Ultrasensitive quantum dots-based DNA detection and hybridization kinetics analysis with evanescent wave biosensing platform

Recent Progress in Functional-Nucleic-Acid-Based Fluorescent Fiber-Optic Evanescent Wave Biosensors

Biosensors capable of onsite and continuous detection of environmental and food pollutants and biomarkers are highly desired, but only a few sensing platforms meet the "2-SAR" requirements (sensitivity, specificity, affordability, automation, rapidity, and reusability). A fiber optic evanescent wave (FOEW) sensor is an attractive type of portable device that has the advantages of high sensitivity, low cost, good reusability, and long-term stability. By utilizing functional nucleic acids (FNAs) such as aptamers, DNAzymes, and rational designed nucleic acid probes as specific recognition ligands, the FOEW sensor has been demonstrated to be a general sensing platform for the onsite and continuous detection of various targets ranging from small molecules and heavy metal ions to proteins, nucleic acids, and pathogens. In this review, we cover the progress of the fluorescent FNA-based FOEW biosensor since its first report in 1995. We focus on the chemical modification of the optical fiber and the sensing mechanisms for the five above-mentioned types of targets. The challenges and prospects on the isolation of high-quality aptamers, reagent-free detection, long-term stability under application conditions, and high throughput are also included in this review to highlight the future trends for the development of FOEW biosensors capable of onsite and continuous detection.

Targeted design of green carbon dot-CA-125 aptamer conjugate for the fluorescence imaging of ovarian cancer cell

Aptamer-Carbon Dot (CD) bioconjugation is an attractive target-tracking strategy in detecting cell surface antigens. This study describes an effective imaging paradigm for CA-125 antigen imaging. Our experience encompasses green CD synthesis and characterization, CD-capture probe conjugation through covalent bonding, the hybridization linkage of CD-probe to aptamer and their coupling confirmation, and fluorescent targeted imaging of ovarian cancer cells. As a result, the synthesized CDs from lemon extract by hydrothermal reaction show average size of 2 nm with maximum fluorescence intensity at excitation/emission 360/450 nm. CD-probe construction was provided by functional group interactions of CD and probe via EDC/NHS chemistry. The linkage of CD-probe to aptamer was conducted by Watson-Crick nucleotide pairing. The assessment of CD-probe and CD-probe-aptamer fabrication was validated by the increase in surface roughness through AFM analysis, the diminish of fluorescence intensity of CD after bioconjugation, and particle size growth of the construct. Conjugates with negligible cytotoxicity, appropriate zeta potential, and good aptamer release were applied in cellular imaging. This targeted diagnosis method was employed the four reported DNA aptamers toward fluorescence intensity. The DOV-3 aptamer showed more qualified detection over other aptamer conjugates during fluorescent microscopy analysis. In conclusion, the CD-probe-aptamer conjugate applications as toxic-free method can open new horizons in fluorescent nano-imaging in the field of targeted cancer cell diagnosis.

Trends in the Design of Intensity-Based Optical Fiber Biosensors (2010-2020)

There exists an increasing interest in monitoring low concentrations of biochemical species, as they allow the early-stage detection of illnesses or the monitoring of the environment quality. Thus, both companies and research groups are focused on the development of accurate, fast and highly sensitive biosensors. Optical fiber sensors have been widely employed for these purposes because they provide several advantages for their use in point-of-care and real-time applications. In particular, this review is focused on optical fiber biosensors based on luminescence and absorption. Apart from the key parameters that determine the performance of a sensor (limit of detection, sensibility, cross-sensibility, etc.), other features are analyzed, such as the optical fiber dimensions, the sensing set ups and the fiber functionalization. The aim of this review is to have a comprehensive insight of the different aspects that must be taken into account when working with this kind of sensors.

