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

Synthetic methodology for asymmetric ferrocene derived bio-conjugate systems via solid phase resin-based methodology

Early detection is a key to successful treatment of most diseases, and is particularly imperative for the diagnosis and treatment of many types of cancer. The most common techniques utilized are imaging modalities such as Magnetic Resonance Imaging (MRI), Positron Emission Topography (PET), and Computed Topography (CT) and are optimal for understanding the physical structure of the disease but can only be performed once every four to six weeks due to the use of imaging agents and overall cost. With this in mind, the development of "point of care" techniques, such as biosensors, which evaluate the stage of disease and/or efficacy of treatment in the clinician's office and do so in a timely manner, would revolutionize treatment protocols.1 As a means to exploring ferrocene based biosensors for the detection of biologically relevant molecules2, methods were developed to produce ferrocene-biotin bio-conjugates described herein. This report will focus on a biotin-ferrocene-cysteine system that can be immobilized on a gold surface.

Bimodal-hybrid heterocyclic amine targeting oxidative pathways and copper mis-regulation in Alzheimer's disease

Oxidative stress resulting from metal-ion misregulation plays a role in the development of Alzheimer's disease (AD). This process includes the production of tissue-damaging reactive oxygen species and amyloid aggregates. Herein we describe the synthesis, characterization and protective capacity of the small molecule, lipoic cyclen, which has been designed to target molecular features of AD. This construct utilizes the biologically compatible and naturally occurring lipoic acid as a foundation for engendering low cellular toxicity in multiple cell lines, radical scavenging capacity, tuning the metal affinity of the parent cyclen, and results in an unexpected affinity for amyloid without inducing aggregation. The hybrid construct thereby shows protection against cell death induced by amyloid aggregates and copper ions. These results provide evidence for the rational design methods used to produce this fused molecule as a potential strategy for the development of lead compounds for the treatment of neurodegenerative disorders.

The optical property of core-shell nanosensors and detection of atrazine based on localized surface plasmon resonance (LSPR) sensing

Three different nanosensors with core-shell structures were fabricated by molecular self-assembly and evaporation techniques. Such closely packed nanoparticles exhibit fine optical properties which are useful for biochemical sensing. The refractive index sensitivity (RIS) of nanosensors was detected by varying the refractive index of the surrounding medium and the decay length of nanosensors was investigated using a layer-by-layer polyelectrolyte multilayer assembly. The results showed that the thickness of the Au shell plays an important role in determining the RIS and the decay length. A system based on localized surface plasmon resonances (LSPR) sensing was constructed in our study. The core-shell nanosensors can detect 10 ng/mL atrazine solutions and are suitable for pesticide residue detection.

Are Hot Spots between Two Plasmonic Nanocubes of Silver or Gold Formed between Adjacent Corners or Adjacent Facets? A DDA Examination

Of all the plasmonic solid nanoparticles, single Ag or Au nanocubes are known to be plasmonic nanoparticles with strong plasmonic fields, which are concentrated around their corners. However, when nanoparticles aggregate, they do so in a face-to face arrangement. The formation of hot spots between plasmonic nanoparticles in close proximity to each other is known to greatly enhance their plasmonic fields which are important in the field of imaging. Thus, what is the structural development of hot spots between two nanocubes in a dimer? Do they form between the corners or are they between the adjacent facets, and what does this depend on? A detailed discrete dipole approximation (DDA) simulation of Au-Au and Ag-Ag dimers suggests that there is a competition between their formation in these two locations, which depends on the polarization direction of the exciting light (with respect to the interparticle axis in the dimer), its intensity and the wavelength as well as the interparticle separation of the dimer.

Localized surface plasmon resonance as a biosensing platform for developing countries

The discovery of the phenomena known as localized surface plasmon resonance (LSPR) has provided the basis for many research areas, ranging from materials science to biosensing. LSPR has since been viewed as a transduction platform that could yield affordable, portable devices for a multitude of applications. This review aims to outline the potential applications within developing countries and the challenges that are likely to be faced before the technology can be effectively employed.

