Distance-dependent emission from dye-labeled oligonucleotides on striped Au/Ag nanowires: effect of secondary structure and hybridization efficiency

Controlling plasmon propagation and enhancement via reducing agent in wet chemistry synthesized silver nanowires

Silver nanowires with varying diameters and submillimeter lengths were obtained by changing a reducing agent used during hydrothermal synthesis. The control over the nanowire diameter turns out to play a critical role in determining their plasmonic properties, including fluorescence enhancement and surface plasmon polariton propagation. Advanced fluorescence imaging of hybrid nanostructures assembled of silver nanowires and photoactive proteins indicates longer propagation lengths for nanowires featuring larger diameters. At the same time, with increasing diameter of the nanowires, we measure a substantial reduction of fluorescence enhancement. The results point at possible ways to control the influence of plasmon excitations in silver nanowires by tuning their morphology.

Asymmetric exponential amplification reaction on a toehold/biotin featured template: an ultrasensitive and specific strategy for isothermal microRNAs analysis

The sensitive and specific analysis of microRNAs (miRNAs) without using a thermal cycler instrument is significant and would greatly facilitate biological research and disease diagnostics. Although exponential amplification reaction (EXPAR) is the most attractive strategy for the isothermal analysis of miRNAs, its intrinsic limitations of detection efficiency and inevitable non-specific amplification critically restrict its use in analytical sensitivity and specificity. Here, we present a novel asymmetric EXPAR based on a new biotin/toehold featured template. A biotin tag was used to reduce the melting temperature of the primer/template duplex at the 5′ terminus of the template, and a toehold exchange structure acted as a filter to suppress the non-specific trigger of EXPAR. The asymmetric EXPAR exhibited great improvements in amplification efficiency and specificity as well as a dramatic extension of dynamic range. The limit of detection for the let-7a analysis was decreased to 6.02 copies (0.01 zmol), and the dynamic range was extended to 10 orders of magnitude. The strategy enabled the sensitive and accurate analysis of let-7a miRNA in human cancer tissues with clearly better precision than both standard EXPAR and RT-qPCR. Asymmetric EXPAR is expected to have an important impact on the development of simple and rapid molecular diagnostic applications for short oligonucleotides.

Nanosilver rainbow: a rapid and facile method to tune different colours of nanosilver through the controlled synthesis of stable spherical silver nanoparticles

A rapid and simple one-pot reaction to synthesize stable, spherically shaped silver nanoparticles of different sizes producing distinct optical properties in aqueous solution at ambient temperature has been developed.

Single nanoporous gold nanowire as a tunable one-dimensional platform for plasmon-enhanced fluorescence

Up to ∼62-fold enhancement of fluorescence can be obtained on individual nanoporous Au nanowires, ∼8-fold higher than that of smooth Au nanowires.

Modulation of fluorescence signals from biomolecules along nanowires due to interaction of light with oriented nanostructures

High aspect ratio nanostructures have gained increasing interest as highly sensitive platforms for biosensing. Here, well-defined biofunctionalized vertical indium arsenide nanowires are used to map the interaction of light with nanowires depending on their orientation and the excitation wavelength. We show how nanowires act as antennas modifying the light distribution and the emitted fluorescence. This work highlights an important optical phenomenon in quantitative fluorescence studies and constitutes an important step for future studies using such nanostructures.

Image decoding of photonic crystal beads array in the microfluidic chip for multiplex assays

Along with the miniaturization and intellectualization of biomedical instruments, the increasing demand of health monitoring at anywhere and anytime elevates the need for the development of point of care testing (POCT). Photonic crystal beads (PCBs) as one kind of good encoded microcarriers can be integrated with microfluidic chips in order to realize cost-effective and high sensitive multiplex bioassays. However, there are difficulties in analyzing them towards automated analysis due to the characters of the PCBs and the unique detection manner. In this paper, we propose a strategy to take advantage of automated image processing for the color decoding of the PCBs array in the microfluidic chip for multiplex assays. By processing and alignment of two modal images of epi-fluorescence and epi-white light, every intact bead in the image is accurately extracted and decoded by PC colors, which stand for the target species. This method, which shows high robustness and accuracy under various configurations, eliminates the high hardware requirement of spectroscopy analysis and user-interaction software, and provides adequate supports for the general automated analysis of POCT based on PCBs array.

