Multicolor Detection Research Articles

Fibered confocal spectroscopy and multicolor imaging system for in vivo fluorescence analysis

We report the design and implementation of spectroscopic and multicolor imaging capabilities into a fibered confocal fluorescence microscope (FCFM) already capable of in vivo imaging. The real time imaging device and the high resolution fiber probe make this system the first reported capable of performing multi color detection in the field of FCFM. The advantages of the system will allow in vivo morphological and functional imaging. Preliminary experiments were carried out in tissue samples to demonstrate the potential of the technique. The quality of the axial sectioning achieved in the confocal fluorescence spectroscopy mode is demonstrated experimentally, and applications to multicolor imaging are shown.

Multicolor Fluorescence Detection on an Electrophoretic Microdevice Using an Acoustooptic Tunable Filter

An acoustooptic tunable filter (AOTF) is used to detect multiple fluorescent signals on a fluidic microdevice. A confocal laser-induced fluorescence detection setup is used to excite fluorescent dyes in glass microchannels, presenting a streamlined and robust detection system consisting of the narrow-bandwidth AO filter and a single photodetector. The flexibility of the filter is demonstrated by alternating between wavelengths for precise microchannel alignment and sweeping through a range of wavelengths for preliminary spectral characterization of subnanoliter probe volumes of target analytes. The AOTF is also coupled with an electrophoretic separation for the multicolor detection of PCR-amplified DNA against a labeled sizing standard, the discrimination of multiple amplicons overlapped in time, and the identification of amplified biowarfare agents in a fluorescent spiking experiment. Finally, to demonstrate the multicolor capability of the system, 19-wavelength detection is performed during the separation of a three-dye sample mixture.

Prism-based multicolor fluorescence correlation spectrometer

We report the design and application of a prism-based detection system for fluorescence (cross) correlation spectroscopy. The system utilizes a single laser wavelength for the simultaneous excitation of several dyes of different emission spectra. Fluorescence light is spectrally separated with a prismatic setup, and wavelengths are selected by scanning a fiber-coupled avalanche photodiode across the image spots. Multicolor autocorrelations are demonstrated with standard and tandem dyes, and fluorescence cross-correlation measurements of biotinylated nanocontainers and streptavidin are presented. This spectrometer offers high optical stability and no focal volume mismatch for the multicolor detection of molecular dynamics and interactions, with single-molecule sensitivity.

Rapid quantitative analysis using a single molecule counting approach

Single molecule detection of target molecules specifically bound by paired fluorescently labeled probes has shown great potential for sensitive quantitation of biomolecules. To date, no reports have rigorously evaluated the analytical capabilities of a single molecule detection platform employing this dual-probe approach or the performance of its data analysis methodology. In this paper, we describe a rapid, automated, and sensitive multicolor single molecule detection apparatus and a novel extension of coincident event counting based on detection of fluorescent probes. The approach estimates the number of dual-labeled molecules of interest from the total number of coincident fluorescent events observed by correcting for unbound probes that randomly pass through the interrogation zone simultaneously. Event counting was evaluated on three combinations of distinct fluorescence channels and was demonstrated to outperform conventional spatial cross-correlation in generating a wider linear dynamic response to target molecules. Furthermore, this approach succeeded in detecting subpicomolar concentrations of a model RNA target to which fluorescently labeled oligonucleotide probes were hybridized in a complex background of RNA. These results illustrate that the fluorescent event counting approach described represents a general tool for rapid sensitive quantitative analysis of any sample analyte, including nucleic acids and proteins, for which pairs of specific probes can be developed.

Specific and Stable Fluorescence Labeling of Histidine-Tagged Proteins for Dissecting Multi-Protein Complex Formation

