reach the maximum of interference for the emission wavelength of the Cy5 fluorescent label. Moreover, SiO2 layer is suitable for the immobilization of single-strand DNA through standard silane chemistry, and probe densities of about 2000 F/um2 are reached. The microarray is investigated in the detection of HBV (Hepatitis B Virus) pathogen with analytical samples, resulting in a dynamic linear range of 0.05–0.5 nM, a sensitivity of about 18000 a.u. nM−1, and a Limit of Detection in the range of 0.031–0.043 Nm as a function of the capture probe sequence.

scholarly journals Hybrid Integrated Nanophotonic Silicon-based Structures

2019 ◽  
Vol 29 (4) ◽  
pp. 481
Author(s):  
Thi Hong Cam Hoang ◽  
Thanh Binh Pham ◽  
Thuy Van Nguyen ◽  
Van Dai Pham ◽  
Huy Bui ◽  
...  
Keyword(s):  
Optical Fiber ◽  
Fiber Laser ◽  
Limit Of Detection ◽  
Signal To Noise Ratio ◽  
Optical Signal ◽  
Integrated System ◽  
Laser Structure ◽  
Wavelength Shift ◽  
On Chip ◽  
Silicon Based

We report nanophotonic silicon-based devices for hybrid integration: 1D photonic crystal (PhC) on optical fiber, i. e. fiber Bragg grating (FBG) sensing probe integrated in fiber laser structure for chemical sensors and slotted planar 2D PhC cavity combined with carbon nanotube (CNT) towards light nanosources. The experiments have been carried out by integrating 1D PhC on optical fiber in fiber laser structure. This structure possesses many advantages including high resolution for wavelength shift, high optical signal-to-noise ratio (OSNR) of about 50~dB, the small full width at half-maximum (FWHM) of about 0.014~nm therefore its accuracy is enhanced, as well as the precision and capability are achieved for remote sensing. Low nitrate concentration in water from 0 to 80 ppm has been used to demonstrate its sensing ability in the experiment. The proposed sensor can work with good repeatability, rapid response, and its sensitivity can be obtained of \(3.2\times 10^{ - 3}\) nm/ppm with the limit of detection (LOD) of 3~ppm. For 2D PhC cavity, enhancement of photoluminescence of CNT emission is observed. The semiconducting single-walled carbon nanotubes (s-SWNTs) solution was prepared by polymer-sorted method and coupled with the confined modes in silicon slotted PhC cavities. The enhancement ratio of 1.15 is obtained by comparing between the PL peaks at two confined modes of the cavity. The PL enhancement result of the integrated system shows the potential for the realization of on-chip nanoscale sources.

scholarly journals Signal Amplification in an Optical and Dielectric Biosensor Employing Liquid Crystal-Photopolymer Composite as the Sensing Medium

Biosensors ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 81
Author(s):  
Hassanein Shaban ◽  
Shih-Chun Yen ◽  
Mon-Juan Lee ◽  
Wei Lee
Keyword(s):  
Dielectric Constant ◽  
Liquid Crystal ◽  
Uv Irradiation ◽  
Signal Amplification ◽  
Limit Of Detection ◽  
Optical Signal ◽  
Uv Exposure ◽  
Dielectric Anisotropy ◽  
Optical Texture ◽  
Potential Development

An optical and dielectric biosensor based on a liquid crystal (LC)–photopolymer composite was established in this study for the detection and quantitation of bovine serum albumin (BSA). When the nematic LC E7 was doped with 4-wt.% NOA65, a photo-curable prepolymer, and photopolymerized by UV irradiation at 20 mW/cm2 for 300 s, the limit of detection determined by image analysis of the LC optical texture and dielectric spectroscopic measurements was 3400 and 88 pg/mL for BSA, respectively, which were lower than those detected with E7 alone (10 μg/mL BSA). The photopolymerized NOA65, but not the prepolymer prior to UV exposure, contributed to the enhanced optical signal, and UV irradiation of pristine E7 in the absence of NOA65 had no effect on the optical texture. The effective tilt angle θ, calculated from the real-part dielectric constant ε’, decreased with increasing BSA concentration, providing strong evidence for the correlation of photopolymerized NOA65 to the intensified disruption in the vertically oriented LC molecules to enhance the optical and dielectric signals of BSA. The optical and dielectric anisotropy of LCs and the photo-curable dopant facilitate novel quantitative and signal amplification approaches to potential development of LC-based biosensors.