Dual labeled Ag@SiO₂ core-shell nanoparticle based optical immunosensor for sensitive detection of E. coli

An optical nanobiosensor is presented using a fluorescent dye and anti-E. coli McAb anchored Ag@Silica core shell nanoparticles, for rapid and sensitive Escherichia coli detection in environmental samples. The synthesized dual labeled core shell (DLCS) nanoparticle shows intense fluorescence at 620 nm in solution, having a narrow emission with full width at half maxima (FWHM) of 10 nm, as a prerequisite to develop a sensitive detection platform for various biosensing applications. The specific E. coli was captured using an anti-E. coli antibody functionalized quartz glass, followed by a treatment with DLCS, where the photoluminescence spectroscopy was used to detect the target pathogen. The fabrication of the quartz glass based optical-immunosensor was monitored, and the results show changes in the photoluminescent patterns, which substantiate that varied species were immobilized on the surface of the antibody modified quartz glass. Consequently, the optical immunosensor demonstrated specificity and improved sensitivity, as compared to the customary methods, and was able to detect as low as 5CFU/mL. The developed DLCS based optical immunosensor was evaluated with environmental water samples, which showed acceptable precision, reproducibility and stability, and could be readily applied to the routine monitoring of pathogenic microorganisms in the environmental samples, and most importantly, demonstrate the potential of a prototype development of a simple and inexpensive diagnostic technique.

Experimental and theoretical study of the distance dependence of metal-enhanced fluorescence, phosphorescence and delayed fluorescence in a single system

Distance dependent singlet and triplet metal-enhanced emission of eosin from silica coated silver island films (SiFs) has been studied by steady-state and time resolved fluorescence techniques, along with theoretical finite difference time domain (FDTD) numerical simulations, to understand how the thickness of the dielectric coating surrounding silver nanoparticles fundamentally affects luminescence enhancement. Our findings suggest that the distance dependence of metal-enhanced phenomena such as fluorescence, phosphorescence and delayed fluorescence is underpinned by the decay of the electric near-field, and depending on the actual silver silica sample embodiment, one can see either decreased or enhanced luminescence. These results not only expand our current MEF thinking but also suggest that one may well be able to approximate plasmon-enhanced luminescence values.

Multiplex detection of B-type natriuretic peptide, cardiac troponin I and C-reactive protein with photonic suspension array

A novel photonic suspension array has been developed for multiplex immunoassay. The carriers of this array were silica colloidal crystal beads (SCCBs). The codes of these carriers have characteristic reflection peaks originating from their structural periodicity; therefore they do not suffer from fading, bleaching, quenching or chemical instability. In addition, the fluorescence background of SCCBs is negligible because no fluorescence materials or dyes are involved. With a sandwich method, the proposed suspension array was used for simultaneous multiplex detection of heart failure (HF) and coronary heart disease (CAD) biomarkers in one test tube. The results showed that the three biomarkers: cardiac troponin I (cTnI), C-reactive protein (CRP) and B-type natriuretic peptide (BNP) could be assayed in the ranges of 0.1-500 ng/ml, 1-500 mg/L and 0.02-50 ng/ml with detection limits of 0.01 ng/ml, 0.36 mg/L and 0.004 ng/ml at 3σ, respectively. There were no significant differences between the photonic suspension array and traditional parallel single-analyte test. This novel method demonstrated acceptable accuracy, high detection sensitivity and reproducibility and excellent storage stability. This technique provides a new strategy for low cost, automated, and simultaneous multiplex immunoassays of bio-markers.

SYBR Green I: fluorescence properties and interaction with DNA

In this study, we have investigated the fluorescence properties of SYBR Green I (SG) dye and its interaction with double-stranded DNA (dsDNA). SG/dsDNA complexes were studied using various spectroscopic techniques, including fluorescence resonance energy transfer and time-resolved fluorescence techniques. It is shown that SG quenching in the free state has an intrinsic intramolecular origin; thus, the observed >1,000-fold SG fluorescence enhancement in complex with DNA can be explained by a dampening of its intra-molecular motions. Analysis of the obtained SG/DNA binding isotherms in solutions of different ionic strength and of SG/DNA association in the presence of a DNA minor groove binder, Hoechst 33258, revealed multiple modes of interaction of SG inner groups with DNA. In addition to interaction within the DNA minor groove, both intercalation between base pairs and stabilization of the electrostatic SG/DNA complex contributed to increased SG affinity to double-stranded DNA. We show that both fluorescence and the excited state lifetime of SG dramatically increase in viscous solvents, demonstrating an approximate 200-fold enhancement in 100 % glycerol, compared to water, which also makes SG a prospective fluorescent viscosity probe. A proposed structural model of the SG/DNA complex is compared and discussed with results recently reported for the closely related PicoGreen chromophore.

