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

Photonic crystal slab sensor with enhanced surface area

In this work, we demonstrate improved molecular detection sensitivity for silicon slab photonic crystal cavities by introducing multiple-hole defects (MHDs), which increase the surface area available for label-free detection without degrading the quality factor. Compared to photonic crystals with L3 defects, adding MHDs into photonic crystal cavities enabled a 44% increase in detection sensitivity towards small refractive index perturbations due to surface monolayer attachment of a small aminosilane molecule. Also, photonic crystals with MHDs exhibited 18% higher detection sensitivity for bulk refractive index changes.

Emerging use of nanostructure films containing capped gold nanoparticles in biosensors

The localized surface plasmon resonance (LSPR) property of gold nanoparticles (GNP) has been exploited in a variety of optical sensor configurations including solution-based bioassays, paper-based colorimetric detection, surface-confined nanoparticle film/array-based sensing, etc. Amongst these, gold nanostructured films are of great interest because of their high stability, good reproducibility, robustness, and cost-effectiveness. The inherent optical characteristics of GNP, are attributed to parameters like size and shape (eg, nanospheres, nanorods, nanostars), eg, LSPR spectral location sensitivity to the local environment, composition (eg, gold-silver or silica-gold nanoshells), sensing volume, mesospacing, and multiplexing. These properties allow sensor tunability, enabling enhanced sensitivity and better performance of these biosensors. Ultrasensitive biosensor designs were realized using gold nanostructured films fabricated by bottom-up as well as top-down approaches. In this review, we describe the past, present, and future trends in the development of GNP-LSPR-based sensors, concentrating on both design (fabrication) and application. In the process, we have discussed various combinations of GNP size and shape, substrate, and application domains.

Recent advancements in optical DNA biosensors: exploiting the plasmonic effects of metal nanoparticles

The emerging field of plasmonics, the study of electromagnetic responses of metal nanostructures, has revealed many novel signal enhancing phenomena. As applied to the development of label-free optical DNA biosensors, it is now well established that plasmon-based surface enhanced spectroscopies on nanostructured metal surfaces or metal nanoparticles can markedly improve the sensitivity of optical biosensors, with some showing great promise for single molecule detection. In this review, we first summarize the basic concepts of plasmonics in metal nanostructures, as well as the characteristic optical phenomena to which plasmons give rise. We will then describe recent advances in optical DNA biosensing systems enabled by metal nanoparticle-derived plasmonic effects, including the use of surface enhanced Raman scattering (SERS), colorimetric methods, "scanometric" processes, and metal-enhanced fluorescence (MEF).

Direct detection and discrimination of double-stranded oligonucleotide corresponding to hepatitis C virus genotype 3a using an electrochemical DNA biosensor based on peptide nucleic acid and double-stranded DNA hybridization

Development of an electrochemical DNA biosensor for the direct detection and discrimination of double-stranded oligonucleotide (dsDNA) corresponding to hepatitis C virus genotype 3a, without its denaturation, using a gold electrode is described. The electrochemical DNA sensor relies on the modification of the gold electrode with 6-mercapto-1-hexanol and a self-assembled monolayer of 14-mer peptide nucleic acid probe, related to the hepatitis C virus genotype 3a core/E1 region. The increase of differential pulse voltammetric responses of methylene blue, upon hybridization of the self-assembled probe with the target ds-DNA to form a triplex is the principle behind the detection and discrimination. Some hybridization experiments with non-complementary oligonucleotides were carried out to assess whether the developed DNA sensor responds selectively to the ds-DNA target. Diagnostic performance of the biosensor is described and the detection limit was found to be 1.8 x 10(-12) M in phosphate buffer solution, pH 7.0. The relative standard deviation of measurements of 100 pM of target ds-DNA performed with three independent probe-modified electrodes was 3.1%, indicating a remarkable reproducibility of the detection method.