Simulation and implementation of a morphology-tuned gold nano-islands integrated plasmonic sensor

This work presents simulation, analysis and implementation of morphology tuning of gold nano-island structures deposited by a novel convective assembly technique. The gold nano-islands were simulated using 3D Finite-Difference Time-Domain (FDTD) techniques to investigate the effect of morphological changes and adsorption of protein layers on the localized surface plasmon resonance (LSPR) properties. Gold nano-island structures were deposited on glass substrates by a novel and low-cost convective assembly process. The structure formed by an uncontrolled deposition method resulted in a nano-cluster morphology, which was annealed at various temperatures to tune the optical absorbance properties by transforming the nano-clusters to a nano-island morphology by modifying the structural shape and interparticle separation distances. The dependence of the size and the interparticle separation distance of the nano-islands on the LSPR properties were analyzed in the simulation. The effect of adsorption of protein layer on the nano-island structures was simulated and a relation between the thickness and the refractive index of the protein layer on the LSPR peak was presented. Further, the sensitivity of the gold nano-island integrated sensor against refractive index was computed and compared with the experimental results.

A facile and cost-effective TEM grid approach to design gold nano-structured substrates for high throughput plasmonic sensitive detection of biomolecules

A commercial TEM grid was used as a mask for the creation of extremely well-organized gold micro-/nano-structures on a glass substrate via a high temperature annealing process at 500 °C. The structured substrate was (bio)functionalized and used for the high throughput LSPR immunosensing of different concentrations of a model protein named bovine serum albumin.

Optical imaging of individual plasmonic nanoparticles in biological samples

Imaging of plasmonic nanoparticles (PNP) with optical microscopy has aroused considerable attention in recent years. The unique localized surface plasmon resonance (LSPR) from metal nanoparticles facilitates the transduction of a chemical or physical stimulus into optical signals in a highly efficient way. It is therefore possible to perform chemical or biological assays at the single object level with the help of standard optical microscopes. Because the source of background noise from different samples is different, distinct imaging modalities have been developed to discern the signals of interest in complex surroundings. With these convenient yet powerful techniques, great improvements in chemical and biological assays have been demonstrated, and many interesting phenomena and dynamic processes have also been elucidated. Further development and application of optical imaging methods for plasmonic probes should lead to many exciting results in chemistry and biology in the future.

Hydrogen peroxide (H₂O₂) detection with nanoprobes for biological applications: a mini-review

Hydrogen peroxide (H2O2) is an important member of the reactive oxygen species, playing various roles in biology and medicine. The conventional detection methods for H2O2 are often restricted by their limited sensitivity, poor selectivity towards H2O2, inappropriate physicochemical properties for detection in biological environments, long response time, etc. We briefly review here some recent nanotechnology--based approaches for H2O2 detection, which present an effective improvement, overcoming some of the limitations of the conventional H2O2 sensing techniques.

Effect of interdome spacing on the resonance properties of plasmonic nanodome arrays for label-free optical sensing

In this paper, we report on experimental and theoretical studies that investigate how the structural properties of plasmonic nanodome array devices determine their optical properties and sensing performance. We examined the effect of the interdome gap spacing within the plasmonic array structures on the performance for detection of change in local refractive index environment for label-free capture affinity biosensing applications. Optical sensing properties were characterized for nanodome array devices with interdome spacings of 14 nm, 40 nm, and 79 nm, as well as for a device where adjacent domes are in contact. For each interdome spacing, the extinction spectrum was measured using a broadband reflection instrumentation, and finite-difference-time-domain (FDTD) simulation was used to model the local electric field distribution associated with the resonances. Based on these studies, we predict that nanodome array devices with gap between 14 nm to 20 nm provide optimal label-free capture affinity biosensing performances, where the dipole resonance mode exhibits the highest overall surface sensitivity, as well as the lowest limit of detection.