Labeling of proteins with fluorescent dyes offers powerful means for monitoring protein interactions in vitro and in live cells. Only a few techniques for noncovalent fluorescence labeling with well-defined localization of the attached dye are currently available. Here, we present an efficient method for site-specific and stable noncovalent fluorescence labeling of histidine-tagged proteins. Different fluorophores were conjugated to a chemical recognition unit bearing three NTA moieties (tris-NTA). In contrast to the transient binding of conventional mono-NTA, the multivalent interaction of tris-NTA conjugated fluorophores with oligohistidine-tagged proteins resulted in complex lifetimes of more than an hour. The high selectivity of tris-NTA toward cumulated histidines enabled selective labeling of proteins in cell lysates and on the surface of live cells. Fluorescence labeling by tris-NTA conjugates was applied for the analysis of a ternary protein complex in solution and on surfaces. Formation of the complex and its stoichiometry was studied by analytical size exclusion chromatography and fluorescence quenching. The individual interactions were dissected on solid supports by using simultaneous mass-sensitive and multicolor fluorescence detection. Using these techniques, formation of a 1:1:1 stoichiometry by independent interactions of the receptor subunits with the ligand was shown. The incorporation of transition metal ions into the labeled proteins upon labeling with tris-NTA fluorophore conjugates provided an additional sensitive spectroscopic reporter for detecting and monitoring protein-protein interactions in real time. A broad application of these fluorescence conjugates for protein interaction analysis can be envisaged.

Nano-oncology: drug delivery, imaging, and sensing

Innovation in the last decade has endowed nanotechnology with an assortment of tools for delivery, imaging, and sensing in cancer research-stealthy nanoparticle vectors circulating in vivo, assembled with exquisite molecular control, capable of selective tumor targeting and potent delivery of therapeutics; intense and photostable quantum dot-based tumor imaging, enabling multicolor detection of cell receptors with a single optical excitation source; arrays of semiconducting nanowire and carbon nanotube sensor elements for selective multiplexed sensing of cancer markers without the need for probe labeling. These rapidly emerging tools are indicative of a burgeoning field ready to expand into medical applications. This review attempts to outline most of the current nanoparticle toolset for therapeutic release by liposomes, dendrimers, smart polymers, and virus-based systems. Advantages of nanoparticle-based imaging and targeting by use of nanoshells and quantum dots are also explored. Finally, emerging nanoelectronics-based sensing and a global discussion on the utility of each nanoparticle system addresses their fundamental advantages and shortcomings in cancer research.

Comparison of real-time PCR and hemagglutination assay for quantitation of human polyomavirus JC

Human polyomavirus JC (JCV), the etiological agent of the disease progressive multifocal leukoencephalopathy (PML) affects immunocompromised patients particularly patients with AIDS. In vitro studies of JCV infection are hampered by the lack of sensitive JCV quantitation tests. Although the hemagglutination (HA) assay has been routinely employed for in vitro quantitation of JCV, its sensitivity is severely limited. We have employed a real-time PCR assay which compares favorably with the HA assay for the in vitro quantitation of JCV. JCV(Mad1), propagated in primary human fetal glial (PHFG) cells in two independent laboratories, was purified and quantitated by the HA assay. Both batches of purified JCV(Mad1) were then serially diluted in Dulbecco's Modified Eagle's Medium to obtain HA titers ranging from 64 to 0.001 HA units (HAU) per 100 μL of virus suspension. DNA was extracted from 100 μL of virus suspension and eluted in 50 μL of buffer, and DNA amplification and quantitation were performed in the Bio-Rad iCycler iQ Multicolor Real-Time PCR Detection System using T-antigen as the target gene. Real-time PCR for quantitation of JCV was sensitive and consistently detected 1.8 × 101 copies of JCV DNA, and as low as 0.001 HAU equivalent of JCV. Moreover, there was a strong linear correlation between the HA assay and the DNA copy number of JCV(Mad1). The intra-run and inter-run coefficients of variation for the JCV standard curve were 0.06% to 4.8% and 2.6% to 5.2%, respectively. Based on these data, real-time PCR can replace the less-sensitive HA assay for the reliable detection, quantitation and monitoring of in vitro JCV replication.

Su.48. Stomatin-Like Protein 2 Stabilizes Tcr-Dependent Signalling Microclusters in Effector T-Cells

Despite significant recent advances in molecular and structural studies of G protein-coupled receptors (GPCRs), an understanding of transmembrane signal transduction with chemical precision requires new approaches. Simple binary receptor–ligand or receptor–G protein complex models cannot adequately describe the relevant macromolecular signaling machineries. GPCR signalosomes undergo complex dynamic assembly–disassembly reactions to create allosteric signaling conduits whose properties cannot necessarily be predicted from individual elements alone. The combinatorial possibilities inherent in a system with hundreds of potential components suggest that high-content miniaturized experimental platforms and computational approaches will be required. To study allosteric effects involved in signalosome reaction pathways, a bottom-up approach using multicolor single-molecule detection fluorescence experiments in biochemically defined systems and complemented by molecular dynamics models of macromolecular complexes is proposed. In bridging the gap between molecular and systems biology, this synthetic approach suggests a way forward from the flatlands to multi-dimensional data collection.