Carbon nanostructure-based field-effect transistors for label-free chemical/biological sensors

Over the past decade, electrical detection of chemical and biological species using novel nanostructure-based devices has attracted significant attention for chemical, genomics, biomedical diagnostics, and drug discovery applications. The use of nanostructured devices in chemical/biological sensors in place of conventional sensing technologies has advantages of high sensitivity, low decreased energy consumption and potentially highly miniaturized integration. Owing to their particular structure, excellent electrical properties and high chemical stability, carbon nanotube and graphene based electrical devices have been widely developed for high performance label-free chemical/biological sensors. Here, we review the latest developments of carbon nanostructure-based transistor sensors in ultrasensitive detection of chemical/biological entities, such as poisonous gases, nucleic acids, proteins and cells.

Rigiflex lithography-based nanodot arrays for localized surface plasmon resonance biosensors

We present a facile and robust means of fabricating metallic nanodot arrays for localized surface plasmon resonance (LSPR) biosensors through the strategic coupling of a polymeric template prepared with rigiflex lithography and a subsequent metallization via electrodeposition. Rigiflex lithography provides the capability to realize large-scale nanosized features as well as process flexibility during contact molding. In addition, the electrodeposition process enables wet-based nanoscale metallization with high pattern fidelity and geometric controllability. Generated metallic nanodot arrays can be used as a general platform for LSPR biosensors via the sequential binding of chemicals and biomolecules. Extinction spectra of the corresponding LSPR signal are measured with UV-vis-NIR spectroscopy, from which the pattern size and shape dependence of LSPR are readily confirmed. The feasibility of a very sensitive biosensor is demonstrated by the targeted binding of human immunoglobulin G, yielding subnanomolar detection capability with high selectivity.

Au nanoparticle based localized surface plasmon resonance substrates fabricated by dynamic shadowing growth

Au nanoparticle (NP) substrates, Au NP/TiO(2)/Au NP sandwich structures, and Ti coated Au NP substrates are fabricated by glancing angle deposition (GLAD) and oblique angle deposition (OAD) methods. Under the same deposition condition, the Au NP substrates produced by GLAD are more uniform and reproducible compared to those fabricated by OAD. The localized surface plasmon resonance (LSPR) wavelength of Au NP substrates can be easily tuned by changing the film thickness, the deposition angle, and the coating of the dielectric layer (TiO(2)) and metallic layer (Ti). In addition, the thickness and the deposition angle of the Ti coating on Au NP also affect the LSPR wavelength. Our results demonstrate that GLAD is a very versatile fabrication technique to produce reproducible and fine-tuned LSPR substrates.

Signal amplification by enzymatic reaction in an immunosensor based on localized surface plasmon resonance (LSPR)

An enzymatic reaction was employed as a means to enhance the sensitivity of an immunosensor based on localized surface plasmon resonance (LSPR). The reaction occurs after intermolecular binding between an antigen and an antibody on gold nano-island (NI) surfaces. For LSPR sensing, the gold NI surface was fabricated on glass substrates using vacuum evaporation and heat treatment. The interferon-γ (IFN-γ) capture antibody was immobilized on the gold NIs, followed by binding of IFN-γ to the antibody. Subsequently, a biotinylated antibody and a horseradish peroxidase (HRP) conjugated with avidin were simultaneously introduced. A solution of 4-chloro-1-naphthol (4-CN) was then used for precipitation; precipitation was the result of the enzymatic reaction catalyzed the HRP on gold NIs. The LSPR spectra were obtained after each binding process. Using this method, the enzyme-catalyzed precipitation reaction on the gold NI surface was found to effectively amplify the change in the signal of the LSPR immunosensor after intermolecular binding.

Application of peptide nucleic acid towards development of nanobiosensor arrays

Peptide nucleic acid (PNA) is the modified DNA or DNA analogue with a neutral peptide backbone instead of a negatively charged sugar phosphate. PNA exhibits chemical stability, resistant to enzymatic degradation inside living cell, recognizing specific sequences of nucleic acid, formation of stable hybrid complexes like PNA/DNA/PNA triplex, strand invasion, extraordinary thermal stability and ionic strength, and unique hybridization relative to nucleic acids. These unique physicobiochemical properties of PNA enable a new mode of detection, which is a faster and more reliable analytical process and finds applications in the molecular diagnostics and pharmaceutical fields. Besides, a variety of unique characteristic features, PNAs replace DNA as a probe for biomolecular tool in the molecular genetic diagnostics, cytogenetics, and various pharmaceutical potentials as well as for the development of sensors/arrays/chips and many more investigation purposes. This review paper discusses the various current aspects related with PNAs, making a new hot device in the commercial applications like nanobiosensor arrays.