Nanoscale Affinity Double Layer Overcomes the Poor Antimatrix Interference Capability of Aptamers

Poor antimatrix interference capability of aptamers is one of the major obstacles preventing their wide applications for real-sample detections. Here, we devise a multiple-function interface, denoted as a nanoscale affinity double layer (NADL), to overcome this bottleneck via in situ simultaneous target enrichment, purification, and detection. The NADL consists of an upper aptamer layer for target purification and sensing and a lower nanoscale solid-phase microextraction (SPME) layer for sample enrichment. The targets flowing through the NADL-functionalized surface are instantly million-fold enriched and purified by the sequential extraction of aptamer and SPME. The formation of the aptamer-target complex is greatly enhanced, enabling ultrasensitive detection of targets with minimized interference from the matrix. Taking the fiber-optic evanescent wave sensor as an example, we demonstrated the feasibility and generality of the NADL. The unprecedented detection of limits of 800, 4.8, 40, and 0.14 fM were, respectively, achieved for three representative small-molecule targets with distinct hydrophobicity (kanamycin A, sulfadimethoxine, and di-(2-ethylhexyl) phthalate) and protein target (human serum albumin), corresponding to 2500 to 3 × 10⁸-fold improvement compared to the sensors without the NADL. Our sensors also showed exceptionally high target specificity (>1000) and tunable dynamic ranges simply by manipulating the SPME layer. With these features comes the ability to directly detect targets in diluted environmental, food, and biological samples at concentrations all well below the tolerance limits.

All-fiber all-optical quantitative polymerase chain reaction (qPCR)

Quantitative polymerase chain reaction (qPCR), the real-time amplification and measurement of a targeted DNA molecule, has revolutionized the biological sciences and is routinely applied in areas such as medical diagnostics, forensics, and agriculture. Despite widescale use of qPCR technology in the lab, the availability of low-cost and high-speed portable systems remains one of the barriers to routine in-field implementation. Here we propose and demonstrate a potential solution using a photonics-based qPCR system. By using an all-optical approach, we achieve ultra-fast temperature response with real-time temperature feedback using nanoliter scale reaction volumes. The system uses a microcavity to act as a nanoliter scale reaction vessel with a laser-driven and optically monitored temperature cycling system for ultrafast thermal cycling and incorporates an all-fiber fluorescence excitation/detection system to achieve real-time, high sensitivity fluorescence monitoring of the qPCR process. Further, we demonstrate the potential of the system to operate as a label-free qPCR system through direct optical measurement of the sample refractive index. Due to advantages in portability and fabrication simplicity, we anticipate that this platform technology will offer a new strategy for fundamental techniques in biochemistry applications, such as point-of-care and remote diagnostics.

Evanescent-Wave Fiber Optic Sensing of the Anionic Dye Uranine Based on Ion Association Extraction

Herein, we propose an evanescent-wave fiber optic sensing technique for the anionic dye uranine based on ion association extraction. The sensor was prepared by removing a section of the cladding from a multimode fiber and hydrophobization of the exposed core surface. Uranine was extracted in association along with hexadecyltrimethylammonium (CTA) ion onto the fiber surface and detected via absorption of the evanescent wave generated on the surface of the exposed fiber core. The effect of CTA+ concentration added for ion association was investigated, revealing that the absorbance of uranine increased with increasing CTA+ concentration. A change in the sensor response as a function of the added uranine concentration was clearly observed. The extraction data were analyzed using a distribution equilibrium model and a Freundlich isotherm. The uranine concentration in the evanescent field of the fiber optic was up to 54 times higher than that in the bulk solution, and the limit of detection (3σ) for uranine was found to be 1.3 nM.

Nucleic acid functionalized fiber optic probes for sensing in evanescent wave: optimization and application

Nucleic acid functionalized evanescent wave fiber optic (EWFO) biosensors have attracted much attention due to their remarkable advantages in both device configuration and sensing performance. One critical technique in EWFO biosensor fabrication is its surface modification, which requires (1) minimal nonspecific adsorption and (2) high-quality DNA immobilization to guarantee satisfactory sensing performances. Focusing on these two requirements, a series of optimizations have been conducted in this work to develop reliable DNA-functionalized EWFO probes. Firstly, the surface planeness of EWFO probes were found to be greatly improved by a novel HF/HNO₃ mixture etching solution. Both atomic force microscopy (AFM) and X-ray photoelectron spectroscopy (XPS) were conducted to investigate the morphological structures and surface chemical compositions. Besides, EWFO sensing performances adopting moderate immobilization of irrelevant DNA were investigated for optimization purposes. Furthermore, a split aptamer based sandwich-type EWFO sensor was developed using adenosine (Ade) as the model target (LOD = 25 μM). To the best of our knowledge, this study is the first case to focus on the optimization of etching solution compositions in the fabrication of combination tapered fibers, which provides experimental basis for the understanding of the silica-etching mechanism using HF/HNO₃ mixture solution and may further inspire related researches.