Rapid PCR Real-Time Genotyping of M-Malton ??1-Antitrypsin Deficiency Alleles by Molecular Beacons

Alpha1-Antitrypsin deficiency is an autosomal codominant inherited disorder, with increased risk of developing lung and liver disease. The large majority of subjects affected by alpha1-antitrypsin deficiency carry the PIZZ or PISZ genotypes, which can be easily detected using several molecular methods. Another pathologic allele, the M-Malton variant (also known as Mnichinan and Mcagliari), can mimic the Pi Z clinical phenotype, but this alpha1-antitrypsin deficiency variant is not easily recognizable and, therefore, seems to be more under-recognized than the Z or S alleles. We report the development of a rapid qualitative fluorescent real-time PCR assay designed for the detection of the M-Malton alpha1-antitrypsin deficiency alleles using 2 specific molecular beacons. The assay is able to detect in a single tube the homozygous as well the heterozygous genotypes. The procedure combines the great sensitivity of the polymerase chain reaction, the specificity provided by allele-specific molecular beacons, and the throughput of a multi-color fluorescence detection procedure. This technique will be useful for research and molecular diagnostic laboratories involved in the study of alpha1-antitrypsin deficiency-related diseases.

Pulsed Interleaved Excitation

In this article, we demonstrate the new method of pulsed interleaved excitation (PIE), which can be used to extend the capabilities of multiple-color fluorescence imaging, fluorescence cross-correlation spectroscopy (FCCS), and single-pair fluorescence resonance energy transfer (spFRET) measurements. In PIE, multiple excitation sources are interleaved such that the fluorescence emission generated from one pulse is complete before the next excitation pulse arrives. Hence, the excitation source for each detected photon is known. Typical repetition rates used for PIE are between ∼1 and 50MHz. PIE has many applications in various fluorescence methods. Using PIE, dual-color measurements can be performed with a single detector. In fluorescence imaging with multicolor detection, spectral cross talk can be removed, improving the contrast of the image. Using PIE with FCCS, we can eliminate spectral cross talk, making the method sensitive to weaker interactions. FCCS measurements with complexes that undergo FRET can be analyzed quantitatively. Under specific conditions, the FRET efficiency can be determined directly from the amplitude of the measured correlation functions without any calibration factors. We also show the application of PIE to spFRET measurements, where complexes that have low FRET efficiency can be distinguished from those that do not have an active acceptor.

Four-color fluorescence correlation spectroscopy realized in a grating-based detection platform

We have developed a filterless multicolor detection unit for fluorescence correlation spectroscopy (FCS). This grating-based setup is continuously tunable for multicolor separation and is thus a powerful alternative to the classical cascade of dichroic mirrors and filters. Our tailored platform allows for accommodation of up to 15 detection channels covering the entire visible spectral range. As a proof of principle, we successfully demonstrate simultaneous FCS of four distinct fluorescent quantum dot species being mixed in aqueous solution. Grating-based detection allows for spectral high-resolution FCS in a stable and compact setup and is a feasible tool for quantitative investigation of complexbiomolecular dynamics on a single molecule level.

A novel multicolor immunofluorescence method using heat treatment.

We describe a novel method for immunofluorescent detection of multiple antigens in a single paraffin-embedded tissue section. We hypothesized that if fluorescent dyes are resistant to heat treatment, then thermal inactivation of immunoglobulins during antigen detection procedures might make it possible to use multicolor immunofluorescence detection even if the primary antibodies are from the same species. We found that several fluorescent dyes, including fluorescein isothiocyanate (FITC), Cy3 and Cy5, were resistant to heating at 90 degrees Celsius for 15 min, whereas the antigenicities of the primary antibodies were lost completely. This novel method, which uses heat treatment between staining steps, has great advantages for multicolor immunofluorescence because unlabeled primary antibodies from the same species can be used. Therefore, by using this method not only 3 unlabeled mouse monoclonal antibodies but also 3 unlabeled rabbit antisera can be used as primary antibodies for multicolor immunofluorescence.

