Influence of nanometric holes on the sensitivity of a waveguide-mode sensor: label-free nanosensor for the analysis of RNA aptamer-ligand interactions

Spiked nanorosette: A novel zinc oxide-gold textured nanostructure for impedance biosensing of target DNA signatures

The creation of nanostructure is profound for the generation of nanobiosensors in several medical diagnosis. Here, we employed an aqueous hydrothermal route using Zinc-oxide (ZnO) and Gold (Au), which under optimal conditions formed an ultra-crystalline rose-like nanostructure textured with nanowires on the surface, coined as "spiked nanorosette." The spiked nanorosette structures was further characterized to possess crystallites of ZnO and Au grains with average sizes of 27.60 and 32.33 nm, respectively. The intensity for both ZnO (002) and Au (111) planes of the nanocomposite was inferred to be controlled by fine-tuning the percentage of Au nanoparticles doped in the ZnO/Au matrix, as referred by X-ray diffraction analysis. The formation of ZnO/Au-hybrid nanorosettes were additionally verified by the distinct corresponding peaks from photoluminescence and X-ray photoelectron spectroscopy, supported by electrical validations. The biorecognition properties of the spiked nanorosettes were also examined using custom targeted and non-target DNA sequences. The DNA targeting capabilities of the nanostructures were analyzed by Fourier Transform Infrared and electrochemical impedance spectroscopy. The fabricated nanowire-embedded nanorosette exhibited a detection limit at the lower picomolar range of 1 × 10-12 M, with high selectivity, stability and reproducibility and good linearity, under optimal conditions. Impedance-based techniques are more sensitive to the detection of nucleic acid molecule whereas this novel spiked nanorosette demonstrate promising attributes as excellent nanostructures for nanobiosensor developments and their potential future application for nucleic-acids or disease diagnostics.

Coordinated Dispersion and Aggregation of Gold Nanorod in Aptamer-Mediated Gestational Hypertension Analysis

Gestational hypertension is one of the complicated disorders during pregnancy; it causes the significant risks, such as placental abruption, neonatal deaths, and maternal deaths. Hypertension is also responsible for the metabolic and cardiovascular issues to the mother after the years of pregnancy. Identifying and treating gestational hypertension during pregnancy by a suitable biomarker is mandatory for the healthy mother and foetus development. Cortisol has been found as a steroid hormone that is secreted by the adrenal gland and plays a pivotal role in gestational hypertension. A normal circulating level of cortisol is involved in the regulation of blood pressure, and it is necessary to monitor the changes in the level of cortisol during pregnancy. In this work, aptamer-based colorimetric assay is demonstrated as a model with gold nanorod to quantify the level of cortisol using the coordinated aggregation (at 500 mM of NaCl) and dispersion (with 10 μM of aptamer), evidenced by the scanning electron microscopy observation and UV-visible spectroscopy analysis. This colorimetric assay is an easier visual detection and reached the limit of detection of cortisol at 0.25 mg/mL. This method is reliable to identify the condition of gestational hypertension during the pregnancy period.

Amine-Aldehyde Chemical Conjugation on a Potassium Hydroxide-Treated Polystyrene ELISA Surface for Nanosensing an HIV-p24 Antigen

The enzyme-linked immunosorbent assay (ELISA) has been widely used for disease surveillance and drug screening due to its relatively higher accuracy and sensitivity. Fine-tuning the ELISA is mandatory to elevate the specific detection of biomolecules at a lower abundance. Towards this end, higher molecular capture on the polystyrene (PS) ELISA surface is crucial for efficient detection, and it could be attained by immobilizing the molecules in the correct orientation. It is highly challenging to immobilize protein molecules in a well-aligned manner on an ELISA surface due to charge variations. We employed a 3-(aminopropyl) triethoxysilane (APTES)- and glutaraldehyde (GLU)-coupled PS surface chemical strategy to demonstrate the high performance with ELISA. A potassium hydroxide treatment followed by an equal ratio of 1% APTES and GLU attachment was found to be optimal, and a longer incubation with GLU favored maximum sensitivity. p24 is a vital early secreting antigen for diagnosing human immunodeficiency virus (HIV), and it has been used for efficient detection with the above chemistry. Three different procedures were followed, and they led to the improved detection of the HIV-p24 antigen at 1 nM, which is a 30-fold higher level compared to a conventional ELISA surface. The surface chemical functionalization shown here also displays a higher specificity with human serum and HIV-TAT. The above approach with the designed surface chemistry could also be recommended for disease diagnosis on other sensing surfaces involving the interaction of the probe and the analyte in heterogeneous test samples.

