Label-Free Detection of Peptide Nucleic Acid−DNA Hybridization Using Localized Surface Plasmon Resonance Based Optical Biosensor

Fabrication of localized surface plasmon resonance sensors with scalable polyvinyltetrazole/copper cluster hybrid ring-array for Cu(II) detection

The bottom of a hole-array photoresist template deposited with a hydrophobic atom-transfer radical polymerization (ATRP) initiator was wetted by treatment with oxygen plasma. After the removal of the photoresist template, ring patterns of the ATRP initiator were formed at the interface between the hydrophobic and wetting regions. Polyacrylonitrile (PAN) was grafted from the initiator ring array to covert to polyvinyltetrazole (PVT) rings via a cyano-to-tetrazole reaction, which could adsorb Cu(II) at various concentrations. The Cu(II) ions within the PVT rings were reduced to form a PVT-copper hybrid ring (VCHR), resulting in a blue-shift of the localized surface plasmon resonance (LSPR) peak as the Cu(II) was adsorbed by the PVT rings. The blue-shift and Cu(II) concentration were linearly correlated, with a detection limit of ∼25 pg mL^-1 and a linear range of 25-400 pg mL^-1 for Cu(II) detection. Although the PVT rings also chelated Pb(II) and Cr(III), these ions did not exhibit obvious LSPR peaks. The VCHR LSPR sensor exhibited excellent selectivity for Cu(II) detection. Combining lithography and plasma technology provides a versatile platform for developing the scalable ring structure of copper for highly sensitive and selective Cu(II) sensing.

LSPR Sensing of Epithelial Cell Adhesion Molecules through Sphere and Cavity Plasmons of a Composite Ring Array of Poly[2-(dimethylamino)ethyl methacrylate]/Gold Nanoparticles

Self-organization facilitates the formation of specific structures as a result of constituent interactions. In this study, the bottom of a 600 nm hole array photoresist template, which was deposited with a hydrophobic atom transfer radical polymerization (ATRP) initiator, was wetted by treatment with oxygen plasma. After the removal of the photoresist template, ring patterns of the ATRP initiator were formed at the interface between the hydrophobic and wetting regions. Poly[2-(dimethylamino)ethyl methacrylate] (PDMAEMA) was grafted from the ring array of the initiator to immobilize gold nanoparticles (AuNPs) as a uniform ring array on a silicon substrate via repeated swelling/shrinking cycles. The localized surface plasmon resonance (LSPR) peak of the PDMAEMA-AuNP hybrid ring (PAHR) red-shifted after 12 swelling/shrinking cycles. In comparison to gold nanoparticles, scalable gold nanorings can effectively develop a variety of nanostructures to design LSPR-based sensors and optimize the sensing accuracy and stability. To detect epithelial cell adhesion molecules (EpCAM) during the structural change from a ring to a disk, antiEpCAM was anchored onto the PAHR as a biosensor during swelling/shrinking. The coupling of antiEpCAM and EpCAM led to asymptotical convergence from rings to disks as well as blue shifts of the LSPR peaks. Linear correlation between the blue shift and EpCAM concentration showed a limit of detection of ∼27 pg mL^-1 and a linear range of 25-200 pg mL^-1 for the detection of EpCAM within 30 min. The simple method of combining lithography and plasma technology provides a versatile platform for developing the scalable ring structure of AuNPs for highly sensitive and selective biosensing.

Detection of Alpha-Fetoprotein Using Aptamer-Based Sensors

Alpha-fetoprotein (AFP) is widely-known as the most commonly used protein biomarker for liver cancer diagnosis at the early stage. Therefore, developing the highly sensitive and reliable method of AFP detection is of essential demand for practical applications. Herein, two types of aptamer-based AFP detection methods, i.e., optical and electrochemical biosensors, are reviewed in detail. The optical biosensors include Raman spectroscopy, dual-polarization interferometry, resonance light-scattering, fluorescence, and chemiluminescence. The electrochemical biosensors include cyclic voltammetry, electrochemical impedance spectroscopy, and giant magnetic impedance. Looking into the future, methods for AFP detection that are high sensitivity, long-term stability, low cost, and operation convenience will continue to be developed.

Fabrication of Gold Nanostructures on Quartz Crystal Microbalance Surface Using Nanoimprint Lithography for Sensing Applications

A quartz crystal microbalance (QCM) is a sensor that uses the piezoelectric properties of quartz crystals sandwiched between conductive electrodes. Localized surface plasmon resonance (LSPR) is an analytical technique that uses the collective vibration of free electrons on metal surfaces. These measurements are known as analysis techniques that use metal surfaces and have been applied as biosensors because they allow for the label-free monitoring of biomolecular binding reactions. These measurements can be used in combination to analyze the reactions that occur on metal surfaces because different types of information can be obtained from them. However, as different devices are used for these measurements, the results often contain device-to-device errors and are not accurately evaluated. In this study, we directly fabricated gold nanostructures on the surface of a QCM to create a device that can simultaneously measure the mass and refractive index information of the analyte. In addition, the device could be easily fabricated because nanoimprint lithography was used to fabricate gold nanostructures. As a proof of concept, the nanoparticle adsorption on gold nanostructures was evaluated, and it was observed that mass and refractive index information were successfully obtained without device-to-device errors.