Detection of Single Bacterial Pathogens with Semiconductor Quantum Dots

Semiconductor quantum dots (QDs) have been used in a simple fluorometric assay to detect single cells of the pathogenic Escherichia coli O157:H7 serotype. Composed of CdSe/ZnS core/shell QDs conjugated to streptavidin, this system exhibits 2 orders of magnitude more sensitivity than a similar assay using a common organic dye. Selectivity for this pathogenic bacterial strain over a common lab strain (E. coli DH5alpha), which is gained from the use of specific biotinylated antibodies, is also demonstrated for QD labeling. Under continuous excitation, these QDs retain high fluorescence intensities for hours, whereas a typical organic dye bleaches within seconds, allowing for more rapid and accurate identification of E. coli O157:H7 in single-cell fluorescence-based assays. This indirect QD labeling method, based on antibody-antigen and streptavidin-biotin interactions, is flexible enough to expand to other systems and has great potential for use in simultaneous multicolor detection schemes.

Highly Efficient, Wavelength-Tunable, Gold Nanoparticle Based Optothermal Nanoconvertors

A photon-to-thermal energy conversion nanosystem based the near-infrared irradiation of one-dimensional gold nanoparticles (nanorods) is highly efficient and tunable to the incident wavelength. Using ambient photothermal detection, we observed a temperature rise of ca. 30 degrees C upon irradiating an aliquot of an aqueous nanoparticle suspension with a laser for 5 s. The temperature can be elevated even higher by embedding the particles into a poorly thermally conducting solid medium. The illuminated area of a sample containing nanorod particles embedded in a polyurethane matrix can be heated to >100 degrees C upon irradiation for 1 min. This optothermal conversion efficiency can be turned on selectively by tuning the wavelength to match that of the surface plasmon resonance of the particles. This specificity, with respect to the wavelength of the incident light, makes these highly efficient, particle-based, optothermal nanoconvertors suitable for potential use in multicolor detection on biochips and related sensors and as ideal contrasting agents for optoacoustic biomedical imaging applications.

Designs and applications of corrugated QWIPs

In this paper, we will describe the performance of two long wavelength 1024 × 1024 corrugated quantum well infrared photodetector focal plane arrays (C-QWIP FPAs) with cutoff wavelengths at 8.6 and 9.0 μm, respectively. The FPAs are background limited (BLIP) at around 76 K in an f/1.8 optical system. In addition to the high performance of these C-QWIPs, the corresponding FPAs are also easily producible, making them ideal for large production. We will discuss the optimization of the detectors for different applications. Since corrugated coupling is wavelength insensitive, it is capable of broadband and multi-color detection. We will present a GaAs/AlGaAs broadband detector based on a binary superlattice design. Incorporating the broadband characteristic in a high gain InGaAs/InP material, C-QWIPs with large background photocurrent can be obtained for high speed applications. For multi-color detection, we have investigated two different approaches. One is based on a voltage-tunable, two-color QWIP material, which can be switched between two detection wavelengths simply by changing the detector bias. Stacking two of these similar QWIPs together and separating them with a middle contact layer, a voltage tunable, four-color detector array can be fabricated. A second approach is to combine a broadband QWIP material with a wavelength-selective light coupling method. Using a light coupling geometry to control the detection wavelength of individual pixels, a large number of wavelengths can be detected based on a single broadband detector material.

Interchange of aequorin and obelin bioluminescence color is determined by substitution of one active site residue of each photoprotein

The bioluminescence spectra from the Ca2+-regulated photoproteins aequorin (λmax=469nm) and obelin (λmax=482nm) differ because aequorin has an H-bond from its Tyr82 to the bound coelenteramide, not present in obelin at the corresponding Phe88. Substitutions of this Phe88 by Tyr, Trp, or His shifted the obelin bioluminescence to shorter wavelength with F88Y having λmax=453nm. Removal of the H-bond by the substitution of Y82F in aequorin shifted its bioluminescence to λmax=501nm. All mutants were stable with good activity and were expressible in mammalian cells, thereby demonstrating potential for monitoring multiple events in cells using multi-color detection.