RNA aptamer-based optical nanostructured sensor for highly sensitive and label-free detection of antigen-antibody reactions

Developments of optical protein sensors with nanostructure based on the noble metals have currently received great attention for their high efficiency and simultaneous analysis of various important biomolecules from proteomics to genetics. In this study, we exploited the absorbance spectra of gold-capped nanoparticles substrate for label-free detections of antigen-antibody reactions using a specific thiolated RNA aptamer. These synthesized RNA aptamers have been optimized to bind to the Fc portion of the human IgG1 subclass, due to their ability to orient antibodies direction on the gold surface. After attaching the anti-fibrinogen antibodies on the surface via these linkers, our thiolated RNA aptamer-based nanostructured sensors were easily applicable to specific detections of fibrinogen with a limit of detection of 0.1 ng/mL. These nanostructured sensor-based models will open a way to display numerous immunosensors as well as to develop other functionally similar sensors which could then be expanded into multi-arrays assay systems.

Self-assembly of gibberellic amide assemblies and their applications in the growth and fabrication of ordered gold nanoparticles

Gibberellins are a group of naturally occurring diterpenoid based phytohormones that play a vital role in plant growth and development. In this work, we have studied the self-assembly of gibberellic acid, a phytohormone, which belongs to the family of gibberellins, and designed amide derivatives of gibberellic acid (GA(3)) for the facile, green synthesis of gold nanoparticles. It was found that the derivatives self-assembled into nanofibers and nanoribbons in aqueous solutions at varying pH. Further, upon incubation with tetrachloroaurate, the self-assembled GA(3)-amide derivatives efficiently nucleated and formed gold nanoparticles when heated to 60 degrees C. Energy dispersive x-ray spectroscopy, transmission electron microscopy and scanning electron microscopy analyses revealed that uniform coatings of gold nanoparticles in the 10-20 nm range were obtained at low pH on the nanowire surfaces without the assistance of additional reducing agents. This simple method for the development of morphology controlled gold nanoparticles using a plant hormone derivative opens doors for a new class of plant biomaterials which can efficiently yield gold nanoparticles in an environmentally friendly manner. The gold encrusted nanowires formed using biomimetic methods may lead on to the formation of conductive nanowires, which may be useful for a wide range of applications such as in optoelectronics and sensors. Further, the spontaneous formation of highly organized nanostructures obtained from plant phytohormone derivatives such as gibberellic acid is of particular interest as it might help in further understanding the supramolecular assembly mechanism of more highly organized biological structures.

Creating a library of complex metallic nanostructures via harnessing pattern transformation of a single PDMS membrane

By harnessing the elastic instability in a single PDMS membrane consisting of a square lattice array of circular pores, we fabricated a library of complex nanostructures in Au with variable feature size, connectivity, and geometry, including arrays of diamond-plate patterns (or elliptic herringbones), compound structures of circular dots and elliptical lines, heartbeat waves, aligned ovals, and a rhombus lattice of holes and lines. This was achieved first by swelling the PDMS membrane, followed by convective assembly of nanoparticles on the membrane. By taking advantage of the unique 3-D topography of the nanoparticle film and its photoresist replica, we could gradually etch the photoresist film to vary the feature size and connectivity of the underlying Au patterns. Further, through a combination of mechanical stretching (at different strain levels and stretching angles) and solvent swelling of the same PDMS membrane, we created a richer library of complex patterns in Au without application of new masters.