Adjusting the Structure of a Peptide Nucleic Acid (PNA) Molecular Beacon and Promoting Its DNA Detection by a Hybrid with Quencher-Modified DNA

In this study, we performed an elaborate adjustment of the structure of peptide nucleic acid (PNA) molecular beacons as probes for detecting nucleic acids. We synthesized the PNA beacons with various numbers of Glu, Lys, and dabcyl (Dab) quenchers in them, and we investigated their fluorescence changes (F1/1/F0) with and without full-match DNA. As the numbers of Glu/Lys or Dab increased, the F1/1/F0 tended to decrease. Among the different beacons, the PNA beacon with one Glu and one Lys (P1Q1) showed the largest F1/1/F0. On the other hand, a relatively large F1/1/F0 was obtained when the number of Glu/Lys and the number of Dab were the same, and the balance between the numbers of Glu/Lys and Dab seemed to affect the F1/1/F0. We also investigated the DNA detection by the prehybrid of P1Q1, which consists of the T790M base sequence, [P1Q1(T790M)], with quencher-modified DNA (Q-DNA). We examined the DNA detection with single-base mismatch by P1Q1(T790M), and we clarified that there was difficulty in detecting the sequence with P1Q1 alone, but that the sequence was successfully detected by the prehybrid of P1Q1 with the Q-DNA.

Au Nanoparticle-Based Amplified DNA Detection on Poly-l-lysine Monolayer-Functionalized Electrodes

Affinity sensing of nucleic acids is among the most investigated areas in biosensing due to the growing importance of DNA diagnostics in healthcare research and clinical applications. Here, we report a simple electrochemical DNA detection layer, based on poly-l-lysine (PLL), in combination with gold nanoparticles (AuNPs) as a signal amplifier. The layer shows excellent reduction of non-specific binding and thereby high contrast between amplified and non-amplified signals with functionalized AuNPs; the relative change in current was 10-fold compared to the non-amplified signal. The present work may provide a general method for the detection of tumor markers based on electrochemical DNA sensing.

Plasmonic Nanoparticle Conjugation for Nucleic Acid Biosensing

This chapter details the use of gold nanorods conjugated with peptide nucleic acid probes for sequence-specific detection of circulating tumor DNA (ctDNA). ctDNA is gaining increased attention as a biomarker for liquid biopsy, the process of detecting molecules in the peripheral blood rather than a tissue sample. It has wide ranging applications as a diagnostic and prognostic biomarker with a similar mutational profile as the tumor. Plasmonic nanoparticles offer a relatively rapid, amplification-free method for detection of ctDNA through the use of sequence-specific peptide nucleic acid (PNA) probes. In this chapter, we discuss methods for probe design, conjugation to plasmonic particles, and ctDNA quantitation with the resulting sensor. This chapter is a resource for those looking to use plasmonic gold particles for sensing in a solution format for a range of applications.

Nanoplasmonic immunosensor for the detection of SCG2, a candidate serum biomarker for the early diagnosis of neurodevelopmental disorder

The neural circuits of the infant brain are rapidly established near 6 months of age, but neurodevelopmental disorders can be diagnosed only at the age of 2-3 years using existing diagnostic methods. Early diagnosis is very important to alleviate life-long disability in patients through appropriate early intervention, and it is imperative to develop new diagnostic methods for early detection of neurodevelopmental disorders. We examined the serum level of secretogranin II (SCG2) in pediatric patients to evaluate its potential role as a biomarker for neurodevelopmental disorders. A plasmonic immunosensor performing an enzyme-linked immunosorbent assay (ELISA) on a gold nanodot array was developed to detect SCG2 in small volumes of serum. This nanoplasmonic immunosensor combined with tyramide signal amplification was highly sensitive to detect SCG2 in only 5 μL serum samples. The analysis using the nanoplasmonic immunosensor revealed higher serum SCG2 levels in pediatric patients with developmental delay than in the control group. Overexpression or knockdown of SCG2 in hippocampal neurons significantly attenuated dendritic arborization and synaptic formation. These results suggest that dysregulated SCG2 expression impairs neural development. In conclusion, we developed a highly sensitive nanoplasmonic immunosensor to detect serum SCG2, a candidate biomarker for the early diagnosis of neurodevelopmental disorders.

Application of DNA sequences in anti-counterfeiting: Current progress and challenges

Counterfeiting has never been more challenging than during the COVID-19 pandemic as counterfeit test kits and therapeutics have been discovered in the market. Current anti-counterfeiting labels have weaknesses: they can either be duplicated easily, are expensive or ill-suited for the existing complex supply chains. While RFID tags provide for an excellent alternative to current anti-counterfeiting methods, they can prove to be expensive and other routes involving nanomaterials can be difficult to encrypt. A DNA based anticounterfeiting system has significant advantages such as relative ease of synthesis and vast data storage abilities, along with great potential in encryption. Although DNA is equipped with such beneficial properties, major challenges that limit its real-world anti-counterfeiting applications include protection in harsh environments, rapid inexpensive sequence determination, and its attachment to products. This review elaborates the current progress of DNA based anti-counterfeiting systems and identifies technological gaps that need to be filled for its practical application. Progress made on addressing the primary challenges associated with the use of DNA, and potential solutions are discussed.