Development of an Optical Fiber Sensor with a D-shaped Fiber Bragg Grating Integrated in a Loop-mirror Optical Fiber Laser as a High Sensitivity Refractometer

2021 ◽  
Vol 32 ◽  
Author(s):  
Binh Pham Thanh ◽  
Thuy Van Nguyen ◽  
Van Hoi Pham ◽  
Huy Bui ◽  
Thi Hong Cam Hoang ◽  
...  
Keyword(s):  
Refractive Index ◽  
Optical Fiber ◽  
Fiber Laser ◽  
Fiber Bragg Grating ◽  
Limit Of Detection ◽  
Optical Fiber Sensor ◽  
High Sensitivity ◽  
Optical Signal ◽  
Bragg Grating ◽  
Loop Mirror

In this paper, we report a new type of refractometer based on a D-shaped fiber Bragg grating (FBG) integrated in a loop-mirror optical fiber laser. This proposed sensor is used in wavelength interrogation method, in which the D-shaped FBG is applied as a refractive index (RI) sensing probe and a mirror to select mode of laser. The D-shaped FBG is prepared by the removal of a portion of the fiber cladding covering the FBG by means of side-polishing technique. The D-shaped FBG sensing probe integrated in a loop-mirror optical fiber laser with saturated pump technique, the characteristics of sensing signals have been improved to obtain stable intensity, narrower bandwidth and higher optical signal-to-noise ratio compare to normal reflection configuration. The limit of detection (LOD) of this sensor can be achieved to 2.95 x 10-4 RIU in the refractive index (RI) range of 1.42-1.44. Accordingly, we believe that the proposed refractometer has a huge potential for applications in biochemical-sensing technique.

scholarly journals Optical Signal Processing in Silicon-Based Integrated Devices

2018 ◽  
Author(s):  
C. Lacava ◽  
T.D. Bucio ◽  
A.Z. Khokhar ◽  
D.J. Richardson ◽  
F. Parmigiani ◽  
...  
Keyword(s):  
Signal Processing ◽  
Optical Signal Processing ◽  
Optical Signal ◽  
Integrated Devices ◽  
Silicon Based

scholarly journals A novel fluorescent biosensor based on dendritic DNA nanostructure in combination with ligase reaction for ultrasensitive detection of DNA methylation

2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Shu Zhang ◽  
Jian Huang ◽  
Jingrun Lu ◽  
Min Liu ◽  
Yan Li ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Limit Of Detection ◽  
Fluorescent Dye ◽  
Fluorescence Signal ◽  
Target Sequence ◽  
Capture Probe ◽  
Detection Range ◽  
Fluorescent Biosensor ◽  
Dna Nanostructure ◽  
Reporter Probe

Background DNA methylation detection is indispensable for the diagnosis and prognosis of various diseases including malignancies. Hence, it is crucial to develop a simple, sensitive, and specific detection strategy. Methods A novel fluorescent biosensor was developed based on a simple dual signal amplification strategy using functional dendritic DNA nanostructure and signal-enriching polystyrene microbeads in combination with ligase detection reaction (LDR). Dendritic DNA self-assembled from Y-DNA and X-DNA through enzyme-free DNA catalysis of a hairpin structure, which was prevented from unwinding at high temperature by adding psoralen. Then dendritic DNA polymer labeled with fluorescent dye Cy5 was ligated with reporter probe into a conjugate. Avidin-labeled polystyrene microbeads were specifically bound to biotin-labeled capture probe, and hybridized with target sequence and dendritic DNA. LDR was triggered by adding Taq ligase. When methylated cytosine existed, the capture probe and reporter probe labeled with fluorescent dye perfectly matched the target sequence, forming a stable duplex to generate a fluorescence signal. However, after bisulfite treatment, unmethylated cytosine was converted into uracil, resulting in a single base mismatch. No fluorescence signal was detected due to the absence of duplex. Results The obtained dendritic DNA polymer had a large volume. This method was time-saving and low-cost. Under the optimal experimental conditions using avidin-labeled polystyrene microbeads, the fluorescence signal was amplified more obviously, and DNA methylation was quantified ultrasensitively and selectively. The detection range of this sensor was 10−15 to 10−7 M, and the limit of detection reached as low as 0.4 fM. The constructed biosensor was also successfully used to analyze actual samples. Conclusion This strategy has ultrasensitivity and high specificity for DNA methylation quantification, without requiring complex processes such as PCR and enzymatic digestion, which is thus of great value in tumor diagnosis and biomedical research.

