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

Microsystems technology and biosensing

This review addresses the recent developments in miniaturized microsystems or lab-on-a-chip devices for biosensing of different biomolecules: DNA, proteins, small molecules, and cells, especially at the single-molecule and single-cell level. In order to sense these biomolecules with sensitivity we have fabricated chip devices with respect to the biomolecule to be analyzed. The details of the fabrication are also dealt with in this review. We mainly developed microarray and microfluidic chip devices for DNA, protein, and cell analyses. In addition, we have introduced the porous anodic alumina layer chip with nanometer scale and gold nanoparticles for label-free sensing of DNA and protein interactions. We also describe the use of microarray and microfluidic chip devices for cell-based assays and single-cell analysis in drug discovery research.

Enzyme-based colorimetric detection of nucleic acids using peptide nucleic acid-immobilized microwell plates

The development of label-free or nonlabeling assays for nucleic acids is important in basic biological research and biomedical diagnosis. In this study, we have developed an enzyme-based colorimetric assay for nucleic acids, which combines the robustness of nonlabeling of DNA and RNA samples and the adequate sensitivity of enzymatic reactions. The core of this assay is the use of neutral peptide nucleic acid (PNA) as capture probe and the electrostatic adsorption of horseradish peroxidase (HRP) on hybridized, negatively charged nucleic acids to report the hybridization events, through HRP-catalyzed color reactions of 3,3',5,5'-tetramethylbenzidine and H(2)O(2). The proposed assay has been validated with fully complementary and single base-mismatched DNAs of different chain lengths. The proposed assay has also been validated with total RNA samples extracted from two human cancer cell lines (A 549 lung cancer cell and HeLa cell) for microRNA detection in real samples. Through extensive optimizations of HRP adsorption and nucleic acid hybridization conditions, detection limits of 0.1-0.2 nM for DNA (depending on chain length) and approximately 2 microg of total RNA have been achieved. Surface plasmon resonance spectroscopy has been used to elucidate the HRP adsorption and PNA-nucleic acid hybridizations through real-time measurements and to provide guidance for the development of the colorimetric assay.

Label-Free Single-Nucleotide Polymorphism Detection Using a Cationic Tetrahedralfluorene and Silica Nanoparticles

We developed a simple method that is able to provide label-free sequence-specific DNA detection with single-nucleotide polymorphism (SNP) detection selectivity. This method makes use of both DNA probe immobilized silica nanoparticles and optically amplifying light harvesting molecules. The recognition is accomplished by sequence-specific hybridization between the DNA probes on the silica nanoparticles and the targets of interest. After subsequent treatment with ethidium bromide (EB), a cationic tetrahedralfluorene was added to electrostatically associate with the DNA molecules on the nanoparticle surface, leading to sensitized EB emission via fluorescence resonance energy transfer (FRET). Because of the selective response of the tetrahedralfluorene to intercalated EB, the perfectly matched DNA targets were distinctively differentiated from those with mutations. The presence of tetrahedralfluorene provides improved detection sensitivity and selectivity, as compared to the use of EB alone as a signal reporter. The demonstrated highly selective label-free detection method laid the ground work for the future development of disposable and real-time testing kits in SNP screenings.

Effect of molecular crowding on the response of an electrochemical DNA sensor

E-DNA sensors, the electrochemical equivalent of molecular beacons, appear to be a promising means of detecting oligonucleotides. E-DNA sensors are comprised of a redox-modified (here, methylene blue or ferrocene) DNA stem-loop covalently attached to an interrogating electrode. Because E-DNA signaling arises due to binding-induced changes in the conformation of the stem-loop probe, it is likely sensitive to the nature of the molecular packing on the electrode surface. Here we detail the effects of probe density, target length, and other aspects of molecular crowding on the signaling properties, specificity, and response time of a model E-DNA sensor. We find that the highest signal suppression is obtained at the highest probe densities investigated, and that greater suppression is observed with longer and bulkier targets. In contrast, sensor equilibration time slows monotonically with increasing probe density, and the specificity of hybridization is not significantly affected. In addition to providing insight into the optimization of electrochemical DNA sensors, these results suggest that E-DNA signaling arises due to hybridization-linked changes in the rate, and thus efficiency, with which the redox moiety collides with the electrode and transfers electrons.