Multiplex analysis of tumor multidrug-resistance genes expression with photonic suspension array

An easy-operated suspension array based on silica colloidal crystal beads is developed for multiplex analysis of tumor multidrug-resistance genes expression, such as multidrug resistance 1 (MDR1) and multidrug resistance-associated protein 1 (MRP1), and potentially single nucleotide polymorphism. In order to obtain high fluorescence intensity, controlled PCR was used to amplify targets at the samples pretreatment stage. By optimizing the conditions a hybridization procedure, which is similar to nucleic acids analysis with binary probes, was established. Small amounts of analytes 10(-19) M could be detected by the method. The K562 cell, human myeloma cell, and its multidrug-resistance string, adriamycin-selected P-glycoprotein-overexpressed K562/A02, were analyzed by using an established procedure to validate feasibility. Clinical blood samples were detected by our method and real-time PCR simultaneously to validate accuracy. Moreover, when combined with multiplex controlled PCR, the method successfully meets the requirements of multiplex analysis. Hence, the method presented is a good method for multiplex analysis of tumor multidrug-resistance genes expression.

Recent trends in molecular beacon design and applications

A molecular beacon (MB) is a hairpin-structured oligonucleotide probe containing a photoluminescent species (PLS) and a quencher at different ends of the strand. In a recognition and detection process, the hybridization of MBs with target DNA sequences restores the strong photoluminescence, which is quenched before hybridization. Making better MBs involves reducing the background photoluminescence and increasing the brightness of the PLS, which therefore involves the development of new PLS and quenchers, as well as innovative PLS-quencher systems. Heavy-metal complexes, nanocrystals, pyrene compounds, and other materials with excellent photophysical properties have been applied as PLS of MBs. Nanoparticles, nanowires, graphene, metal films, and many other media have also been introduced to quench photoluminescence. On the basis of their high specificity, selectivity, and sensitivity, MBs are developed as a general platform for sensing, producing, and carrying molecules other than oligonucleotides.

Fluorescent metal nanoshell and CK19 detection on single cell image

In this article, we report the synthesis strategy and optical properties of a novel type of fluorescence metal nanoshell when it was used as imaging agent for fluorescence cell imaging. The metal nanoshells were made with 40 nm silica cores and 10nm silver shells. Unlike typical fluorescence metal nanoshells which contain the organic dyes in the cores, novel metal nanoshells were composed of Cy5-labelled monoclonal anti-CK19 antibodies (mAbs) on the external surfaces of shells. Optical measurements to the single nanoparticles showed that in comparison with the metal free labelled mAbs, the mAb-Ag complexes displayed significantly enhanced emission intensity and dramatically shortened lifetime due to near-field interactions of fluorophores with metal. These metal nanoshells were found to be able to immunoreact with target cytokeratin 19 (CK19) molecules on the surfaces of LNCAP and HeLa cells. Fluorescence cell images were recorded on a time-resolved confocal microscope. The emissions from the metal nanoprobes could be clearly isolated from the cellular autofluorescence backgrounds on the cell images as either individuals or small clusters due to their stronger emission intensities and shorter lifetimes. These emission signals could also be precisely counted on single cell images. The count number may provide an approach for quantifying the target molecules in the cells.

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.