Single molecule studies of quantum dot conjugates in a submicrometer fluidic channel

A microfluidic and optical system was created for the detection and analysis of single molecules in solution. Fluidic channels with submicrometer dimensions were used to isolate, detect and identify individual quantum dots conjugated with organic fluorophores. The channels were fabricated in fused silica with a 500 nm square cross section. The resulting focal volume of approximately 500 aL reduced fluorescent background and increased the signal to noise ratio of single molecule detection. The channels also enabled the rapid detection of 99% of quantum dots and organic fluorophores traversing the focal volume. Conjugates were driven through the channels electrokinetically at 2.3 kV cm(-1), excited with a single 476 nm wavelength laser and detected with a confocal microscope. Fluorescence emission was collected simultaneously from green (500-590 nm) and red (610-680 nm) regions of the spectrum. Signal rejection was minimized by the narrow and symmetric emission spectra of the quantum dots. To demonstrate efficient multicolor detection and characterization of single molecule binding, Qdot 655 Streptavidin Conjugates were bound to Alexa Fluor 488 molecules and individually detected. Photon counting histogram analysis was used to quantify coincident detection and degree of binding. Fluorescence correlation spectroscopy was used to measure the mobility of bound and unbound species. The union of fluidic channels with submicrometer dimensions and quantum dots as fluorescent labels resulted in efficient and rapid multiplexed single molecule detection and analysis.

Quantitative protein profiling using antibody arrays

Traditional approaches to microarrays rely on direct binding assays where the extent of hybridisation and the signal detected are a measure of the analyte concentration in the experimental sample. This approach, directly imported from the nucleic acid field, may fail if applied to antibody-antigen interactions due to the shortage of characterised antibodies, the significant heterogeneity of antibody affinities, their dependence on the extent of protein modification during labelling and the inherent antibody cross-reactivity. These problems can potentially limit the multiplexing capabilities of protein affinity assays and in many cases rule out quantitative protein profiling using antibody microarrays. A number of approaches aimed at achieving quantitative protein profiling in a multiplex format have been reported recently. Of those reported, the three most promising routes include signal amplification, multicolour detection and competitive displacement approaches to multiplex affinity assays. One in particular, competitive displacement, also overcomes the problems associated with quantitation of affinity interactions and provides the most generic approach to highly parallel affinity assays, including antibody arrays.

Multiplexed fluorescence detection of phosphorylation, glycosylation, and total protein in the proteomic analysis of breast cancer refractoriness.

The Multiplexed Proteomics (MP) technology is a new approach that permits quantitative, multicolor fluorescence detection of proteins in one-dimensional or two-dimensional gels. This methodology allows for multiplexed identification and differential analysis of phosphoproteins, glycoproteins, and total proteins within a single gel electrophoresis experiment. Here the MP system was applied to the differential proteomic analysis of pregnancy-induced refractoriness to breast cancer using a rat model system. Differential analyses identified multiple proteins with altered phosphorylation, glycosylation, or protein expression patterns.

DNA mapping using microfluidic stretching and single-molecule detection of fluorescent site-specific tags.

We have developed a rapid molecular mapping technology--Direct Linear Analysis (DLA)--on the basis of the analysis of individual DNA molecules bound with sequence-specific fluorescent tags. The apparatus includes a microfluidic device for stretching DNA molecules in elongational flow that is coupled to a multicolor detection system capable of single-fluorophore sensitivity. Double-stranded DNA molecules were tagged at sequence-specific motif sites with fluorescent bisPNA (Peptide Nucleic Acid) tags. The DNA molecules were then stretched in the microfluidic device and driven in a flow stream past confocal fluorescence detectors. DLA provided the spatial locations of multiple specific sequence motifs along individual DNA molecules, and thousands of individual molecules could be analyzed per minute. We validated this technology using the 48.5 kb lambda phage genome with different 8-base and 7-base sequence motif tags. The distance between the sequence motifs was determined with an accuracy of +/-0.8 kb, and these tags could be localized on the DNA with an accuracy of +/-2 kb. Thus, DLA is a rapid mapping technology, suitable for analysis of long DNA molecules.