Diagnosing human blood clotting deficiency

There are different clotting factors present in blood, carries the clotting cascade and excessive bleeding may cause a deficiency in the clotting Diagnosis of this deficiency in clotting drastically reduces the potential fatality. For enabling a sensor to detect the clotting factors, suitable probes such as antibody and aptamer have been used to capture these targets on the sensing surface. Two major clotting factors were widely studied for the diagnosis of clotting deficiency, which includes factor IX and thrombin. In addition, factor IX is considered as the substitute for heparin and the prothrombotic associated with the increased thrombin generation are taking into account their prevalence. The biosensors, surface plasmon resonance, evanescent-field-coupled waveguide-mode sensor, metal-enhanced PicoGreen fluorescence and electrochemical aptasensor were well-documented and improvements have been made for high-performance sensing. We overviewed detecting factor IX and thrombin using these biosensors, for the potential application in medical diagnosis.

Characterization of Gold-Sputtered Zinc Oxide Nanorods-a Potential Hybrid Material

Generation of hybrid nanostructures has been attested as a promising approach to develop high-performance sensing substrates. Herein, hybrid zinc oxide (ZnO) nanorod dopants with different gold (Au) thicknesses were grown on silicon wafer and studied for their impact on physical, optical and electrical characteristics. Structural patterns displayed that ZnO crystal lattice is in preferred c-axis orientation and proved the higher purities. Observations under field emission scanning electron microscopy revealed the coverage of ZnO nanorods by Au-spots having diameters in the average ranges of 5-10 nm, as determined under transmission electron microscopy. Impedance spectroscopic analysis of Au-sputtered ZnO nanorods was carried out in the frequency range of 1 to 100 MHz with applied AC amplitude of 1 V RMS. The obtained results showed significant changes in the electrical properties (conductance and dielectric constant) with nanostructures. A clear demonstration with 30-nm thickness of Au-sputtering was apparent to be ideal for downstream applications, due to the lowest variation in resistance value of grain boundary, which has dynamic and superior characteristics.

Cell-targeting aptamers act as intracellular delivery vehicles

Aptamers are single-stranded nucleic acids or peptides identified from a randomized combinatorial library through specific interaction with the target of interest. Targets can be of any size, from small molecules to whole cells, attesting to the versatility of aptamers for binding a wide range of targets. Aptamers show drug properties that are analogous to antibodies, with high specificity and affinity to their target molecules. Aptamers can penetrate disease-causing microbial and mammalian cells. Generated aptamers that target surface biomarkers act as cell-targeting agents and intracellular delivery vehicles. Within this context, the "cell-internalizing aptamers" are widely investigated via the process of cell uptake with selective binding during in vivo systematic evolution of ligands by exponential enrichment (SELEX) or by cell-internalization SELEX, which targets cell surface antigens to be receptors. These internalizing aptamers are highly preferable for the localization and functional analyses of multiple targets. In this overview, we discuss the ways by which internalizing aptamers are generated and their successful applications. Furthermore, theranostic approaches featuring cell-internalized aptamers are discussed with the purpose of analyzing and diagnosing disease-causing pathogens.

Biotin-Streptavidin Competition Mediates Sensitive Detection of Biomolecules in Enzyme Linked Immunosorbent Assay

Enzyme Linked Immunosorbent Assay (ELISA) is the gold standard assay for detecting and identifying biomolecules using antibodies as the probe. Improving ELISA is crucial for detecting disease-causing agents and facilitating diagnosis at the early stages of disease. Biotinylated antibody and streptavidin-conjugated horse radish peroxide (streptavidin-HRP) often are used with ELISA to enhance the detection of various kinds of targets. In the present study, we used a competition-based strategy in which we pre-mixed free biotin with streptavidin-HRP to generate high-performance system, as free biotin occupies some of the biotin binding sites on streptavidin, thereby providing more chances for streptavidin-HRP to bind with biotinylated antibody. ESAT-6, which is a protein secreted early during tuberculosis infection, was used as the model target. We found that 8 fM of free biotin mixed with streptavidin-HRP anchored the higher detection level of ESAT-6 by four-fold compared with detection without free biotin (only streptavidin-HRP), and the limit of detection of the new method was 250 pM. These results suggest that biotin-streptavidin competition can be used to improve the diagnosis of analytes in other types of sensors.

Aptamer-based 'point-of-care testing'

Aptamers are single-stranded oligonucleotides that can be artificially generated by a method called Systematic evolution of ligands by exponential enrichment (SELEX). The generated aptamers have been assessed for high-performance sensing applications due to their appealing characteristics. With either aptamers alone or complementing with antibodies, several high sensitive and portable sensors have been demonstrated for use in 'point-of-care testing'. Due to their high suitability and flexibility, aptamers are conjugated with nanostructures and utilized in field applications. Moreover, aptamers are more amenable to chemical modifications, making them capable of utilization with most developed sensors. In this overview, we discuss novel, portable, and aptamer-based sensing strategies that are suitable for 'point-of-care testing'.