Direct observation of chemokine receptors 5 on T-lymphocyte cell surfaces using fluorescent metal nanoprobes 2: Approximation of CCR5 populations

Metal nanoparticle probes were used as molecular imaging agents to detect the expression levels and spatial distributions of the CCR5 receptors on the cell surfaces. Alexa Fluor 647-labeled anti-CCR5 monoclonal antibodies (mAbs) were covalently bound to 20 nm silver nanoparticles to synthesize the mAb-metal complexes. We measured the single nanoparticle emission of the mAb-metal complexes, showing that the complexes displayed enhanced intensities and reduced lifetimes in comparison with the metal-free mAbs. Six HeLa cell lines with various CCR5 expressions were incubated with the mAb-metal complexes for the target-specific binding to the cell surfaces. Fluorescence cell images were recorded on a time-resolved confocal microscope. The collected images expressed clear CCR5 expression-dependent optical properties. Two regression curves were obtained on the basis of the emission intensity and lifetime over the entire cell images against the number of the CCR5 expression on the cells. The emission from the single mAb-metal complexes could be distinctly identified from the cellular autofluorescence on the cell images. The CCR5 spatial distributions on the cells were analyzed on the cell images and showed that the low-expression cells have the CCR5 receptors as individuals or small clusters but the high expression cells have them as the dense and discrete clusters on the cell surfaces.

Fluorescent Metal Nanoshells: Lifetime-Tunable Molecular Probes in Fluorescent Cell Imaging

We reported the preparation of lifetime-tunable fluorescent metal nanoshells and used them as lifetime imaging agents for potential detection of multiple target molecules by a single cell imaging scan. These metal nanoshells were generated to have 40 nm silica cores and 10 nm silver shells. Three kinds of metal-ligand complexes tris(5-amino-1,10-phenanthroline)ruthenium(II) (Ru(NH(2)-Phen)(3) (2+)), tris(2,2'-bipyridine) ruthenium(II) (Ru(bpy)(3) (2+)), and tris(2,3-bis(2-pyridyl)pyrazine))ruthenium(II) (Ru(dpp)(3) (2+)) that have similar excitation and emission wavelengths but different lifetimes were respectively encapsulated in the cores of metal nanoshells for the purpose of fluorescence. Compared with the metal-free silica spheres, these metal nanoshells were found to display enhanced emission intensities and shortened lifetimes due to near-field interactions of Ru(II) complexes with the metal shells. The shortened lifetimes of these metal nanoshells were definitely unique relevant to the Ru(II) complexes: 10 ns for the Ru(Phen-NH(2))(3) (2+)-Ag nanoshells, 45 ns for the Ru(bpy)(3) (2+)-Ag nanoshells, and 200 ns for the Ru(dpp)(3) (2+)-Ag nanoshells. These lifetimes were longer than the lifetime of cellular autofluorescence (2 - 5 ns), so the emission signals of these metal nanoshells could be distinctly isolated from the cellular background on the lifetime cell images. Moreover, these lifetimes were also different from one another, resulting in the emission signals of three metal nanoshells could be distinguished from one another on the cell images. This feature may offer an opportunity to detect multiple target molecules in a single cell imaging scan when the metal nanoshells are bound with various targets in the cells.

Electric field assisted surface plasmon-coupled directional emission: an active strategy on enhancing sensitivity for DNA sensing and efficient discrimination of single base mutation

We have demonstrated the proof-of-principle of electric field assisted surface plasmon-coupled directional emission (E-SPCDE). The combination of SPCDE and electric field control produced a significant synergistic effect to amplify the right signal and suppress the wrong signal intelligently in an active strategy. A novel hairpin structured DNA biosensor based on the quenching and enhancing of fluorescence in SPCDE has been designed. With modulation of the fluorescence coupling efficiency, a high discrimination ratio up to more than 20-fold has been achieved by enhancing the signal of match and suppressing that of mismatch. E-SPCDE has shown a successful application in DNA sensing, eliminating false positives and false negatives in the detection. E-SPCDE should provide an opportunity to create a new generation of miniaturized high-performance sensing platforms especially in chip-based microarrays and to make the manipulation of the nanometer-scale processes more accessible and detectable.

Hybridization efficiency of molecular beacons bound to gold nanowires: effect of surface coverage and target length