Photo-genosensor for Trichomonas vaginalis based on gold nanoparticles-genomic DNA

Trichomoniasis, an infectious disease caused by a parasite called Trichomonas vaginalis (T. vaginalis), enhances the risk of HIV infection, cervical and prostate cancer, and infertility. Therefore, efforts have to be made for accurate, specific, and rapid diagnosise and treatment of trichomoniasis. Today, optical nanosensors have created an opportunity for diagnosis without sophisticated and expensive tools and the need for expertise; at the same time, they are highly sensitive and fast. An optical nano-genosensor was designed by conjugation of gold nanoparticles and a specific oligonucleotide (AuNPs-probe) from repeated DNA target for specific and sensitive polymerase chain reaction diagnosis of T. vaginalis gene sequence (L23861.1). The hybridization of AuNPs-probe was investigated with different concentrations of complementary sequence in synthesized target, gene sequence of standard T. vaginalis genomic DNA extraction, and PCR products of genomic DNA samples extracted from patients. Negative samples including synthesized non-complementary sequence, genomics DNA of other pathogens, and genomics DNA of healthy persons were considered for proof of the accuracy of the sensor function. The occurrence of correct hybridization was detected by adding acid to the medium and observing the changes in the color of the medium and spectroscopic spectrum. Based on spectrophotometric results, the fabricated genosensor had detection limits of 35.16 and 31 pg μL^-1 for the detection of synthetic target and genomic DNA sequences, respectively. The results confirmed the correct function of genosensor for the detection of T. vaginalis in clinical samples. Advantages such as low cost, visual detection, speed, and easy diagnosis encourage the use of this sensor in pathogen detection in the future.

Application of Core/Shell Nanoparticles in Smart Farming: A Paradigm Shift for Making the Agriculture Sector More Sustainable

Modern agriculture has entered an era of technological plateau where intervention of smarter technology like nanotechnology is imminently required for making this sector economically and environmentally sustainable. Throughout the world, researchers are trying to exploit the novel properties of several nanomaterials to make agricultural practices more efficient. Core/shell nanoparticles (CSNs) have attracted much attention because of their multiple attractive novel features like high catalytic, optical, and electronic properties for which they are being widely used in sensing, imaging, and medical applications. Though it also has the promise to solve a number of issues related to agriculture, its full potential still remains mostly unexplored. This review provides a panoramic view on application of CSNs in solving several problems related to crop production and precision farming practices where the wastage of resources can be minimized. This review also summarizes different classes of CSNs and their synthesis techniques. It emphasizes and analyzes the probable potential applications of CSNs in the field of crop improvement and crop protection, detection of plant diseases and agrochemical residues, and augmentation of chloroplast mediated photosynthesis. In a nutshell, there is enormous scope to formulate and design CSN-based smart tools for applications in agriculture, making this sector more sustainable.

Attenuated Total Reflection for Terahertz Modulation, Sensing, Spectroscopy and Imaging Applications: A Review

Terahertz (THz) technique has become one of the most promising analytical methods and has been applied in many fields. Attenuated total reflection (ATR) technique applied in THz spectroscopy and imaging has been proven to be superior in functionalities such as modulation, sensing, analyzing, and imaging. Here, we first provide a concise introduction to the principle of ATR, discuss the factors that impact the ATR system, and demonstrate recent advances on THz wave modulation and THz surface plasmon sensing based on the THz-ATR system. Then, applications on THz-ATR spectroscopy and imaging are reviewed. Towards the later part, the advantages and limitations of THz-ATR are summarized, and prospects of modulation, surface plasmon sensing, spectroscopy and imaging are discussed.

Single Cell Analysis of Neutrophils NETs by Microscopic LSPR Imaging System

A simple microengraving cell monitoring method for neutrophil extracellular traps (NETs) released from single neutrophils has been realized using a polydimethylsiloxane (PDMS) microwell array (MWA) sheet on a plasmon chip platform. An imbalance between NETs formation and the succeeding degradation (NETosis) are considered associated with autoimmune disease and its pathogenesis. Thus, an alternative platform that can conduct monitoring of this activity on single cell level at minimum cost but with great sensitivity is greatly desired. The developed MWA plasmon chips allow single cell isolation of neutrophils from 150 µL suspension (6.0 × 10⁵ cells/mL) with an efficiency of 36.3%; 105 microwells with single cell condition. To demonstrate the utility of the chip, trapped cells were incubated between 2 to 4 h after introducing with 100 nM phorbol 12-myristate 13-acetate (PMA) before measurement. Under observation using a hyperspectral imaging system that allows high-throughput screening, the neutrophils stimulated by PMA solution show a significant release of fibrils and NETs after 4 h, with observed maximum areas between 314–758 µm². An average absorption peak wavelength shows a redshift of Δλ = 1.5 nm as neutrophils release NETs.

A Review: Evolution and Diversity of Optical Fibre Plasmonic Sensors

The purpose of this review is to bring to the attention of the wider research community how two quite different optical sensory techniques were integrated resulting in a sensor device of exceptional sensitivity with wide ranging capability. Both authors have collaborated over a 20 year period, each researching initially surface plasmon resonance (SPR) and optical fibre Bragg grating devices. Our individual research, funded in part by EPSRC and industry into these two areas, converged, resulting in a device that combined the ultra-sensitive working platform of SPR behavior with that of fibre Bragg grating development, which provided a simple method for SPR excitation. During this period, they developed a new approach to the fabrication of nano-structured metal coatings for plasmonic devices and demonstrated on fibre optic platform, which has created an ultra-sensitive optical sensing platform. Both authors believe that the convergence of these two areas will create opportunities in detection and sensing yet to be realised. Furthermore, giving the reader "sign-post" research articles to help to construct models to design sensors and to understand their experimental results.