Reliable DNA-functionalized optic probes for sensing in evanescent wave have been developed based a series of optimizations on the etching solution and immobilization chemistry.

Rapid detection of cocaine using aptamer-based biosensor on an evanescent wave fibre platform

The rapid detection of cocaine has received considerable attention because of the instantaneous and adverse effects of cocaine overdose on human health. Aptamer-based biosensors for cocaine detection have been well established for research and application. However, reducing the analytic duration without deteriorating the sensitivity still remains as a challenge. Here, we proposed an aptamer-based evanescent wave fibre (EWF) biosensor to rapidly detect cocaine in a wide working range. At first, the aptamers were conjugated to complementary DNA with fluorescence tag and such conjugants were then immobilized on magnetic beads. After cocaine was introduced to compete against the aptamer-DNA conjugants, the released DNA in supernatant was detected on the EWF platform. The dynamic curves of EWF signals could be interpreted by the first-order kinetics and saturation model. The semi-log calibration curve covered a working range of 10-5000 µM of cocaine, and the limit of detection was approximately 10.5 µM. The duration of the full procedure was 990 s (16.5 min), and the detection interval was 390 s (6.5 min). The specified detection of cocaine was confirmed from four typical pharmaceutic agents. The analysis was repeated for 50 cycles without significant loss of sensitivity. Therefore, the aptamer-based EWF biosensor is a feasible solution to rapidly detect cocaine.

An Optical Biosensor-Based Quantification of the Microcystin Synthetase A Gene: Early Warning of Toxic Cyanobacterial Blooming

The monitoring and control of toxic cyanobacterial strains, which can produce microcystins, is critical to protect human and ecological health. We herein reported an optical-biosensor-based quantification of the microcystin synthetase A (mcyA) gene so as to discriminate microcystin-producing strains from nonproducing strains. In this assay, the mcyA-specific ssDNA probes were designed in silico with an on-line tool and then synthesized to be covalently immobilized on an optical-fiber surface. Production of fluorescently modified target DNA fragment amplicons was accomplished through the use of Cy5-tagged deoxycytidine triphosphates (dCTPs) in the polymerase chain reaction (PCR) method, which resulted in copies with internally labeled multiple sites per DNA molecule and delivered great sensitivity. With a facile surface-based hybridization process, the PCR amplicons were captured on the optical-fiber surface and were induced by an evanescent-wave field into fluorescence emission. Under the optimum conditions, the detection limit was found to be 10 pM (S/N ratio = 3) and equaled 10³ gene copies/mL. The assay was triumphantly demonstrated for PCR amplicons of mcyA detection and showed satisfactory stability and reproducibility. Moreover, the sensing system exhibited excellent selectivity with quantitative spike recoveries from 87 to 102% for M. aeruginosa species in the mixed samples. There results confirmed that the method would serve as an accurate, cost-effective, and rapid technique for in-field testing of toxic Microcystis sp. in water, giving early information for water quality monitoring against microcystin-producing cyanobacteria.

Evanescent wave aptasensor for continuous and online aminoglycoside antibiotics detection based on target binding facilitated fluorescence quenching

The biosensors capable for on-site continuous and online monitoring of pollutants in environment are highly desired due to their practical importance and convenience. The group specific detection of pollutants is especially attractive due to the diversity of environmental pollutants. Here we devise an evanescent wave aptasensor based on target binding facilitated fluorescence quenching (FQ-EWA) for the online continuous and group-specific detection of aminoglycoside antibiotics (AMGAs). In FQ-EWA, a fluorophore labeled DNA aptamer selected against kanamycin was used for both the target recognition in solution and signal transduction on optical fiber of EWA. The aptamers form multiple-strand complex (M-Apt) in the absence of AMGAs. The binding between AMGA and the aptamer disrupts M-Apt and leads to the formation of AMGA -aptamer complex (AMGA-Apt). The photo-induced electron transfer between the fluorophore and AMGA partially quenches the fluorescence of AMGA-Apt. The structure-selective absorption of AMGA-Apt over M-Apt on the graphene oxide further quenches the fluorescence of AMGA-Apt. Meanwhile, the unbound aptamers in solution assemble with the unlabeled aptamers immobilized on the fiber to form M-Apt. The amount of M-Apt on the fiber is inversely proportional to the concentration of AMGAs, enabling the signal-off detection of AMGAs from 200nM to 200μM with a detection limit of 26nM. The whole detection process is carried out in an online mode without any offline operation, providing a great benefit for system automation and miniaturization. FQ-EWA also shows great surface regeneration capability and enables the continuous detection more than 60 times.