Localized Surface Plasmon Resonance Spectroscopy and Sensing

Localized surface plasmon resonance (LSPR) spectroscopy of metallic nanoparticles is a powerful technique for chemical and biological sensing experiments. Moreover, the LSPR is responsible for the electromagnetic-field enhancement that leads to surface-enhanced Raman scattering (SERS) and other surface-enhanced spectroscopic processes. This review describes recent fundamental spectroscopic studies that reveal key relationships governing the LSPR spectral location and its sensitivity to the local environment, including nanoparticle shape and size. We also describe studies on the distance dependence of the enhanced electromagnetic field and the relationship between the plasmon resonance and the Raman excitation energy. Lastly, we introduce a new form of LSPR spectroscopy, involving the coupling between nanoparticle plasmon resonances and adsorbate molecular resonances. The results from these fundamental studies guide the design of new sensing experiments, illustrated through applications in which researchers use both LSPR wavelength-shift sensing and SERS to detect molecules of chemical and biological relevance.

Silicon Nanowire Arrays for Label-Free Detection of DNA

Arrays of highly ordered n-type silicon nanowires (SiNW) are fabricated using complementary metal-oxide semiconductor (CMOS) compatible technology, and their applications in biosensors are investigated. Peptide nucleic acid (PNA) capture probe-functionalized SiNW arrays show a concentration-dependent resistance change upon hybridization to complementary target DNA that is linear over a large dynamic range with a detection limit of 10 fM. As with other SiNW biosensing devices, the sensing mechanism can be understood in terms of the change in charge density at the SiNW surface after hybridization, the so-called "field effect". The SiNW array biosensor discriminates satisfactorily against mismatched target DNA. It is also able to monitor directly the DNA hybridization event in situ and in real time. The SiNW array biosensor described here is ultrasensitive, non-radioactive, and more importantly, label-free, and is of particular importance to the development of gene expression profiling tools and point-of-care applications.

Label-Free DNA Biosensor Based on Localized Surface Plasmon Resonance Coupled with Interferometry

In this report, we developed a new optical biosensor in connection with a gold-deposited porous anodic alumina (PAA) layer chip. In our sensor, we observed that the gold deposition onto the chip surface formed a "caplike" layer on the top of the oxide nanostructures in an orderly fashion, so we called this new surface formation a "gold-capped oxide nanostructure". As a result of its interferometric and localized surface plasmon resonance properties, the relative reflected intensity (RRI) at surface of the chip resulted in an optical pattern that was highly sensitive to the changes in the effective thickness of the biomolecular layer. We demonstrated the method on the detection of picomolar quantities of untagged oligonucleotides and the hybridization with synthetic and PCR-amplified DNA samples. The detection limit of our PAA layer chip was determined as 10 pM synthetic target DNA. The capability of observing both RRI increment and wavelength shift upon biomolecular interactions promises to make our chip widely applicable in various analytical tests.

Analysis of recombinant protein expression using localized surface plasmon resonance (LSPR)

The localized surface plasmon resonance (LSPR)-based optical biosensor using nano-structures of noble metals has been considered as a useful tool for label-free detection of DNA hybridization and protein-protein interactions. We fabricated LSPR-based optical biosensors using gold nano-islands (nominal thickness; 75 A) on glass substrates that were easily made using the conventional fabrication methods. The formation of gold nano-islands on glass substrates was realized by heat treatment of thin gold film deposited with a low deposition rate (approximately 0.05 A/s). The morphologies of sensor surfaces composed of gold nano-islands were observed using an atomic force microscope (AFM) with a non-contact mode. To investigate the sensing capacity of the gold nano-island sensor for the binding of proteins by affinity interactions, the streptavidin and biotin interaction was used as a model system. In addition, detection of recombinant glutathione-S-transferase (GST)-tagged human interleukin-6 (hIL6) expressed in Escherichia coli was carried out by LSPR. It is expected that the LSPR sensors composed of gold nano-islands can be an alternative to traditional methods such as SDS-polyacrylamide gel electrophoresis (SDS-PAGE) for fast analysis of protein expression.

Multiple Label-Free Detection of Antigen−Antibody Reaction Using Localized Surface Plasmon Resonance-Based Core−Shell Structured Nanoparticle Layer Nanochip

In this research, a localized surface plasmon resonance (LSPR)-based bioanalysis method for developing multiarray optical nanochip suitable for screening bimolecular interactions is described. LSPR-based label-free monitoring enables to solve the problems of conventional methods that require large sample volumes and time-consuming labeling procedures. We developed a multiarray LSPR-based nanochip for the label-free detection of proteins. The multiarray format was constructed by a core-shell-structured nanoparticle layer, which provided 300 nanospots on the sensing surface. Antibodies were immobilized onto the nanospots using their interaction with Protein A. The concentrations of antigens were determined from the peak absorption intensity of the LSPR spectra. We demonstrated the capability of the array measurement using immunoglobulins (IgA, IgD, IgG, IgM), C-reactive protein, and fibrinogen. The detection limit of our label-free method was 100 pg/mL. Our nanochip is readily transferable to monitor the interactions of other biomolecules, such as whole cells or receptors, with a massively parallel detection capability in a highly miniaturized package. We anticipate that the direct label-free optical immunoassay of proteins reported here will revolutionize clinical diagnosis and accelerate the development of hand-held and user-friendly point-of-care devices.