ERASE: a novel surface reconditioning strategy for single-molecule experiments

While surface-based single-molecule experiments have revolutionized our understanding of biology and biomolecules, the workflow in preparing for such experiments, especially surface cleaning and functionalization, remains labor-intensive and time-consuming. Even worse, meticulously assembled flow channels can be used only once for most experiments. A reusable surface would thus dramatically increase productivity and efficiency of single-molecule experiments. In this paper, we report a novel surface reconditioning strategy termed ERASE (Epitaxial Removal Aided by Strand Exchange) that allows a single flow cell to be used for vast repetition of single-molecule experiments. In this method, biomolecules immobilized to the surface through a nucleic acid duplex are liberated when a competing DNA strand disrupts the duplex via toehold-mediated strand displacement. We demonstrate the wide-range applicability of this method with various common surface preparation techniques, fluorescent dyes, and biomolecules including the bacterial ribosome. Beyond time and cost savings, we also show ERASE can assort molecules based on a nucleic acid barcode sequence, thus allowing experiments on different molecules in parallel. Our method increases the utility of prepared surfaces and is a significant improvement to the current single-use paradigm.

Real-time monitoring of DNA immobilization and detection of DNA polymerase activity by a microfluidic nanoplasmonic platform

DNA polymerase catalyzes the replication of DNA, one of the key steps in cell division. The control and understanding of this reaction owns great potential for the fundamental study of DNA-enzyme interactions. In this context, we developed a label-free microfluidic biosensor platform based on the principle of localized surface plasmon resonance (LSPR) to detect the DNA-polymerase reaction in real-time. Our microfluidic LSPR chip integrates a polydimethylsiloxane (PDMS) channel bonded with a nanoplasmonic substrate, which consists of densely packed mushroom-like nanostructures with silicon dioxide stems (~40 nm) and gold caps (~22 nm), with an average spacing of 19 nm. The LSPR chip was functionalized with single-stranded DNA (ssDNA) template (T30), spaced with hexanedithiol (HDT) in a molar ratio of 1:1. The DNA primer (P8) was then attached to T30, and the second strand was subsequently elongated by DNA polymerase assembling nucleotides from the surrounding fluid. All reaction steps were detected in-situ inside the microfluidic LSPR chip, at room temperature, in real-time, and label-free. In addition, the sensor response was successfully correlated with the amount of DNA and HDT molecules immobilized on the LSPR sensor surface. Our platform represents a benchmark in developing microfluidic LSPR chips for DNA-enzyme interactions, further driving innovations in biosensing technologies.

Film-Spotting chiral miniPEG-γPNA array for BRCA1 gene mutation detection

Peptide nucleic acids array technology is a method of greatly increasing the throughput of laboratory processes to efficiently perform large-scale genetic tests. Diethylene glycol-containing chiral γPNA (miniPEG-γPNA) is considered to be the best PNA derivative and one of the best candidates for gene detection, because it can hybridize DNA with greater affinity and sequence selectivity than DNA and ordinary aminoethylglycyl PNA (aegPNA). Herein, miniPEG-γPNA probes are synthesized by 9-fluorenylmethyloxycarbonyl (Fmoc) solid phase peptide synthesis (SPPS) in a mild condition, and a new biochip fabrication method "Film-Spotting" is invented, by which γPNA arrays with regular pattern, uniform luminance, and very low fluorescence background are obtained easily and cheaply. The miniPEG-γPNA array can effectively distinguish the full matched and mismatched targets in SSarc buffer, serum and urine, and the detection limit of complementary DNA is less than 5.97 nM. A miniPEG-γPNA array for BRCA1 gene mutation (3099delT) detection is also fabricated with a very good detection performance. This work provides an effective avenue for the diagnosis of breast cancer biomarker and expands the application of miniPEG-γPNA in the field of biochip.

Ultrasensitive chemiluminescence biosensors using nucleic acid-functionalized silver-cysteine nanowires as signal amplifying labels

Ultrasensitive chemiluminescence (CL) sensors for biomolecules (DNA and proteins) have been developed by adopting DNA-functionalized silver-cysteine hybrid nanowires (p-SCNWs) as signal amplifying labels. The sensing is established from a sandwich-type DNA hybridization, where the target DNA strands are initially hybridized with the capture DNA located at paramagnetic microspheres (PMs) and subsequently hybridized with p-SCNWs functionalized with the signal DNA probe. After magnetic separation, p-SCNWs on the hybrids were completely decomposed with HNO3 to release numerous silver ions. The powerful catalysis of silver ions toward the redox reaction of K2S2O8-Mn2+-H3PO4 causes the generation of KMnO4 that is capable of oxidizing luminol at high pH, triggering an amplified chemiluminescent signal emission. The sensing combines the extraordinary sensitivity of the catalytic chemiluminescence technology and the amplifying strategy via releasing large quantities of silver ions as the catalyst from each hybrid, enabling the assay of target DNA strands at a concentration as low as 0.34 fM. The CL signals associated with single-base pair mismatched DNA strands and non-complementary DNA strands are able to be discriminated well from the CL signal related to the complementary DNA hybridization. Likewise, the combination of p-SCNWs functionalized with an aptamer and PMs/aptamer/thrombin complex allowed the chemiluminescence sensing of thrombin with a low limit of detection corresponding to 0.17 pM.