scholarly journals Detection of severe acute respiratory syndrome coronavirus 2 and influenza viruses based on CRISPR-Cas12a

2020 ◽  
pp. 153537022096379
Author(s):  
Oraphan Mayuramart ◽  
Pattaraporn Nimsamer ◽  
Somruthai Rattanaburi ◽  
Naphat Chantaravisoot ◽  
Kritsada Khongnomnan ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Severe Acute Respiratory Syndrome ◽  
Influenza A ◽  
Limit Of Detection ◽  
Cross Reactivity ◽  
Influenza Viruses ◽  
Influenza B Virus ◽  
Influenza B ◽  
Influenza Virus A ◽  
B Virus

Due to the common symptoms of COVID-19, patients are similar to influenza-like illness. Therefore, the detection method would be crucial to discriminate between SARS-CoV-2 and influenza virus-infected patients. In this study, CRISPR-Cas12a-based detection was applied for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A virus, and influenza B virus which would be a practical and attractive application for screening of patients with COVID-19 and influenza in areas with limited resources. The limit of detection for SARS-CoV-2, influenza A, and influenza B detection was 10, 103, and 103 copies/reaction, respectively. Moreover, the assays yielded no cross-reactivity against other respiratory viruses. The results revealed that the detection of influenza virus and SARS-CoV-2 by using RT-RPA and CRISPR-Cas12a technology reaches 96.23% sensitivity and 100% specificity for SARS-CoV-2 detection. The sensitivity for influenza virus A and B detections was 85.07% and 94.87%, respectively. In addition, the specificity for influenza virus A and B detections was approximately 96%. In conclusion, the RT-RPA with CRISPR-Cas12a assay was an effective method for the screening of influenza viruses and SARS-CoV-2 which could be applied to detect other infectious diseases in the future.

scholarly journals Disposable silicon-based all-in-one micro-qPCR for rapid on-site detection of pathogens

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Estefania Nunez-Bajo ◽  
Alexander Silva Pinto Collins ◽  
Michael Kasimatis ◽  
Yasin Cotur ◽  
Tarek Asfour ◽  
...  
Keyword(s):  
Real Time ◽  
Limit Of Detection ◽  
Low Cost ◽  
High Specificity ◽  
Rapid Screening ◽  
Quantitative Detection ◽  
The Novel ◽  
Novel Coronavirus ◽  
Silicon Based ◽  
Specific Sequences

AbstractRapid screening and low-cost diagnosis play a crucial role in choosing the correct course of intervention when dealing with highly infectious pathogens. This is especially important if the disease-causing agent has no effective treatment, such as the novel coronavirus SARS-CoV-2, and shows no or similar symptoms to other common infections. Here, we report a disposable silicon-based integrated Point-of-Need transducer (TriSilix) for real-time quantitative detection of pathogen-specific sequences of nucleic acids. TriSilix can be produced at wafer-scale in a standard laboratory (37 chips of 10 × 10 × 0.65 mm in size can be produced in 7 h, costing ~0.35 USD per device). We are able to quantitatively detect a 563 bp fragment of genomic DNA of Mycobacterium avium subspecies paratuberculosis through real-time PCR with a limit-of-detection of 20 fg, equivalent to a single bacterium, at the 35th cycle. Using TriSilix, we also detect the cDNA from SARS-CoV-2 (1 pg) with high specificity against SARS-CoV (2003).