Evaluation of anti-A/Udorn/307/1972 antibody specificity to influenza A/H3N2 viruses using an evanescent-field coupled waveguide-mode sensor

Discrimination of closely related strains is a key issue, particularly for infectious diseases whose incidence fluctuates according to variations in the season and evolutionary changes. Among infectious diseases, influenza viral infections are a worldwide cause of pandemic disease and mortality. With the emergence of different influenza strains, it is vital to develop a method using antibodies that can differentiate between viral types and subtypes. Ideally, such a system would also be user friendly. In this study, a polyclonal antibody generated against A/Udorn/307/1972 (H3N2) was used as a probe to distinguish between influenza H3N2 viruses based on the interaction between the antibody and hemagglutinin, demonstrating its applicability for viral discrimination. Clear discrimination was demonstrated using an evanescent-field-coupled waveguide-mode sensor, which has appealing characteristics over other methods in the viewpoint of improving the sensitivity, measurement time, portability and usability. Further supporting evidence was obtained using enzyme-linked immunosorbent assays, hemagglutination-inhibition assays, and infectivity neutralization assays. The results obtained indicate that the polyclonal antibody used here is a potential probe for distinguishing influenza viruses and, with the aid of a handheld sensor it could be used for influenza surveillance.

Observations of immuno-gold conjugates on influenza viruses using waveguide-mode sensors

Gold nanoparticles were conjugated to an antibody (immuno-AuNP) against A/Udorn/307/1972 (H3N2) influenza virus to detect viruses on a sensing plate designed for an evanescent field-coupled waveguide-mode sensor. Experiments were conducted using human influenza A/H3N2 strains, and immuno-AuNP could detect 8×10(5) PFU/ml (40 pg/µl) intact A/Udorn/307/1972 and 120 pg/µl A/Brisbane/10/2007. Furthermore, increased signal magnitude was achieved in the presence of non-ionic detergent, as the virtual detection level was increased to 8×10(4) PFU/ml A/Udorn/307/1972. Immuno-AuNPs were then complexed with viruses to permit direct observation, and they formed a ring of confined nanodots on the membrane of both intact and detergent-treated viruses as directly visualized by scanning electron microscopy. With this complex the detection limit was improved further to 8×10(3) PFU/ml on anti-rabbit IgG immobilized sensing plate. These strategies introduce methods for observing trapped intact viruses on the sensing plates generated for optical systems.

Neu5Acα2,6Gal and Neu5Acα2,3Gal receptor specificities on influenza viruses determined by a waveguide-mode sensor

To characterize the differences in the receptor-binding specificities of human and avian influenza viruses with glycan chains, the authors performed binding analyses using an evanescent field-coupled waveguide-mode biosensor. The experiments were performed on intact viruses and hemagglutinin proteins, using gold-nanoparticle-conjugated Neu5Acα2,6Gal and Neu5Acα2,3Gal glycan chains. Several influenza viruses belonging to subtypes H3N2 (A/Udorn/307/1972, A/Shandong/9/1993, A/Kiev/301/1994, A/Panama/2007/1999, A/Wisconsin/67/2005 and A/Brisbane/10/2007), H1N1 (A/Brisbane/59/2007 and A/California/07/2009) and H5N1 (A/chicken/India/NIV33487/2006) were used. High levels of glycan-based discrimination were observed with the H3N2 strain A/Brisbane/10/2007 due to its specificity with Neu5Acα2,6Gal, but not with Neu5Acα2,3Gal. Possible amino acid residues responsible for the discrimination of human and avian influenza viruses are discussed. These types of sensor-based discriminatory analyses would be very useful for distinguishing between influenza pandemics, especially during the transition and overlapping periods of human and avian influenza viruses with evolutionary changes.

Surface functionalization chemistries on highly sensitive silica-based sensor chips

The surfaces of silica-based sensor chips, designed for evanescent-field-coupled waveguide-mode sensors, were functionalized using various surface chemistries. The immobilization of molecular entities on the functionalized silica surfaces was monitored using various microscopic techniques (scanning electron, fluorescence, and atomic force microscopies). Further, gold nanoparticle-based signal enhancement analyses were performed with protein conjugation on different functionalized surfaces using a waveguide-mode sensor. Based on these analyses, the sensor surfaces modified with glutaraldehyde (Glu) and carbonyldiimidazole were found to be good for molecules of different sizes. In addition, it can be inferred that the Glu-modified surface may be suitable for small molecules with diameters around 5 nm owing to its surface roughness. The modified surface with carbonyldiimidazole is suitable for the direct immobilization of larger molecules especially for biomolecular assemblies without intermediate chemical modifications.