Ω-Shaped Fiber-Optic Probe-Based Localized Surface Plasmon Resonance Biosensor for Real-Time Detection of Salmonella Typhimurium

A novel, Ω-shaped fiber-optic localized surface plasmon resonance (FOLSPR) biosensor was designed for sensitive real-time and label-free bacterial detection. The designed Ω-shaped fiber-optic probe exhibits an outstanding sensitivity, due to the effect of unique geometry on performance. The results show that refractive index (RI) sensitivity of the Ω-shaped fiber-optic probe is 14 times and 2.5 times higher than those of the straight-shaped and the U-shaped FOLSPR, respectively. In addition, the reason for the geometry and the bending radius effects on RI sensitivity was discussed by investigating the relationship between RI sensitivity and the bending area. The results show that RI sensitivity was enhanced with the increase of bending area, and the best RI sensitivity obtained by Ω-shaped FOLSPR was 64.582 (a.u.)/RIU. Combined with this newly designed Ω-shaped FOLSPR biosensor, a real-time, label-free, sensitive, and highly selective bacterial detection method was established. In this work, the aptamers immobilized on the surface of FOLSPR could specifically capture Salmonella Typhimurium, resulting in an intense change of the absorption peak. In line with this principle, the FOLSPR biosensor achieved high detection sensitivity for Salmonella Typhimurium down to 128 CFU/mL within a linear range from 5 × 10² to 1 × 10⁸ CFU/mL and showed good selectivity for Salmonella Typhimurium detection compared to other bacteria. Furthermore, the FOLSPR biosensor was successfully applied to the detection of Salmonella Typhimurium in a chicken sample with the recoveries of 85-123%. With these characteristics, the novel biosensor is a potential alternative tool in food analysis and environmental monitoring.

Photonic crystals on copolymer film for label-free detection of DNA hybridization

The presence of a single-nucleotide polymorphism in Apolipoprotein E4 gene is implicated with the increased risk of developing Alzheimer's disease (AD). In this study, detection of AD-related DNA oligonucleotide sequence associated with Apolipoprotein E4 gene sequence was achieved using localized-surface plasmon resonance (LSPR) on 2D-Photonic crystal (2D-PC) and Au-coated 2D-PC surfaces. 2D-PC surfaces were fabricated on a flexible copolymer film using nano-imprint lithography (NIL). The film surface was then coated with a dual-functionalized polymer to react with surface immobilized DNA probe. DNA hybridization was detected by monitoring the optical responses of either a Fresnel decrease in reflectance on 2D-PC surfaces or an increase in LSPR on Au-coated 2D-PC surfaces. The change in response due to DNA hybridization on the modified surfaces was also investigated using mismatched and non-complementary oligonucleotides sequences. The proof-of-concept results are promising towards the development of 2D-PC on copolymer film surfaces as miniaturized and wearable biosensors for various diagnostic and defense applications.

Development of a new method based on unmodified gold nanoparticles and peptide nucleic acids for detecting bovine viral diarrhea virus-RNA

A simple colorimetric assay is presented for detecting bovine viral diarrhea virus (BVDV)-RNA based on aggregation of gold nanoparticles (AuNPs) in the presence of charge-neutral peptide nucleic acids (PNA). Free charge-neutral PNA oligomers tended to be adsorbed onto AuNPs and act as a coagulant, whereas hybridizing complementary RNA with PNA disrupted PNA-induced AuNP aggregation, and the NPs remained stable. However, non-complementary RNA did not have this effect, and PNA induced aggregation of the AuNPs that resulted in a color change of the reaction from red to blue. The label-free colorimetric assay developed was estimated to have a 10.48 ng/reaction BVDV-RNA detection limit for the visual assay and 1.05 ng/reaction BVDV-RNA using a spectrophotometer. Diagnostic sensitivity and specificity for the assay was in accordance with real-time reverse transcriptase–polymerase chain reaction (RT-PCR) and nested RT-PCR results were 98 and 100%, respectively. Absorption of the 520/620 nm ratio was linear, along with an increase in the target RNA concentration of 1.64–52.4 ng/reaction (R² = 0.992), which showed a linear correlation for the quantitative assay. This study established a rapid visual label and enzyme-free diagnostic assay for detecting BVDV that is applicable in any clinical laboratory.

An Assay Using Localized Surface Plasmon Resonance and Gold Nanorods Functionalized with Aptamers to Sense the Cytochrome-c Released from Apoptotic Cancer Cells for Anti-Cancer Drug Effect Determination

To determine the degree of cancer cell killing after treatment with chemotherapeutic drugs, we have developed a sensitive platform using localized surface plasmon resonance (LSPR) and aptamers to detect the extracellular cytochrome-c (cyto-c), a mitochondrial protein released from cancer cells for the induction of apoptosis after treatment, to evaluate the effectiveness of cancer therapy. In this assay, a short single-stranded 76-mer DNA aptamer with a unique DNA sequence, which binds towards the cyto-c like an antibody with a high binding affinity and specificity, was conjugated to gold nanorods (AuNR) for LSPR sensing. Practically, cyto-c was first grabbed by a capturing antibody functionalized on the surface of micro-magnetic particles (MMPs). Subsequently, the AuNR-conjugated aptamer was added to form a complex sandwich structure with cyto-c (i.e., (MMP-Ab)-(cyto-c)-(AuNR-aptamer)) after washing away the non-target impurities, such as serum residues and intracellular contents, in a microfluidic chip. The sandwich complex led to formation of AuNR aggregates, which changed the LSPR signals in relation to the amount of cyto-c. With the LSPR signal enhancement effects from the AuNRs, the detection limit of cyto-c, sparked in human serum or culture medium, was found to be 0.1 ng/mL in our platform and the whole sensing process could be completed within two hours. Moreover, we have applied this assay to monitor the apoptosis in leukemia cancer cells induced by a potential anti-cancer agent phenylarsine oxide.