Surface-bound nucleic acid probes designed to adopt specific secondary structures are becoming increasingly important in a range of biosensing applications but remain less well characterized than traditional single-stranded probes, which are typically designed to avoid secondary structure. We report the hybridization efficiency for surface-immobilized hairpin DNA probes. Our probes are molecular beacons, carrying a 3' dye moiety and a 5' thiol for attachment to gold nanowires, which serve as both scaffolds for probe attachment and quenchers. Hybridization efficiency was dependent on probe surface coverage, reaching a maximum of ∼90% at intermediate coverages of (1-2) × 10(12) probes/cm(2) and dropping to ≤20% at higher or lower coverages. Fluorescence intensity did not track with the number of target molecules bound, and was highest for high probe coverage despite the lower bound targets per square centimeter. Backfilling with short thiolated oligoethylene glycol spacers increased hybridization efficiency at low hairpin probe coverages (∼(3-4) × 10(11) probes/cm(2)), but not at higher probe coverages (1 × 10(12)/cm(2)). We also evaluated the effect of target length by adding up to 50 nonhybridizing nucleotides to the 3' or 5' end of the complementary target sequence. Additional nucleotides on the 3' end of the complementary target sequence (i.e., the end near the nanowire surface) had a much greater impact on hybridization efficiency as compared to nucleotides added to the 5' end. This work provides guidance in designing sensors in which surface-bound probes designed to adopt secondary structures are used to detect target sequences from solution.

Tailoring DNA structure to increase target hybridization kinetics on surfaces

We report a method for increasing the rate of target hybridization on DNA-functionalized surfaces using a short internal complement DNA (sicDNA) strand. The sicDNA causes up to a 5-fold increase in association rate by inducing a conformational change that extends the DNA away from the surface, making it more available to bind target nucleic acids. The sicDNA-induced kinetic enhancement is a general phenomenon that occurred with all sequences and surfaces investigated. Additionally, the process is selective and can be used in multicomponent systems to controllably and orthogonally "turn on" specific sequences by the addition of the appropriate sicDNA. Finally, we show that sicDNA is compatible with systems used in gene regulation, intracellular detection, and microarrays, suggesting several potential therapeutic, diagnostic, and bioinformatic applications.

Nanoscale interfaces to biology

Nanotechnology has held great promise for revolutionizing biology. The biological behavior of nanomaterials depends primarily on how they interface to biomolecules and their surroundings. Unfortunately, interface issues like non-specific adsorption are still the biggest obstacles to the success of nanobiotechnology and nanomedicine, and have held back widespread practical use of nanotechnology in biology. Not only does the biological interface of nanoparticles (NPs) need to be understood and controlled, but also NPs must be treated as biological entities rather than inorganic ones. Furthermore, one can adopt an engineering perspective of the NP-biological interface, realizing that it has unique, exploitable properties.

Nanowire-based sensors

Nanowires are important potential candidates for the realization of the next generation of sensors. They offer many advantages such as high surface-to-volume ratios, Debye lengths comparable to the target molecule, minimum power consumption, and they can be relatively easily incorporated into microelectronic devices. Accordingly, there has been an intensified search for novel nanowire materials and corresponding platforms for realizing single-molecule detection with superior sensing performance. In this work, progress made towards the use of nanowires for achieving better sensing performance is critically reviewed. In particular, various nanowires types (metallic, semiconducting, and insulating) and their employment either as a sensor material or as a template material are discussed. Major obstacles and future steps towards the ultimate nanosensors based on nanowires are addressed.

Understanding the role of thiol and disulfide self-assembled DNA receptor monolayers for biosensing applications

A detailed study of the immobilization of three differently sulfur-modified DNA receptors for biosensing applications is presented. The three receptors are DNA-(CH)n-SH-, DNA-(CH)n-SS-(CH)n-DNA, and DNA-(CH)n-SS-DMTO. Nanomechanical and surface plasmon resonance biosensors and fluorescence and radiolabelling techniques were used for the experimental evaluation. The results highlight the critical role of sulfur linker type in DNA self-assembly, affecting the kinetic adsorption and spatial distribution of DNA chains within the monolayer and the extent of chemisorption and physisorption. A spacer (mercaptohexanol, MCH) is used to evaluate the relative efficiencies of chemisorption of the three receptors by analysing the extent to which MCH can remove physisorbed molecules from each type of monolayer. It is demonstrated that -SH derivatization is the most suitable for biosensing purposes as it results in densely packed monolayers with the lowest ratio of physisorbed probes.

Highly controlled silica coating of PEG-capped metal nanoparticles and preparation of SERS-encoded particles

Thiol-modified poly(ethylene glycol) (mPEG-SH) has been used to replace standard capping agents from the surfaces of gold nanoparticles with different sizes and shapes. Upon PEG stabilization, the nanoparticles can be transferred into ethanol, where silica can be directly grown on the particle surfaces through the standard Stober process. The obtained silica shells are uniform and homogeneous, and the method allows a high degree of control over shell thickness for any particle size and shape. Additionally, Raman-active molecules can be readily incorporated within the composite nanoparticles during silica growth so that SERS/SERRS-encoded nanoparticles can be fabricated containing a variety of tags, thereby envisaging multiplexing capability.