Waveguide-mode sensors as aptasensors

Aptamers are artificial nucleic acid ligands that can be generated by in vitro selection through partition and amplification. Aptamers can be generated against a wide range of biomolecules through the formation of versatile stem-loop structures. Because aptamers are potential substitutes for antibodies and drugs, the development of an aptamer-based sensor (aptasensor) is mandatory for diagnosis. We previously reported that waveguide-mode sensors are useful in the analysis of a wide range of biomolecular interactions, including aptamers. The advantages of the waveguide-mode sensor that we developed include physical and chemical stability and that higher sensitivity can be achieved with ease by perforating the waveguide layer or using colored materials such as dyes or metal nanoparticles as labels. Herein, we provide an overview of the strategies and applications for aptamer-based analyses using waveguide-mode sensors.

Optical detection systems using immobilized aptamers

Advances in the development and the applications of optical biosensing systems based on immobilized aptamers are presented. These nucleic acid sequences have been used as new molecular recognition elements to develop heterogeneous assays, biosensors and microarrays. Among different detection modes that have been employed, optical ones which are described here are among the most used. Since their first report in 1996, numerous optical detection systems using aptamers and mainly based on fluorescence have been developed. Two main approaches have been used: label-based (using fluorophore, luminophore, enzyme, nanoparticles) or aptamer label-free detection systems (e.g. surface plasmon resonance, optical resonance). Most methods are based on a labeling approach. Some targets can be optically detected using not only colorimetry, chemiluminescence or the most developed fluorescence mode but also more recent non conventional optical methods such as surface plasmon-coupled directional emission (SPCDE). The first SPCDE-based aptasensor for thrombin detection has recently been reported in 2009. Aptasensors based on surface-enhanced Raman scattering spectroscopy (SERS) which presents advantages compared to fluorescence have also been described. Different label-free techniques have recently been shown to be suitable for developing performant aptasensors or aptamer-based microarrays, such as surface plasmon resonance (SPR), diffraction grating, evanescent-field-coupled (EFC) waveguide-mode, optical resonance or Brewster angle straddle interferometry (BASI). Important advances have been realized on optical aptamer-based detection systems that appear as highly efficient devices with enormous potential.

Evaluation of nucleic acid duplex formation on gold over layers in biosensor fabricated using Czochralski-grown single-crystal silicon substrate

With a view to developing an economical and elegant biosensor chip, we compared the efficiencies of biosensors that use gold-coated single-crystal silicon and amorphous glass substrates. The reflectivity of light over a wide range of wavelengths was higher from gold layer coated single-crystal silicon substrates than from glass substrates. Furthermore, the efficiency of reflection from gold layers of two different thicknesses was examined. The thicker gold layer (100 nm) on the single-crystal silicon showed a higher reflectivity than the thinner gold film (10 nm). The formation of a nucleic acid duplex and aptamer-ligand interactions were evaluated on these gold layers, and a crystalline silicon substrate coated with the 100-nm-thick gold layer is proposed as an alternative substrate for studies of interactions of biomolecules.

Strategies for the design of RNA-binding small molecules

Bacterial ribosomal RNA is the target of clinically important antibiotics, while biologically important RNAs in viral and eukaryotic genomes present a range of potential drug targets. The physicochemical properties of RNA present difficulties for medicinal chemistry, particularly when oral availability is needed. Peptidic ligands and analysis of their RNA-binding properties are providing insight into RNA recognition. RNA-binding ligands include far more chemical classes than just aminoglycosides. Chemical functionalities from known RNA-binding small molecules are being exploited in fragment- and ligand-based projects. While targeting of RNA for drug design is very challenging, continuing advances in our understanding of the principles of RNA–ligand interaction will be necessary to realize the full potential of this class of targets.

A sensitive multilayered structure suitable for biosensing on the BioDVD platform

Several technologies are currently available for the analysis of biomolecular interactions with high sensitivity and efficiency. However, these instruments are invariably expensive and, thus, are not suitable for bedside analyses. To circumvent this issue, we have previously reported a BioDVD platform that allowed us to use a DVD mechanism to monitor various biomolecular interactions [Gopinath et al., 2008, ACS Nano 2, 1885-1895]. In the present study, to improve the sensitivity of the BioDVD platform for various analyses, we have performed computer simulations to optimize the ZnS-SiO(2) layer thicknesses and determined an optimized optical interferometric response after adjusting the ZnS-SiO(2) layer thickness to 65 and 60 nm for the inner and outer layer thicknesses, respectively. Biomolecular interaction analyses performed with the optimized BioDVD disks revealed a 3-fold improvement in the sensitivity, compared to our previously reported multilayered structure. In this study, we have also shown that the BioDVD platform is suitable not only for analyzing nucleic acid hybridization and interactions between RNA-small ligands and RNA-proteins, but also for antigen-antibody interactions. Furthermore, our evaluations revealed that each sample required no more than 10 tracks of data to analyze the biomolecular interactions on the BioDVD platform, which permits a greater number of spots per BioDVD disk and also reduces the time needed to measure the biomolecular interactions.