Optical sensor for fluoride determination in tea sample based on evanescent-wave interaction and fiber-optic integration

In this work, a miniaturized optical sensor was developed for fluoride determination in tea samples to evaluate their specific risks of fluorosis for public health based on evanescent-wave interaction. The sensor design was integrated on the optical fiber by utilizing the evanescent wave produced on the fiber surface to react with sensing reagents. According to the absorption change at 575nm, fluoride could be determined by colorimetric method and evaluated by Beer's law. With improved performances of small detection volume (1.2μL), fast analysis (0.41min), wide linear range (0.01-1.4mgL^-1), low detection limit (3.5μgL^-1, 3σ) and excellent repeatability (2.34%), the sensor has been applied to fluoride determination in six different tea samples. Conventional spectrophotometry and ion chromatography were employed to validate the sensor's accuracy and potential application. Furthermore, this sensor fabrication provided a miniaturized colorimetric detection platform for other hazardous species monitoring based on evanescent wave interaction.

Fluorescence based fiber optic and planar waveguide biosensors. A review

The application of optical biosensors, specifically those that use optical fibers and planar waveguides, has escalated throughout the years in many fields, including environmental analysis, food safety and clinical diagnosis. Fluorescence is, without doubt, the most popular transducer signal used in these devices because of its higher selectivity and sensitivity, but most of all due to its wide versatility. This paper focuses on the working principles and configurations of fluorescence-based fiber optic and planar waveguide biosensors and will review biological recognition elements, sensing schemes, as well as some major and recent applications, published in the last ten years. The main goal is to provide the reader a general overview of a field that requires the joint collaboration of researchers of many different areas, including chemistry, physics, biology, engineering, and material science.

A novel sensitive pathogen detection system based on Microbead Quantum Dot System

A fast and accurate detection system for pathogens can provide immediate measurements for the identification of infectious agents. Therefore, the Microbead Quantum-dots Detection System (MQDS) was developed to identify and measure target DNAs of pathogenic microorganisms and eliminated the need of PCR amplifications. This nanomaterial-based technique can detect different microorganisms by flow cytometry measurements. In MQDS, pathogen specific DNA probes were designed to form a hairpin structure and conjugated on microbeads. In the presence of the complementary target DNA sequence, the probes will compete for binding with the reporter probes but will not interfere with the binding between the probe and internal control DNA. To monitor the binding process by flow cytometry, both the reporter probes and internal control probes were conjugated with Quantum dots that fluoresce at different emission wavelengths using the click reaction. When MQDS was used to detect the pathogens in environmental samples, a high correlation coefficient (R=0.994) for Legionella spp., with a detection limit of 0.1 ng of the extracted DNAs and 10 CFU/test, can be achieved. Thus, this newly developed technique can also be applied to detect other pathogens, particularly viruses and other genetic diseases.

Portable optical aptasensor for rapid detection of mycotoxin with a reversible ligand-grafted biosensing surface

As food safety is gaining prominence as a global issue, the demand for developing rapid, simple, on-site, accurate and low-cost biosensor technologies will continue to grow. This study demonstrates an evanescent wave optical aptasensor with a reversible ligand-grafted biosensing surface for rapid, sensitive and highly selective detection of ochratoxin A (OTA) in food. In this system, the OTA molecules were covalently immobilized onto the surface of an optical fiber using glutaraldehyde and ethylenediamine as space linkers. An integrated evanescent wave all-fiber (EWA) biosensing platform was developed for investigating the binding kinetics between the tethered ligand and free OTA-aptamer, the performance of the aptamer-based bioassay and the reversibility of biosensing surface. The affinity constant (Ka) of aptamer with tethered OTA was measured to be 2.2 × 10(8)M(-1) based on the EWA biosensing platform. With a competitive detection mode, the quantification of OTA over concentration ranges from 0.73 μg L(-1) to 12.50 μg L(-1) with a detection limit of 0.39 μg L(-1). The performance of the aptasensor with other interfering mycotoxins and spiked real wheat samples shows high specificity and selectivity, good recovery, precision, and accuracy, indicating that it can be applied for on-site, inexpensive and easy-to-use monitoring of OTA in real samples. Moreover, since the organic ligands are grafted onto the fiber surface, this strategy may avoid the potential disadvantages caused by immobilizing the nucleic acid biomolecules, such as weak restoration to the original DNA conformation after repeated uses.