Quantitative real-time imaging of protein-protein interactions by LSPR detection with micropatterned gold nanoparticles

Localized surface plasmon resonance (LSPR) offers powerful means for sensitive label-free detection of protein-protein interactions in a highly multiplexed format. We have here established self-assembly and surface modification of plasmonic nanostructures on solid support suitable for quantitative protein-protein interaction analysis by spectroscopic and microscopic LSPR detection. These architectures were obtained by layer-by-layer assembly via electrostatic attraction. Gold nanoparticles (AuNP) were adsorbed on a biocompatible amine-terminated poly(ethylene glycol) (PEG) polymer brush and further functionalized by poly-l-lysine graft PEG (PLL-PEG) copolymers. Stable yet reversible protein immobilization was achieved via tris(nitrilotriacetic acid) groups incorporated into the PLL-PEG coating. Thus, site-specific immobilization of His-tagged proteins via complexed Ni(II) ions was achieved. Functional protein immobilization on the surface was confirmed by real-time detection of LSPR scattering by reflectance spectroscopy. Association and dissociation rate constants obtained for a reversible protein-protein interaction were in good agreement with the data obtained by other surface-sensitive detection techniques. For spatially resolved detection, AuNP were assembled into micropatterns by means of photolithographic uncaging of surface amines. LSPR imaging of reversible protein-protein interactions was possible in a conventional wide field microscope, yielding detection limits of ∼30 protein molecules within a diffraction-limited surface area.

Nanoplasmonic quantitative detection of intact viruses from unprocessed whole blood

Infectious diseases such as HIV and hepatitis B pose an omnipresent threat to global health. Reliable, fast, accurate, and sensitive platforms that can be deployed at the point-of-care (POC) in multiple settings, such as airports and offices, for detection of infectious pathogens are essential for the management of epidemics and possible biological attacks. To the best of our knowledge, no viral load technology adaptable to the POC settings exists today due to critical technical and biological challenges. Here, we present for the first time a broadly applicable technology for quantitative, nanoplasmonic-based intact virus detection at clinically relevant concentrations. The sensing platform is based on unique nanoplasmonic properties of nanoparticles utilizing immobilized antibodies to selectively capture rapidly evolving viral subtypes. We demonstrate the capture, detection, and quantification of multiple HIV subtypes (A, B, C, D, E, G, and subtype panel) with high repeatability, sensitivity, and specificity down to 98 ± 39 copies/mL (i.e., HIV subtype D) using spiked whole blood samples and clinical discarded HIV-infected patient whole blood samples validated by the gold standard, i.e., RT-qPCR. This platform technology offers an assay time of 1 h and 10 min (1 h for capture, 10 min for detection and data analysis). The presented platform is also able to capture intact viruses at high efficiency using immuno-surface chemistry approaches directly from whole blood samples without any sample preprocessing steps such as spin-down or sorting. Evidence is presented showing the system to be accurate, repeatable, and reliable. Additionally, the presented platform technology can be broadly adapted to detect other pathogens having reasonably well-described biomarkers by adapting the surface chemistry. Thus, this broadly applicable detection platform holds great promise to be implemented at POC settings, hospitals, and primary care settings.

DNAzyme-functionalized gold nanoparticles for biosensing

Recent progress in using DNAzyme-functionalized gold nanoparticles (AuNPs) for biosensing is summarized in this chapter. A variety of methods, including those for attaching DNA on AuNPs, detecting metal ions and small molecules by DNAzyme-functionalized AuNPs, and intracellular applications of DNAzyme-functionalized AuNPs are discussed. DNAzyme-functionalized AuNPs will increasingly play more important roles in biosensing and many other multidisciplinary applications. This chapter covers the recent advancement in biosensing applications of DNAzyme-functionalized gold nanoparticles, including the detection of metal ions, small molecules, and intracellular imaging.

A sandwich-type DNA electrochemical biosensor for hairpin-stem-loop structure based on multistep temperature-controlling method

A highly sensitive and selective method for amplified electrochemical detection for hairpin-stem-loop structured target sequences was developed based on the temperature regulation of DNA hybrids on a sandwich-type electrochemical DNA sensor. Multistep hybridization was applied to promote the hybridization efficiency of each section of sandwich structure. The results showed that both multistep and temperature-controlling hybridization techniques were both especially made to fabricate the sensor for the tendency of internal hybridization of target gene sequences. This strategy provides significantly enhanced hybridization efficiency and sequence specificity of electrochemical detection.