Luminescent Silica Core / Silver Shell Encapsulated with Eu(III) Complex

In this paper we studied the metal-enhanced emission from long-lifetime lanthanide dyes that were encapsulated in the silver nanoshells. The metal nanoshells were synthesized with the silica spherical cores of 50 nm diameters and the silver shells of 5 - 60 nm. The optical properties of luminescent metal shells were performed on the either ensemble fluorescence spectroscopy or single particle imaging. The emission intensity from the encapsulated lanthanides was observed to enhance significantly by the metal nanoshell. The enhancement efficiency initially increased with the metal shell thickness and then decreased. The maximal enhancement occurred at the 20 - 30 nm thickness. The lifetime of encapsulated Eu(III) complexes was shorten dramatically indicating that they were coupled efficiently with the metal shells. The increased brightness and reduced lifetime of this core-shell structure demonstrate that the lanthanides are favorable for the single target molecule detections after encapsulating into the metal nanoshells.

Nano-flares for mRNA regulation and detection

We build off the previously described concept of a nanoflare to develop an oligonucleotide gold nanoparticle conjugate that is capable of both detecting and regulating intracellular levels of mRNA. We characterize the binding rate and specificity of these materials using survivin, a gene associated with the diagnosis and treatment of cancer, as a target. The nanoconjugate enters cells and binds mRNA, thereby decreasing the relative abundance of mRNA in a dose- and sequence-dependent manner, resulting in a fluorescent response. This represents the first demonstration of a single material capable of both mRNA regulation and detection. Further, we investigate the intracellular biochemistry of the nanoconjugate, elucidating its mechanism of gene regulation. This work is important to the study of biologically active nanomaterials such as the nanoflare and is a first step toward the development of an mRNA responsive "theranostic".

Viral detection using DNA functionalized gold filaments

Early detection of pediatric viruses is critical to effective intervention. A successful clinical tool must have a low detection limit, be simple to use and report results quickly. No current method meets all three of these criteria. In this report, we describe an approach that combines simple, rapid processing and label free detection. The method detects viral RNA using DNA hairpin structures covalently attached to a gold filament. In this design, the gold filament serves both to simplify processing and enable fluorescence detection. The approach was evaluated by assaying for the presence of respiratory syncytial virus (RSV) using the DNA hairpin probe 5' [C6Thiol]TTTTTTTTTTCGACGAAAAATGGGGCAAATACGTCG[CAL] 3' covalently attached to a 5 cm length of a 100 microm diameter gold-clad filament. This sequence was designed to target a portion of the gene end-intergenic gene start signals which is repeated multiple times within the negative-sense genome giving multiple targets for each strand of genomic viral RNA present. The filament functionalized with probes was immersed in a 200 microm capillary tube containing viral RNA, moved to subsequent capillary tubes for rinsing and then scanned for fluorescence. The response curve had a typical sigmoidal shape and plateaued at about 300 plaque forming units (PFU) of viral RNA in 20 microL. The lower limit of detection was determined to be 11.9 PFU. This lower limit of detection was approximately 200 times better than a standard comparison ELISA. The simplicity of the core assay makes this approach attractive for further development as a viral detection platform in a clinical setting.

Fluorescent avidin-bound silver particle: a strategy for single target molecule detection on a cell membrane

Cy5-avidin conjugate-bound silver nanoparticles were prepared as a fluorescence molecular reagent for the cell imaging. Compared with the metal-free avidin conjugate, the avidin-metal complex was observed to display a stronger emission intensity, shorter lifetime, and better photostability. The avidin-metal complexes were conjugated with the biotin-sites on the surfaces of PM1 cell lines, and the cell images were recorded using scanning confocal microscopy. It was noticed that the avidin-metal complexes bound on the cell surfaces could be identified as the isolated emission spots distinct from the cellular autofluorescence. The emission intensity over the cell image was increased with an increase of the number of avidin-metal complexes on the cell surface but the lifetime was decreased. A quantitative regression curve was achieved between the amount of avidin-metal complex on the cell surface and the emission intensity or lifetime over the entire cell image. On the basis of this curve, we expect to develop an approach that can be used to quantify the amount of target molecules on the cell surfaces using the cell intensity and lifetime images at the single cell level.