Quantum dots and graphene oxide fluorescent switch based multivariate testing strategy for reliable detection of Listeria monocytogenes

Graphene oxide (GO) and quantum dots (QDs), as burgeoning types of nanomaterials, have gained tremendous interest in the biosensor field. In this work, we designed a novel multivariate testing strategy that depends on the fluorescence resonance energy transfer (FRET) effect between quantum dots (QDs) and graphene oxide (GO). It integrates the QD-GO FRET principle and QD probes with different emission peaks into a platform, aims at multiplex gene detection of a human infectious and highly pathogenic pathogen, Listeria monocytogenes (L. monocytogenes). With the development of a multiplex linear-after-the-exponential (LATE) polymerase chain reaction (PCR) system, the single-stranded DNA (ssDNA) products of hlyA genes and iap genes are obtained by simultaneous amplification of the target genes. Then with the hybridization of ssDNA products and QD probes, simultaneous homogeneous detection of two gene amplification products can be achieved by using GO as a fluorescence switch and monitoring the relevant emissions excited by a single light source. Distinguishable signals corresponding to target genes are obtained. With this developed approach, genomic DNA from L. monocytogenes can be detected as low as 100 fg/μL. Moreover, this platform has a good dynamic range from 10(2) to 10(6) fg/μL. It is indicated that this platform has potential to be a reliable complement for rapid gene detection technologies and is capable of reducing the false-negative and false-dismissal probabilities in routine tests.

Optic fiber-based immunosensor for the rapid and sensitive detection of hepatitis C virus in serum

A portable optic fiber-based immunosensor is developed to achieve rapid and sensitive hepatitis C virus detection in serum.

Development of stable and reproducible biosensors based on electrochemical impedance spectroscopy: three-electrode versus two-electrode setup

This work focuses on the development of electrochemical impedance biosensors based on capacitance readout, for the detection of biomolecules in small sample volumes. We performed electrochemical impedance spectroscopy (EIS) measurements of DNA hybridization in electrochemical cells with microfabricated gold electrodes. The time stability of the device was tested in two different configurations: two microelectrodes in a microfluidic channel; two microelectrodes plus a reference electrode in an electrochemical cell. Our results demonstrate that the three-electrode setup is more stable, more reproducible, and suitable for real-time measurements. In the last part of the work we perform a test study of DNA hybridization in real time, and we show that the three-electrode configuration can measure the process in situ and in real time.

Monitoring DNA hybridization using optical microcavities

The development of DNA analysis methods is rapidly expanding as interest in characterizing subtle variations increases in biomedicine. A promising approach is based on evanescent field sensors that monitor the hybridization process in real time. However, one challenge is discriminating between nonspecific and specific attachment. Here, we demonstrate a hybridization sensor based on an integrated toroidal optical microcavity. The surface is functionalized with ssDNA using an epoxide method, and the evanescent wave of the microresonator excites a fluorescent label on the complementary ssDNA during hybridization. Based on a temporal analysis, the different binding regimes can be identified.

Recent advances in optical biosensors for environmental monitoring and early warning

The growing number of pollutants requires the development of innovative analytical devices that are precise, sensitive, specific, rapid, and easy-to-use to meet the increasing demand for legislative actions on environmental pollution control and early warning. Optical biosensors, as a powerful alternative to conventional analytical techniques, enable the highly sensitive, real-time, and high-frequency monitoring of pollutants without extensive sample preparation. This article reviews important advances in functional biorecognition materials (e.g., enzymes, aptamers, DNAzymes, antibodies and whole cells) that facilitate the increasing application of optical biosensors. This work further examines the significant improvements in optical biosensor instrumentation and their environmental applications. Innovative developments of optical biosensors for environmental pollution control and early warning are also discussed.