Real-time label-free immunoassay of interferon-gamma and prostate-specific antigen using a Fiber-Optic Localized Surface Plasmon Resonance sensor

A Fiber-Optic Localized Surface Plasmon Resonance (FO LSPR) sensor was fabricated using spherical gold nanoparticles (Au NPs) on a flattened end-face of the optical fiber. The Au NPs were easily synthesized by the Turkevich method and were immobilized on the end-face of the optical fiber by using a self-assembled monolayer (SAM). In order to examine the possibility of its application as a biosensor for label-free immunoassays, the fabricated FO LSPR sensor was used for the detection of the antibody-antigen reaction of interferon-gamma (IFN-γ) and the limit of detection (LOD) was approximately 2pg/ml. Herein, The antibodies and bovine serum albumins (BSAs) were immobilized on the Au NPs by physisorption. Also, the FO LSPR sensor was used for the detection of a prostate-specific antigen (PSA) and the LOD was 1pg/ml below. The fabricated FO LSPR sensor can be used for real-time label-free immunoassay having fast detection time, high resolution and sensitivity. In addition, the proposed sensor platform has the advantages of low cost, simple optical setup, remote sensing, simple fabrication, real-time detection, low sample volume, and potential application to in-vivo detection systems.

Applications of peptide nucleic acids (PNAs) and locked nucleic acids (LNAs) in biosensor development

Nucleic acid biosensors have a growing number of applications in genetics and biomedicine. This contribution is a critical review of the current state of the art concerning the use of nucleic acid analogues, in particular peptide nucleic acids (PNA) and locked nucleic acids (LNA), for the development of high-performance affinity biosensors. Both PNA and LNA have outstanding affinity for natural nucleic acids, and the destabilizing effect of base mismatches in PNA- or LNA-containing heterodimers is much higher than in double-stranded DNA or RNA. Therefore, PNA- and LNA-based biosensors have unprecedented sensitivity and specificity, with special applicability in DNA genotyping. Herein, the most relevant PNA- and LNA-based biosensors are presented, and their advantages and their current limitations are discussed. Some of the reviewed technology, while promising, still needs to bridge the gap between experimental status and the harder reality of biotechnological or biomedical applications.

Peptide nucleic acids tagged with four lysine residues for amperometric genosensors

A homothymine PNA decamer bearing four lysine residues has been synthesized as a probe for the development of amperometric sensors. On one hand, the four amino groups introduced make this derivative nine times more soluble than the corresponding homothymine PNA decamer and, on the other hand, allow the stable anchoring of this molecule on Au nanostructured surface through the terminal -NH₂ moieties. In particular, XPS and electrochemical investigations performed with hexylamine, as a model molecule, indicate that the stable deposition of primary amine derivatives on such a nanostructured surface is possible and involves the free electron doublet on the nitrogen atom. This finding indicates that this PNA derivative is suitable to act as the probe molecule for the development of amperometric sensors.

 

Thanks to the molecular probe chosen and to the use of a nanostructured surface as the substrate for the sensor assembly, the device proposed makes possible the selective recognition of the target oligonucleotide sequence with very high sensitivity.

Nano-islands integrated evanescence-based lab-on-a-chip on silica-on-silicon and polydimethylsiloxane hybrid platform for detection of recombinant growth hormone

Integration of nano-materials in optical microfluidic devices facilitates the realization of miniaturized analytical systems with enhanced sensing abilities for biological and chemical substances. In this work, a novel method of integration of gold nano-islands in a silica-on-silicon-polydimethylsiloxane microfluidic device is reported. The device works based on the nano-enhanced evanescence technique achieved by interacting the evanescent tail of propagating wave with the gold nano-islands integrated on the core of the waveguide resulting in the modification of the propagating UV-visible spectrum. The biosensing ability of the device is investigated by finite-difference time-domain simulation with a simplified model of the device. The performance of the proposed device is demonstrated for the detection of recombinant growth hormone based on antibody-antigen interaction.