Poly-silicon nanowire field-effect transistor for ultrasensitive and label-free detection of pathogenic avian influenza DNA

Enhanced surveillance of influenza requires rapid, robust, and inexpensive analytical techniques capable of providing a detailed analysis of influenza virus strains. Functionalized poly-crystalline silicon nanowire field-effect transistor (poly-SiNW FET) was demonstrated to achieve specific and ultrasensitive (at fM level) detection of high pathogenic strain virus (H5 and H7) DNA of avian influenza (AI) which is an important infectious disease and has an immediate need for surveillance. The poly-SiNW FET was prepared by a simple and low-cost method that is compatible with current commercial semiconductor process without expensive E-beam lithography tools for large-scale production. Specific electric changes were observed for AI virus DNA sensing when nanowire surface of poly-SiNW FET was modified with complementary captured DNA probe and target DNA (H5) at fM to pM range could be distinguished. With its excellent electric properties and potential for mass commercial production, poly-SiNW FET can be developed to become a portable biosensor for field use and point-of-care diagnoses.

An interference localized surface plasmon resonance biosensor based on the photonic structure of Au nanoparticles and SiO2/Si multilayers

This paper presents the experimental and simulation analysis of an original nanostructure design constructed with plasmonic gold nanoparticles and photonic thin-film multilayers of silicon dioxide (500 nm in thickness) and silicon on a substrate. Our nanostructure substrate showed a high sensitivity for various refractive index RI solutions and a prominent capacity for functionalizing alkanethiol molecules on the gold surface and demonstrates great potential in the development of a microfluidic-based biosensor for monitoring biotin-avidin interactions in real-time.

Methods for assessing DNA hybridization of peptide nucleic acid-titanium dioxide nanoconjugates

We describe the synthesis of peptide nucleic acid (PNA)-titanium dioxide (TiO(2)) nanoconjugates and several novel methods developed to investigate the DNA hybridization behaviors of these constructs. PNAs are synthetic DNA analogs resistant to degradation by cellular enzymes that hybridize to single-stranded DNA (ssDNA) with higher affinity than DNA oligonucleotides, invade double-stranded DNA (dsDNA), and form different PNA/DNA complexes. Previously, we developed a DNA-TiO(2) nanoconjugate capable of hybridizing to target DNA intracellularly in a sequence-specific manner with the ability to cleave DNA when excited by electromagnetic radiation but susceptible to degradation that may lower its intracellular targeting efficiency and retention time. PNA-TiO(2) nanoconjugates described in the current article hybridize to target ssDNA, oligonucleotide dsDNA, and supercoiled plasmid DNA under physiological-like ionic and temperature conditions, enabling rapid, inexpensive, sequence-specific concentration of nucleic acids in vitro. When modified by the addition of imaging agents or peptides, hybridization capabilities of PNA-TiO(2) nanoconjugates are enhanced, providing essential benefits for numerous in vitro and in vivo applications. The series of experiments shown here could not be done with either TiO(2)-DNA nanoconjugates or PNAs alone, and the novel methods developed will benefit studies of numerous other nanoconjugate systems.

SPR study of DNA hybridization with DNA and PNA probes under stringent conditions

Surface plasmon resonance (SPR) spectroscopy has been used for studying on-chip DNA hybridization to a PNA probe and its counterpart DNA probe of a 22-mer sequence. Two stringency control strategies are used for single base mismatch discrimination, namely (1) adding a denaturant, i.e. formamide (FA), into hybridization buffer and (2) coupling negative potentials for selective dehybridization of mismatch DNA. These two strategies have either not been used before or been less-well studied in SPR detection. An end-point SPR measurement protocol (no real-time hybridization profile recorded) is developed for detecting DNA hybridization in the presence of FA, to circumvent the problem that the refractive index of FA is out of the detectable range of the SPR equipment. The missing of real-time measurement of hybridization profile is compensated with QCM measurement. Under optimal conditions, i.e. 10mM PBS with 30% FA and 1mM PBS with 50% FA, single base mismatch DNA is detected with 1.7 and 2.8 times less hybridization signals compared with the perfect match DNA, with the DNA probe and PNA probe, respectively. Under negative potential of -0.2 to -0.4V (vs. Ag/AgCl), mismatch DNA dissociates more than perfect match DNA by 1.7-2.5 times from the DNA probe and 2.1-3.5 times from the PNA probe. The higher mismatch discrimination efficiency of the PNA probe under stringent conditions would be attributable to its higher intrinsic sequence selectivity.