Patterned arrays of au rings for localized surface plasmon resonance

In this paper, we examined the characteristic behavior of localized surface plasmon resonances (LSPR) of Au dot and ring arrays in response to the selective binding of biomolecules. To do this, patterned arrays of Au rings and dots with various feature scales were fabricated over large areas by an imprint lithography technique. Our results showed that the LSPR spectra of the Au nanorings exhibited a blue shift with increase in the ring widths and asymptotically converged to those for Au nanodots. This clearly implies that the LSPR spectra can be tuned over an extended wavelength range by varying the ring width. For an illustrative purpose, the patterned Au structures were used to detect the binding of streptavidin to biotin. In doing this, the Au patterns were chemically modified with G4 dendrimers of amine terminated poly(amidoamine), which facilitated the tethering of biotin onto the Au pattern. Exposure of the biotinylated Au nanorings to aqueous streptavidin solution induced both red-shifts of the LSPR spectra and changes in the peak intensities. The sensitivity of the LSPR spectra to the binding of the biomolecules was enhanced as the ring width of Au rings was decreased.

Biomedical applications of plasmon resonant metal nanoparticles

The strong optical absorption and scattering of noble metal nanoparticles is due to an effect called localized surface plasmon resonance, which enables the development of novel biomedical applications. The resonant extinction, which can be tuned to the near-infrared, allows the nanoparticles to act as molecular contrast agents in a spectral region where tissue is relatively transparent. The localized heating due to resonant absorption, also tunable into the near-infared, enables new thermal ablation therapies and drug delivery mechanisms. The sensitivity of these resonances to their environment leads to simple affinity sensors for the detection of low-level molecular analytes. Coupled with their general lack of toxicity, these applications suggest that noble metal nanoparticles are a highly promising class of nanomaterials for new biomedical applications.

Label-Free Electrochemical Immunoassay for the Detection of Human Chorionic Gonadotropin Hormone

Here we report on a new and rapid immunoassay for the label-free voltammetric detection of human chorionic gonadotropin hormone (hCG) in urine. Monitoring the changes in the current signals of antibodies (Abs) before and after the binding of the antigen (Ag) provides the basis for an immunoassay that is simple, rapid, and cost-effective. Since hCG is found at highly elevated levels in pregnant female urine with the range of 30,000-200,000 mIU/mL (approximately 30-200 nM) by 8-10 weeks into pregnancy, its label-free electrochemical detection was achieved by using our method. The coverage of the electrode surface with the Ab and the incubation time with the target Ag were optimized for the detection of hCG. The limit of detection of our method was calculated to be 15 pM (n = 3, approximately 15 mIU/mL) in synthetic hCG samples and 20 pM (n = 3, approximately 20 mIU/mL) in human urine. The electrochemical results for the detection of hCG in the urine samples were in agreement with the results obtained using a reference system, enzyme-linked immunosorbent assay. Further research about the intrinsic electroactivity of Abs and their target molecules would surely provide new and sensitive screening assays, as well as extensive data regarding their interaction mechanisms.

Single-nucleotide polymorphism genotyping by nanoparticle-enhanced surface plasmon resonance imaging measurements of surface ligation reactions

A sensitive method for the analysis of single nucleotide polymorphisms (SNPs) in genomic DNA that utilizes nanoparticle-enhanced surface plasmon resonance imaging (SPRI) measurements of surface enzymatic ligation reactions on DNA microarrays is demonstrated. SNP identification was achieved by using sequence-specific surface reactions of the enzyme Taq DNA ligase, and the presence of ligation products on the DNA microarray elements was detected using SPRI through the hybridization adsorption of complementary oligonucleotides attached to gold nanoparticles. The use of gold nanoparticles increases the sensitivity of the SPRI so that single bases in oligonucleotides can be successfully identified at a concentration of 1 pM. This sensitivity is amply sufficient for performing multiplexed SNP genotyping by using multiple PCR amplicons and should also allow for the direct detection and identification of SNP sequences from 1 pM unamplified genomic DNA samples with this array-based and label-free SPRI methodology. As a first example of SNP genotyping, three different human genomic DNA samples were screened for a possible point mutation in the BRCA1 gene that is associated with breast cancer.