Graphene-based single-bacterium resolution biodevice and DNA transistor: interfacing graphene derivatives with nanoscale and microscale biocomponents

Establishing "large-contact-area" interfaces of sensitive nanostructures with microbes and mammalian cells will lead to the development of valuable tools and devices for biodiagnostics and biomedicine. Chemically modified graphene (CMG) nanostructures with their microscale area, sensitive electrical properties, and modifiable chemical functionality are excellent candidates for such biodevices at both biocellular and biomolecular scale. Here, we report on the fabrication and functioning of a novel CMG-based (i) single-bacterium biodevice, (ii) label-free DNA sensor, and (iii) bacterial DNA/protein and polyelectrolyte chemical transistor. The bacteria biodevice was highly sensitive with a single-bacterium attachment generating approximately 1400 charge carriers in a p-type CMG. Similarly, single-stranded DNA tethered on graphene hybridizes with its complementary DNA strand to reversibly increase the hole density by 5.61 x 1012 cm(-2). We further demonstrate (a) a control on the device sensitivity by manipulating surface groups, (b) switching of polarity specificity by changing surface polarity, and (c) a preferential attachment of DNA on thicker CMG surfaces and sharp CMG wrinkles.

Enhanced fluorescence images for labeled cells on silver island films

Silver island films (SIFs) were deposited on glass substrates to serve as supports. T-Lymphocytic (PM1) cell lines were labeled by Alexa Fluor 680-dextran conjugates on the membranes or by YOYO in the nuclei. The fluorescence images of the cell lines were recorded in the emission intensity and lifetime using scanning confocal microscopy. The fluorescence signals by the fluorophores bound on the cell membranes were enhanced significantly by SIF supports as compared with those on the glass. In addition to the increase in the intensity, there was a dramatic shortening of the emission lifetime. In contrast to the Alexa Fluor 680 fluorophores on the membranes, the YOYO fluorophores intercalated in the cell nuclei were not influenced significantly by the silver islands. This result can be interpreted by an effect of the distance on coupling between the fluorophores and metal particles: the fluorophores on the cell membranes are localized within, but the fluorophores in the cell nuclei are beyond the region of metal-enhanced fluorescence. Thus, the metal supports can be used to improve the detection sensitivity for target molecules on cell surfaces when they are fluorescently labeled.

Molecular beacon-metal nanowire interface: effect of probe sequence and surface coverage on sensor performance

We report the effect of surface coverage and sequence on the performance of 5' thiolated, 3' fluorophore-labeled DNA hairpin probes bound to Au/Ag striped ("barcoded") metal nanowires. Coverage was controlled by varying probe concentration, buffer ionic strength, and by addition of short hydroxy-terminated alkanethiol diluent molecules during probe assembly onto the nanowire surface. Surface dilution of the surface-bound probes with a omega-hydroxyl alkanethiol, a commonly accepted practice in the surface-bound DNA literature, did not appreciably improve sensor performance as compared to similar probe coverages without hydroxyalkanethiol diluents; this finding underscores the differences between the molecular beacon probes used here and more traditional nonfluorescent, random coil probes. We found that intermediate probe coverage of approximately 10 (12) molecules/cm (2) gave the best discrimination between presence and absence of a target sequence. Because we are interested in multiplexed assays, we also compared several beacon probe sequences having different stabilities for secondary structure formation in solution; we found that both probe surface coverage and sensor performance varied for different probe sequences. When five different molecular beacon probes, each bound to barcoded nanowires, were used in a multiplexed, wash-free assay for target oligonucleotides corresponding to viral nucleic acid sequences, these differences in probe performance did not prevent accurate target identification. We anticipate that the findings described here will also be relevant to other applications involving molecular beacons or other structured nucleic acid probes immobilized on metal surfaces.