scholarly journals Distortion losses of high-speed single-photon avalanche diode optical receivers approaching quantum sensitivity

2020 ◽  
Vol 378 (2169) ◽  
pp. 20190194 ◽  
Author(s):  
John Kosman ◽  
Kevin Moore ◽  
Harald Haas ◽  
Robert K. Henderson
Keyword(s):  
High Speed ◽  
Limit Of Detection ◽  
Single Photon ◽  
Visible Light Communication ◽  
Optical Signal ◽  
Quantum Limit ◽  
Modulation Scheme ◽  
Communication Link ◽  
Nonlinear Behaviour ◽  
Error Performance

The high internal gain of single-photon avalanche diodes (SPADs) operating in Geiger mode allows the quantum limit of detection to be approached. This offers a significantly improved sensitivity for optical communication over existing photodiodes. A fully integrated CMOS SPAD array receiver (RX) is presented which achieves 500 Mb s −1 four-level pulse amplitude modulation in a visible light communication link within 15.2 dB of the quantum limit. However, SPAD dead time induces around 5.7 dB of transient distortion which restricts error performance and data rate. We propose a model describing a discrete photon counting system which exhibits this nonlinear behaviour and compare it to practical measurements with the RX. A unipolar intensity modulated optical signal is considered, as opposed to bipolar electric fields in conventional radio frequency wireless systems. Intermodulation between the DC and harmonic components of the data-carrying waveform is investigated, and the resulting degradation of signal-to-noise-and-distortion ratio and bit error rate is evaluated. The model is developed as a tool for understanding distortion to ultimately allow rectification through RX architecture, modulation scheme, coding and equalization techniques. This article is part of the theme issue ‘Optical wireless communication’.

All – Optical Signal Processing on Silicon – Based Platforms

2016 ◽  
Author(s):  
D. T. H. Tan ◽  
G. F. R. Chen ◽  
K. J. A. Ooi ◽  
J. W. Choi ◽  
B. U. Sohn ◽  
...  
Keyword(s):  
Signal Processing ◽  
Optical Signal Processing ◽  
Optical Signal ◽  
All Optical ◽  
Silicon Based

scholarly journals A Label-Free Fluorescent DNA Machine for Sensitive Cyclic Amplification Detection of ATP

Materials ◽  
2018 ◽  
Vol 11 (12) ◽  
pp. 2408
Author(s):  
Jingjing Zhang ◽  
Jialun Han ◽  
Shehong Feng ◽  
Chaoqun Niu ◽  
Chen Liu ◽  
...  
Keyword(s):  
Human Urine ◽  
Limit Of Detection ◽  
Logic Gates ◽  
Fluorescent Label ◽  
Label Free ◽  
Background Signal ◽  
Detection Range ◽  
Signal Suppression ◽  
Dna Machine ◽  
Recycling Amplification

In this study, a target recycled amplification, background signal suppression, label-free fluorescent, enzyme-free deoxyribonucleic acid (DNA) machine was developed for the detection of adenosine triphosphate (ATP) in human urine. ATP and DNA fuel strands (FS) were found to trigger the operation of the DNA machine and lead to the cyclic multiplexing of ATP and the release of single stranded (SS) DNA. Double-stranded DNA (dsDNA) was formed on graphene oxide (GO) from the combination of SS DNA and complementary strands (CS′). These double strands then detached from the surface of the GO and in the process interacted with PicoGreen dye resulting in amplifying fluorescence intensity. The results revealed that the detection range of the DNA machine is from 100 to 600 nM (R2 = 0.99108) with a limit of detection (LOD) of 127.9 pM. A DNA machine circuit and AND-NOT-AND-OR logic gates were successfully constructed, and the strategy was used to detect ATP in human urine. With the advantage of target recycling amplification and GO suppressing background signal without fluorescent label and enzyme, this developed strategy has great potential for sensitive detection of different proteins and small molecules.

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