Using Laser Interference Lithography in the Fabrication of a Simplified Micro- and Nanofluidic Device for Label-free Detection

Recently, we developed a label-free detection method based on optical diffraction, and implemented it in on our fabricated micro- and nanofluidic device. This detection method is simple and useful for detecting biomolecules, but the device fabrication consists of complicated processes. In this paper, we propose a simple method for fabricating the micro- and nanofluidic device; the fabrication combines laser interference lithography with conventional photolithography. The performance of a device fabricated by the proposed method is comparable to the performance of the device in our previous study.

Magnetic Nanoparticles for Antibiotics Detection

Widespread use of antibiotics has led to pollution of waterways, potentially creating resistance among freshwater bacterial communities. Microorganisms resistant to commonly prescribed antibiotics (superbug) have dramatically increased over the last decades. The presence of antibiotics in waters, in food and beverages in both their un-metabolized and metabolized forms are of interest for humans. This is due to daily exposure in small quantities, that, when accumulated, could lead to development of drug resistance to antibiotics, or multiply the risk of allergic reaction. Conventional analytical methods used to quantify antibiotics are relatively expensive and generally require long analysis time associated with the difficulties to perform field analyses. In this context, electrochemical and optical based sensing devices are of interest, offering great potentials for a broad range of analytical applications. This review will focus on the application of magnetic nanoparticles in the design of different analytical methods, mainly sensors, used for the detection of antibiotics in different matrices (human fluids, the environmental, food and beverages samples).

Selective detection of Mg2+ ions via enhanced fluorescence emission using Au-DNA nanocomposites

The biophysical properties of DNA-modified Au nanoparticles (AuNPs) have attracted a great deal of research interest for various applications in biosensing. AuNPs have strong binding capability to the phosphate and sugar groups in DNA, rendering unique physicochemical properties for detection of metal ions. The formation of Au-DNA nanocomposites is evident from the observed changes in the optical absorption, plasmon band, zeta potential, DLS particle size distribution, as well as TEM and AFM surface morphology analysis. Circular dichroism studies also revealed that DNA-functionalized AuNP binding caused a conformational change in the DNA structure. Due to the size and shape dependent plasmonic interactions of AuNPs (33-78 nm) with DNA, the resultant Au-DNA nanocomposites (NCs) exhibit superior fluorescence emission due to chemical binding with Ca²⁺, Fe²⁺ and Mg²⁺ ions. A significant increase in fluorescence emission (λ_ex = 260 nm) of Au-DNA NCs was observed after selectively binding with Mg²⁺ ions (20-800 ppm) in an aqueous solution where a minimum of 100 ppm Mg²⁺ ions was detected based on the linearity of concentration versus fluorescence intensity curve (λ_em = 400 nm). The effectiveness of Au-DNA nanocomposites was further verified by comparing the known concentration (50-120 ppm) of Mg²⁺ ions in synthetic tap water and a real life sample of Gelusil (300-360 ppm Mg²⁺), a widely used antacid medicine. Therefore, this method could be a sensitive tool for the estimation of water hardness after careful preparation of a suitably designed Au-DNA nanostructure.

Colorimetric Detection Based on Localised Surface Plasmon Resonance Optical Characteristics for the Detection of Hydrogen Peroxide Using Acacia Gum-Stabilised Silver Nanoparticles

The use of nanoparticles in sensing is attracting the interest of many researchers. The aim of this work was to fabricate Acacia gum–stabilised silver nanoparticles (SNPs) using green chemistry to use them as a highly sensitive and cost-effective localised surface plasmon resonance (LSPR) colorimeter sensor for the determination of reactive oxygen species, such as hydrogen peroxide (H₂O₂). Silver nanoparticles were fabricated by the reduction of an inorganic precursor silver nitrate solution (AgNO₃) using white sugar as the reducing reagent and Acacia gum as the stabilising reagent and a sonication bath to form uniform silver nanoparticles. The fabricated nanoparticles were characterised by visual observation, ultraviolet-visible (UV-Vis) spectrophotometry, transmission electron microscopy (TEM) analysis, energy-dispersive X-ray spectroscopy (EDAX), thermogravimetric analysis (TGA), and Fourier transform infrared spectroscopy (FT-IR). The TEM micrographs of the synthesised nanoparticles showed the presence of spherical nanoparticles with sizes of approximately 10 nm. The EDAX spectrum result confirmed the presence of silver (58%), carbon (30%), and oxygen (12%). Plasmon colorimetric sensing of H₂O₂ solution was investigated by introducing H₂O₂ solution into Acacia gum–capped SNP dispersion, and the change in the LSPR band in the UV-Vis region of spectra was monitored. In this study, it was found that the yellow colour of Acacia gum–stabilised SNPs gradually changed to transparent, and moreover, a remarkable change in the LSPR absorbance strength was observed. The calibration curve was linear over 0.1–0.00001 M H₂O₂, with a correlation estimation (R²) of .953. This was due to the aggregation of SNPs following introduction of the H₂O₂ solution. Furthermore, the fabricated SNPs were successfully used to detect H₂O₂ solution in a liquid milk sample, thereby demonstrating the ability of the fabricated SNPs to detect H₂O₂ solution in liquid milk samples. This work showed that Acacia gum–stabilised SNPs may have the potential as a colour indicator in medical and environmental applications.