Probing the electromagnetic field distribution within a metallic nanodisk

A Co nanolayer is used as a local probe to evaluate the vertical inhomogeneous distribution of the electromagnetic (EM) field within a resonant metallic nanodisk. Taking advantage of the direct relation between the magneto-optical activity and the electromagnetic field intensity in the Co layer, it is shown that the nonuniform EM distribution within the nanodisk under plasmon resonant conditions has maximum values close to the upper and lower flat faces, and a minimum value in the middle.

Development of a mass-producible on-chip plasmonic nanohole array biosensor

We have developed a polymer film based plasmonic device whose optical properties are tuned for measuring biological samples. The device has a circular nanohole array structure fabricated with a nanoimprint technique using a UV curable polymer, and then gold thin film is deposited by electron beam deposition. Therefore, the device is mass-producible, which is also very important for bioaffinity sensors. First the gold film thickness and hole depth were optimized to obtain the maximum dip shift for the reflection spectra. The dip shift is equivalent to the sensitivity to refractive index changes at the plasmonic device surface. We also calculated the variation in reflection spectra by changing the above conditions using the finite-difference time domain method, and we obtained agreement between the theoretical and experimental curves. The nanohole periodicity was adjusted from 400 to 900 nm to make it possible to perform measurements in the visible wavelength region to measure the aqueous samples with less optical absorption. The tuned bottom filled gold nanohole array was incorporated in a microfluidic device covered with a PDMS based microchannel that was 2 mm wide and 20 μm deep. As a proof of concept, the device was used to detect TNF-α by employing a direct immunochemical reaction on the plasmonic array, and a detection limit of 21 ng mL(-1) was obtained by amplification with colloidal gold labeling instead of enzymatic amplification.

Size-dependent plasmonic responses of single gold nanoparticles for analysis of biorecognition

We report the use of plasmonic responses of single gold nanoparticles (AuNPs) with various sizes for the analysis of biomolecular recognition. We also describe the relationship between particle size and plasmonic response induced by the binding of receptors and target analytes. To investigate the plasmonic response of AuNPs, Rayleigh light scattering spectra were collected from individual AuNPs using a dark-field microspectroscopy system. Using prostate-specific antigen (PSA) as a model, the linear dynamic range was obtained in the concentration range of 10(-4) to 10 ng/ml, with the smallest detectable concentration at 0.1 pg/ml corresponding to localized surface plasmon resonance (LSPR) λ(max) shifts of approximately 2.95 nm. This result indicates that individual AuNPs can be used for development of a very sensitive, robust, simple, and label-free biosensor to detect protein biomarkers. Furthermore, the method possesses great potential for monitoring other biological interactions.

Reflection spectroscopy for the determination of Au nanostructure formation on carbon surfaces

Au electrodeposition has been performed on carbon electrodes to fabricate Au nanostructures on the working electrode of screen-printed carbon chips. The amount of Au deposited was characterized using the raw reflection spectra obtained by detecting UV-Vis spectrum reflected from the electrode surface. SEM images at different deposition time points provided evidence for the growth of Au nanostructures. The increase in deposition time led to an increase in the intensity of the spectrum obtained for both chips. The acquired optical properties of the carbon chips provide a promising platform for simultaneous optical and electrochemical measurements.

Biosensing in a microelectrofluidic system using optical whispering-gallery mode spectroscopy