Plasmon-Coupled Fluorescence Probes: Effect of Emission Wavelength on Fluorophore-Labeled Silver Particles

We examined the emission intensity and wavelength of 40 nm diameter silver particles covalently coated with organic fluorophores with different absorption and emission wavelengths. The objective of this study is to use the interactions of fluorophores with the plasmon in the metal particles to create the brightest possible probes. We refer to the complexes as plasmon-coupled fluorescence probes (PCPs). The fluorophores were separated from the metal cores by 10 nm long polymer backbones. The fluorescence was observed to be enhanced for seven fluorophores with emission wavelength from 450 to 700 nm. The enhancement efficiency was shown to approximately increase with long wavelengths for the silver particle-bound fluorophores. When comparing a single fluorophore free in solution and bound to the silver particle, the emission intensity increases 3- to 17-fold. The relationship between the enhancement efficiency and loading number of fluorophore on each silver particle was studied to optimize the conditions for PCP brightness. Compared with the free single fluorophores in the absence of metal, the optimized single labeled silver particles were even more than 1000-fold brighter, showing their potentials in the applications of sensitive clinical and biological assays.

Single-cell fluorescence imaging using metal plasmon-coupled probe 2: single-molecule counting on lifetime image

Multiple Alexa Fluor 647-conjugated concanavalin A (conA) molecules were covalently bound to a single 20 nm silver particle to synthesize metal plasmon-coupled probes (PCPs). The fluorescence images were recorded by scanning confocal microscopy in both intensity and lifetime. The brightness of PCPs was 30-fold brighter than those of free conA and the lifetime of PCPs was shortened dramatically. PCPs were used to label T-lymphocytic ( PM1) cells. The emission spots by PCPs bound on the cell surfaces were separated clearly from the cell images by autofluorescence due to the brighter signal and shorter lifetime of PCPs. The emission spots by PCPs were also scanned in three dimensions to count the distribution of bound fluorophores on the cell surfaces. The metal-associated fluorophores thus are suggested using as novel molecular imaging agents to quantify the components and describe their distributions on the cell surfaces.

Ultrasensitive optical biodiagnostic methods using metallic nanoparticles

Dramatic progress has been made over the recent decade in the applications of metallic nanoparticles in the field of biomolecule detection. The useful physical and chemical properties (e.g., availability of various synthetic methods of size- and shape-controlled nanoparticles, size- and shape-dependent optical properties, availability of various surface chemistries and biocompatibility) of metallic nanoparticles have brought development to the ultrasensitive detection of biomolecules at the attomolar level and this sensitivity enables the diagnosis of otherwise undetectable biomarkers of many fatal diseases, including Alzheimer’s disease. Furthermore, coupled with the strong physical properties and biocompatible nature of gold nanoparticles in in vivo conditions, the scope of applications for these particles have been broadened into the field of in vivo imaging, such as X-ray contrasting agents, and also cellular tracking. Here, we review synthetic methods and optical properties of metallic nanoparticles and their use in ultrasensitive, in vitro and in vivo biodiagnostic methods.

Metallic barcodes for multiplexed bioassays

Both detection and postdiagnosis monitoring are critical for cancer isolation and treatment. Particle-based sensing strategies could help to address these medical needs. This review describes barcoded metallic nanowires as particle scaffolds for multiplexed detection of antigens or nucleic acids. Barcode patterns are compositionally encoded as stripes of gold and silver metal along the nanowire length during fabrication by templated electrodeposition. Particle identification is accomplished using reflectance optical microscopy and can be coupled with fluorescence readout of antigen- or nucleic acid-binding events. Several approaches to multiplexed biodetection based on barcoded nanowires will be described and the potential for these particles in cancer detection will be discussed.

The synthesis and fabrication of one-dimensional nanoscale heterojunctions

There are a variety of methods for synthesizing or fabricating one-dimensional (1D) nanostructures containing heterojunctions between different materials. Here we review recent developments in the synthesis and fabrication of heterojunctions formed between different materials within the same 1D nanostructure or between different 1D nanostructures composed of different materials. Structures containing 1D nanoscale heterojunctions exhibit interesting chemistry as well as size, shape, and material-dependent properties that are unique when compared to single-component materials. This leads to new or enhanced properties or multifunctionality useful for a variety of applications in electronics, photonics, catalysis, and sensing, for example. This review separates the methods into vapor-phase synthesis, solution-phase synthesis, template-based synthesis, and other approaches, such as lithography, electrospinning, and assembly. These methods are used to form a variety of heterojunctions, including segmented, core/shell, branched, or crossed, from different combinations of semiconductor, metal, carbon, and polymeric materials.