Mechanism of adsorption of single and double stranded DNA on gold and silver nanoparticles: Investigating some important parameters in bio-sensing applications

The mechanism of adsorption of single and double stranded DNAs on colloidal gold and silver nanoparticles has been studied by measuring the resistance of the nanoparticles, surrounded by various oligonucleotides, against salt induced aggregation. It is shown that both single and double stranded DNAs can be adsorbed on the metal nanoparticles and the adsorption strength is determined by the interaction between various bases of DNA and the nanoparticles. By changing the salt concentration, the difference between adsorption of various DNA strands on the nanoparticles can be specified. The results indicate that a key parameter in success of a sensing assay of DNA hybridization is the salt concentration which should be greater than a minimum threshold depending on the nanoparticles characteristics. We have also investigated the interaction mechanism between various DNA bases with the metal nanoparticles. For both gold and silver nanoparticles, adenine has the highest and thymine has the lowest attachment to the nanoparticles. From surface enhanced Raman spectroscopy (SERS) data of various bases in the presence of gold nanoparticles, the probable interaction points in the bases with the nanoparticles have been determined, which are mainly the nitrogen sites of these oligonucleotides.

A novel graphene-based label-free fluorescence 'turn-on' nanosensor for selective and sensitive detection of phosphorylated species in biological samples and living cells

A novel label-free fluorescence 'turn-on' nanosensor has been developed for highly selective and sensitive detection of phosphorylated species (Ps) in biological samples and living cells. The design strategy relies on the use of Ti(4+)-immobilized polydopamine (PDA) coated reduced graphene oxide (rGO@PDA-Ti(4+)) that serves as an attractive platform to bind riboflavin 5'-monophosphate molecules (FMNs) through ion-pair interactions between phosphate groups and Ti(4+). The as-prepared rGO@PDA-Ti(4+)-FMNs (nanosensor), fluoresce only weakly due to the ineffective Förster resonance energy transfer between the FMNs and rGO@PDA-Ti(4+). The experimental findings revealed that the microwave-assisted interaction of the nanosensor with α-, β-casein, ovalbumin, human serum, non-fat milk, egg white, and living cells (all containing Ps) releases FMNs (due to the high formation constant between phosphate groups and Ti(4+)), leading to an excellent fluorescence 'turn-on' response. The fluorescence spectroscopy, confocal microscopy, and MALDI-TOF MS spectrometry were used to detect Ps both qualitatively and quantitatively. Under the optimized conditions, the nanosensor showed a detection limit of ca. 118.5, 28.9, and 54.8 nM for the tryptic digests of α-, β-casein and ovalbumin, respectively. Furthermore, the standard addition method was used as a bench-mark proof for phosphopeptide quantification in egg white samples. We postulate that the present quantitative assay for Ps holds tremendous potential and may pave the way to disease diagnostics in the near future.

Electrostatically tunable plasmonic devices fabricated on multi-photon polymerized three-dimensional microsprings

Electrostatically tunable plasmonic devices on three-dimensional (3D) microsprings were fabricated using multi-photon polymerization followed by metal deposition. These plasmonic devices comprised a nanostructured Au microplate and two 3D microsprings. The maximum plasmon excitation efficiency was 35%, a value achieved with incident light of wavelength 632.8 nm. The efficiency could be continuously changed from almost zero to maximum by inclining the microplates with the application of DC voltage up to 50 V. Such dynamic functionality is useful for the realization of highly integrated optoelectronic devices and tunable metamaterials.

Electrochemical label-free degranulation monitoring for in-situ evaluation of cellular function

We fabricated a degranulation monitoring device, combining ion-sensitive field-effect transistor (ISFET) and microperfusion system. The electrical properties of ISFET were maintained even after immobilization of RBL-2H3 mast cells on the sensor. We successfully demonstrated in-situ monitoring of degranulation from stimulated RBL-2H3 cells by ionomycin. Potential change was induced by the release of acid-granule contents, which result in local pH decrease on the sensor under physiological conditions. This microdevice is expected to contribute as a platform technology for evaluating induced immune responses by chemical compounds.

Label-free fluorescence detection of melamine with a truncated aptamer

The 88 nt melamine aptamer Rd29C33 was truncated to a 34 nt Rd29C33-T7, which is suitable for the label-free detection of melamine.

A Label-free Technique for the Spatio-temporal Imaging of Single Cell Secretions

Inter-cellular communication is an integral part of a complex system that helps in maintaining basic cellular activities. As a result, the malfunctioning of such signaling can lead to many disorders. To understand cell-to-cell signaling, it is essential to study the spatial and temporal nature of the secreted molecules from the cell without disturbing the local environment. Various assays have been developed to study protein secretion, however, these methods are typically based on fluorescent probes which disrupt the relevant signaling pathways. To overcome this limitation, a label-free technique is required.

In this paper, we describe the fabrication and application of a label-free localized surface plasmon resonance imaging (LSPRi) technology capable of detecting protein secretions from a single cell. The plasmonic nanostructures are lithographically patterned onto a standard glass coverslip and can be excited using visible light on commercially available light microscopes. Only a small fraction of the coverslip is covered by the nanostructures and hence this technique is well suited for combining common techniques such as fluorescence and bright-field imaging.

A multidisciplinary approach is used in this protocol which incorporates sensor nanofabrication and subsequent biofunctionalization, binding kinetics characterization of ligand and analyte, the integration of the chip and live cells, and the analysis of the measured signal. As a whole, this technology enables a general label-free approach towards mapping cellular secretions and correlating them with the responses of nearby cells.