Biosensing with plasmonic nanosensors

Recent developments have greatly improved the sensitivity of optical sensors based on metal nanoparticle arrays and single nanoparticles. We introduce the localized surface plasmon resonance (LSPR) sensor and describe how its exquisite sensitivity to size, shape and environment can be harnessed to detect molecular binding events and changes in molecular conformation. We then describe recent progress in three areas representing the most significant challenges: pushing sensitivity towards the single-molecule detection limit, combining LSPR with complementary molecular identification techniques such as surface-enhanced Raman spectroscopy, and practical development of sensors and instrumentation for routine use and high-throughput detection. This review highlights several exceptionally promising research directions and discusses how diverse applications of plasmonic nanoparticles can be integrated in the near future.

Label-free optical detection of aptamer-protein interactions using gold-capped oxide nanostructures

Optical biosensors based on noble nanostructures currently receive attention due to their highly efficient, simultaneous analysis of a number of important biomolecules from proteomics to genomics. In this study, the combination of localized surface plasmon resonance (LSPR) with interferometry in the relative reflected intensity (RRI) spectrum of the gold-capped oxide nanostructure was thoroughly exploited for label-free detection of aptamer-protein interactions. The fabrication of gold-capped oxide nanostructure involved the deposition of gold on the surface of porous anodic alumina (PAA) layer chip. This novel nanomaterial enabled us to simultaneously monitor the changes in both LSPR and interferometric characteristics since the biomolecular interactions occur. After immobilizing the aptamer I on the chip surface, our sensor could be easily applied for specific detection of thrombin and aptamer II with a limit of detection of 1 nM thrombin in the sample. Our optical biosensing device connecting with the gold-capped oxide nanostructure has a high potential for highly sensitive monitoring of the other biomolecular interactions such as protein-protein interactions, DNA-protein interactions, DNA-DNA hybridizations, and ligand-receptor interactions with a massively parallel detection capability in a high-throughput system.

Organic nanocones fabricated by atmospheric plasma polymerization for immobilizing bioprobes

Inspired by the formation process of natural thundershowers, we fabricated an organic nanocone matrix-like bamboo-shoot by using atmospheric plasma polymerization in the absence of any catalyst or template. The discharging characteristics affected the nanocone shape and distribution in an obvious way. The nanocones prepared by helium (He) plasma were about 120 nm in diameter and 80 nm high. The nanostructured surface acted as an adhesion layer immobilizing DNA probes for DNA hybridization assay. The density of NH(2)-DNA probes prepared by He, argon (Ar) and nitrogen (N(2)) plasma was confirmed by the dyed oligonucleotide and was found to be 3.2, 1.0 and 0.6 pM cm(-2), respectively. Each nanocone prepared by helium plasma contains nearly 4 × 10(2) amine groups.

Femtomol SPR detection of DNA-PNA hybridization with the assistance of DNA-guided polyaniline deposition

The inability of surface plasmon resonance (SPR) spectroscopy to detect extremely small refractive index changes has hindered its applications in ultrasensitive DNA analysis. In this study we report a signal amplification strategy that uses DNA-templated polyaniline deposition, suitable for DNA hybridization analysis with charge neutral peptide nucleic acid (PNA) being probes. Under acidic conditions, protonated aniline monomers are adsorbed on DNA backbones through electrostatic interaction. The microenvironment provided by the DNA facilitates oxidative aniline polymerization initialized by H(2)O(2) in the presence of horseradish peroxide. Under optimal conditions, the detection limit is lowered from 5nM for conventional SPR detection to 0.1pM. The significant sensitivity improvement is attributed to the in-situ polymer chain growth along DNA strands, which introduces drastic refractive index increases. This signal amplification approach does not involve secondary hybridization processes. The detection sensitivity obtained is much better than that of gold nanoparticle-based amplification involving a secondary hybridization process and labeled DNA detection probes.