Gold-nanoparticle based electrochemical DNA sensor for the detection of fish pathogen Aphanomyces invadans

Epizootic ulcerative syndrome (EUS) is a devastating fish disease caused by the fungus, Aphanomyces invadans. Rapid diagnosis of EUS is needed to control and treat this highly invasive disease. The current diagnostic methods for EUS are labor intensive. We have developed a highly sensitive and specific electrochemical genosensor towards the 18S rRNA and internal transcribed spacer regions of A. invadans. Multiple layers of latex were synthesized with the help of polyelectrolytes, and labeled with gold nanoparticles to enhance sensitivity. The gold-latex spheres were functionalized with specific DNA probes. We describe here the novel application of this improved platform for detection of PCR product from real sample of A. invadans using a premix sandwich hybridization assay. The premix assay was easier, more specific and gave higher sensitivity of one log unit when compared to the conventional method of step-by-step hybridization. The limit of detection was 0.5 fM (4.99 zmol) of linear target DNA and 1 fM (10 amol) of PCR product. The binding positions of the probes to the PCR amplicons were optimized for efficient hybridization. Probes that hybridized close to the 5' or 3' terminus of the PCR amplicons gave the highest signal due to minimal steric hindrance for hybridization. The genosensor is highly suitable as a surveillance and diagnostic tool for EUS in the aquaculture industry.

Sensitive detection of unlabeled oligonucleotides using a paired surface plasma waves biosensor

Detection of unlabeled oligonucleotides using surface plasmon resonance (SPR) is difficult because of the oligonucleotides' relatively lower molecular weight compared with proteins. In this paper, we describe a method for detecting unlabeled oligonucleotides at low concentration using a paired surface plasma waves biosensor (PSPWB). The biosensor uses a sensor chip with an immobilized probe to detect a target oligonucleotide via sequence-specific hybridization. PSPWB measures the demodulated amplitude of the heterodyne signal in real time. In the meantime, the ratio of the amplitudes between the detected output signal and reference can reduce the excess noise from the laser intensity fluctuation. Also, the common-path propagation of p and s waves cancels the common phase noise induced by temperature variation. Thus, a high signal-to-noise ratio (SNR) of the heterodyne signal is detected. The sequence specificity of oligonucleotide hybridization ensures that the platform is precisely discriminating between target and non-target oligonucleotides. Under optimized experimental conditions, the detected heterodyne signal increases linearly with the logarithm of the concentration of target oligonucleotide over the range 0.5-500 pM. The detection limit is 0.5 pM in this experiment. In addition, the non-target oligonucleotide at concentrations of 10 pM and 10nM generated signals only slightly higher than background, indicating the high selectivity and specificity of this method. Different length of perfectly matched oligonucleotide targets at 10-mer, 15-mer and 20-mer were identified at the concentration of 150 pM.

Reusable evanescent wave DNA biosensor for rapid, highly sensitive, and selective detection of mercury ions

Mercury ions (Hg(2+)) are a highly toxic and ubiquitous pollutants requiring rapid and sensitive on-site detection methods in the environment and foods. Herein, we report an envanescent wave DNA-based biosensor for rapid and very sensitive Hg(2+) detection based on a direct structure-competitive detection mode. In this system, a DNA probe covalently immobilized onto a fiber optic sensor contains a short common oligonucleotide sequences that can hybidize with a fluorescently labeled complementary DNA. The DNA probe also comprises a sequence of T-T mismatch pairs that binds with Hg(2+) to form a T-Hg(2+)-T complex by folding of the DNA segments into a hairpin structure. With a structure-competitive mode, a higher concentration of Hg(2+) leads to less fluorescence-labeled cDNA bound to the sensor surface and thus to lower fluorescence signal. The total analysis time for a single sample, including the measurement and surface regeneration, was under 6 min with a Hg(2+) detection limit of 2.1 nM. The high specificity of the sensor was demonstrated by evaluating its response to a number of potentially interfering metal ions. The sensor's surface can be regenerated with a 0.5% SDS solution (pH 1.9) over 100 times with no significant deterioration of performance. This platform is potentially applicable to detect other heavy metal ions or small-molecule analytes for which DNA/aptamers can be used as specific sensing probes.