Continuously tunable nucleic acid hybridization probes

In silico designed nucleic acid probes and primers often fail to achieve favorable specificity and sensitivity tradeoffs on the first try, and iterative empirical sequence-based optimization is needed, particularly in multiplexed assays. Here, we present a novel, on-the-fly method of tuning probe affinity and selectivity via the stoichiometry of auxiliary species, allowing independent and decoupled adjustment of hybridization yield for different probes in multiplexed assays. Using this method, we achieve near-continuous tuning of probe effective free energy (0.03 kcal·mol⁻¹ granularity). As applications, we enforced uniform capture efficiency of 31 DNA molecules (GC content 0% – 100%), maximized signal difference for 11 pairs of single nucleotide variants, and performed tunable hybrid-capture of mRNA from total RNA. Using the Nanostring nCounter platform, we applied stoichiometric tuning to simultaneously adjust yields for a 24-plex assay, and we show multiplexed quantitation of RNA sequences and variants from formalin-fixed, paraffin-embedded samples (FFPE).

Chemical sensing with nanoparticles as optical reporters: from noble metal nanoparticles to quantum dots and upconverting nanoparticles

A wide variety of biological and medical analyses are based on the use of optical signals to report specific molecular events. Thanks to advances in nanotechnology, various nanostructures have been extensively used as optical reporters in bio- and chemical assays. This review describes recent progress in chemical sensing using noble metal nanoparticles (gold and silver), quantum dots and upconverting nanoparticles. It provides insights into various nanoparticle-based sensing strategies including fluorescence/luminescence resonance energy transfer nanoprobes as well as activatable probes sensitive to specific changes in the biological environment. Finally we list some research challenges to be overcome in order to accelerate the development of applications of nanoparticle bio- and chemical sensors.

Optimizing Nanoplasmonic Biosensor Sensitivity with Orientated Single Domain Antibodies

Localized surface plasmon resonance (LSPR) spectroscopy and imaging are emerging biosensor technologies which tout label-free biomolecule detection at the nanoscale and ease of integration with standard microscopy setups. The applicability of these techniques can be limited by the restrictions that surface-conjugated ligands must be both sufficiently small and orientated to meet analyte sensitivity requirements. We demonstrate that orientated single domain antibodies (sdAb) can optimize nanoplasmonic sensitivity by comparing three anti-ricin sdAb constructs to biotin-neutravidin, a model system for small and highly orientated ligand studies. LSPR imaging of electrostatically orientated sdAb exhibited a ricin sensitivity equivalent to that of the biotinylated LSPR biosensors for neutravidin. These results, combined with the facts that sdAb are highly stable and readily produced in bacteria and yeast, build a compelling case for the increased utilization of sdAbs in nanoplasmonic applications.

The Coupling between Gold or Silver Nanocubes in Their Homo-Dimers: A New Coupling Mechanism at Short Separation Distances

Using the DDA method, we investigated the near-field coupling between two excited Au or Ag 42 nm nanocubes in a face-to-face dimer configuration at small separation distances where the exponential coupling behavior distinctly changes. This could be due to the failure of the dipole approximation at short distances or a change in the electromagnetic field distribution between the adjacent monomers. A detailed calculation of the plasmonic field distribution strongly suggests that the latter mechanism is responsible for the failure of the expected exponential coupling behavior at small separation distances. The results suggest that the observed optical properties of the pair of Au or Ag nanocubes separated by distances larger than 6 nm, result from the electromagnetic coupling between the oscillating dipoles at the corners of the adjacent facets of the nanocubes. At separations smaller than 6 nm, the distribution of the plasmonic dipoles along both the facets and the corners of the adjacent monomers control the plasmonic spectra and the distance dependent optical properties of the dimer.

Electrochemical synthesis of nanostructured gold film for the study of carbohydrate-lectin interactions using localized surface plasmon resonance spectroscopy

Localized surface plasmon resonance (LSPR) spectroscopy is a label-free chemical and biological molecular sensing technique whose sensitivity depends upon development of nanostructured transducers. Herein, we report an electrodeposition method for fabricating nanostructured gold films (NGFs) that can be used as transducers in LSPR spectroscopy. The NGF was prepared by electrodepositing gold from potassium dicyanoaurate solution onto a flat gold surface using two sequential controlled potential steps. Imaging by scanning electron microscopy reveals a morphology consisting of randomly configured block-like nanostructures. The bulk refractive index sensitivity of the prepared NGF is 100±2 nmRIU(-1) and the initial peak in the reflectance spectrum is at 518±1 nm under N2(g). The figure of merit is 1.7. In addition, we have studied the interaction between carbohydrate (mannose) and lectin (Concanavalin A) on the NGF surface using LSPR spectroscopy by measuring the interaction of 8-mercaptooctyl-α-d-mannopyranoside (αMan-C8-SH) with Concanavalin A by first immobilizing αMan-C8-SH in mixed SAMs with 3,6-dioxa-8-mercaptooctanol (TEG-SH) on the NGF surface. The interaction of Con A with the mixed SAMs is confirmed using electrochemical impedance spectroscopy. Finally, the NGF surface was regenerated to its original sensitivity by removing the SAM and the bound biomolecules. The results from these experiments contribute toward the development of inexpensive LSPR based sensors that could be useful for studying glycan-protein interactions and other bioanalytical purposes.