Label-free detection of biomolecules using an optical whispering-gallery mode sensor in a microelectrofluidic channel is simulated. Negatively charged bovine serum albumin is considered as the model protein analyte. The analyte transport in aqueous solution is controlled by an externally applied electrical field. The finite element method is employed for solving the equations of the charged species transport, the Poisson equation of electric potential, the equations of conservation of momentum and energy, and the Helmholtz equations of electromagnetic waves. The adsorption process of the protein molecules on the microsensor head surface is monitored by the resonance frequency shifts. Frequency shift caused by temperature variation due to Joule heating is analyzed and found to be negligible. The induced shifts behave in a manner similar to Langmuir-like adsorption kinetics; but the time constant increases due to the presence of the external electrical field. A correlation of the frequency shift, the analyte feed concentration in the solution, and the applied voltage gradient is obtained, in which an excellent linear relationship between the frequency shift and the analyte concentration is revealed. The applied voltage gradient enhances significantly the analyte concentration in the vicinity of the sensor surface; thus, the sensor sensitivity which has a power function of the voltage gradient with exponent 2.85 in the controlled voltage range. Simulated detection of extremely low protein concentration to the pico-molar level is carried out.

Metal-containing peptide nucleic acid conjugates

Peptide Nucleic Acids (PNAs) are non-natural DNA/RNA analogues with favourable physico-chemical properties and promising applications. Discovered nearly 20 years ago, PNAs have recently re-gained quite a lot of attention. In this Perspective article, we discuss the latest advances on the preparation and utilisation of PNA monomers and oligomers containing metal complexes. These metal- conjugates have found applications in various research fields such as in the sequence-specific detection of nucleic acids, in the hydrolysis of nucleic acids and peptides, as radioactive probes or as modulators of PNA·DNA hybrid stability, and last but not least as probes for molecular and cell biology.

Label-free detection of DNA-binding proteins based on microfluidic solid-state molecular beacon sensor

A solid-state molecular beacon using a gold support as a fluorescence quencher is combined with a polydimethylsiloxane (PDMS) microfluidic channel to construct an optical sensor for detecting single-stranded DNA binding protein (SSBP) and histone protein. The single-stranded DNA-Cy3 probe or double-stranded DNA-Cy3 probe immobilized on the gold surface is prepared for the detection of SSBP or histone, respectively. Due to the different quenching ability of gold to the immobilized single-stranded DNA-Cy3 probe and the immobilized double-stranded DNA-Cy3 probe, low fluorescence intensity of the attached single-stranded DNA-Cy3 is obtained in SSBP detection, whereas high fluorescence intensity of the attached double-stranded DNA-Cy3 is obtained in histone detection. The amounts of SSBP in sample solutions are determined from the degree of fluorescence recovery of the immobilized single-stranded DNA-Cy3 probe, whereas that of histone in sample solutions is determined from the degree of fluorescence quenching of the immobilized double-stranded DNA-Cy3 probe. Using this approach, label-free detection of target proteins at nanomolar concentrations is achieved in a convenient, general, continuous flow format. Our approach has high potential for the highly sensitive label-free detection of various proteins based on binding-induced conformation changes of immobilized DNA probes.

Plasmonics and enhanced magneto-optics in core-shell co-ag nanoparticles

We present theoretical and experimental studies that explain the observed strong enhancement of the magneto-optical (MO) Faraday rotation in all-metal core-shell Co-Ag nanoparticles (NPs) attributed to localized surface plasmon resonance (LSPR). We also explain why the optical absorption and MO spectra peaks appear blue-shifted with increased Co core size while keeping the NP size constant. Further, we demonstrate direct correlation between the strong LSPR induced electromagnetic fields and the enhanced MO activity of the NPs.

Sequence-specific detection of short-length DNA via template-dependent surface-hybridization events

Short-length DNA and RNA, such as mature small RNA, which contains only 17-25 nucleotides, are always a problem in hybridization-based detection assays. In this paper, we report a proof-of-concept for a new short-length DNA detection technology which encompasses a design strategy whereby capture and reporter probes that do not hybridize to each other at 20 degrees C can be made to anneal to each other in the presence of a template via the formation of a stable three-component complex. The thermodynamics of this magnetic bead-based DNA biosensor was then investigated in detail by monitoring chemiluminescence (CL) changes in the absence and presence of targets over a temperature profile. The data show that this new biosensor offers the possibility of highly selective and sensitive detection of the short-length target DNA. In view of these advantages, this template-dependent surface-hybridization assay, as a new CL strategy, might create a universal technology for developing simple biosensors in sensitive and selective detection of short-length DNA and RNA.