Fluorescence lifetime correlation spectroscopic study of fluorophore-labeled silver nanoparticles

In this paper, we introduce the use of fluorescence lifetime correlation spectroscopy to study the metal-fluorophore interactions in solution at the single-fluorophore level. A single-stranded oligonucleotide was chemically bound to a 50-nm-diameter single silver particle, and a Cy5-labeled complementary single-stranded oligonucleotide was hybridized with the silver particle-bound oligonucleotide. The distance between the fluorophore and silver particle was maintained by a rigid hybridized DNA duplex of 8 nm in length. The single Cy5-DNA-Ag particles showed more than 10-fold increase in fluorescence intensity and a 5-fold decrease in emission lifetimes as compared with Cy5-DNA free molecules in the absence of metal. The decrease of lifetime for the Cy5-DNA-Ag particle allowed us to resolve the correlation functions of the two species based on the intensity decays. The increased brightness of the Cy5-DNA-Ag particle as compared to free Cy5-DNA resulted in an increased contribution of Cy5-DNA-Ag to the correlation function of the mixture. These results show that the effects of metal particles on fluorophores can be used to detect the small fractional populations of the metal-bound species in the presence of a larger number of less bright species. Our results also suggest that these bright fluorophores conjugated to silver particles could be used as the fluorescent probes for clinical detection in the biological samples with the high background.     

Particle‐Based Optical Sensing of Intracellular Ions at the Example of Calcium – What Are the Experimental Pitfalls?

Colloidal particles with fluorescence read‐out are commonly used as sensors for the quantitative determination of ions. Calcium, for example, is a biologically highly relevant ion in signaling, and thus knowledge of its spatio‐temporal distribution inside cells would offer important experimental data. However, the use of particle‐based intracellular sensors for ion detection is not straightforward. Important associated problems involve delivery and intracellular location of particle‐based fluorophores, crosstalk of the fluorescence read‐out with pH, and spectral overlap of the emission spectra of different fluorophores. These potential problems are outlined and discussed here with selected experimental examples. Potential solutions are discussed and form a guideline for particle‐based intracellular imaging of ions.     

Dual-view imaging system using a wide-range dichroic mirror for simultaneous four-color single-molecule detection

A dual-view imaging system for simultaneous four-color single-molecule (SM) detection was developed. As for the detection procedure, four species of SM fluorophores, namely, Alexa 488, 555, 647, and 680, are immobilized on different slides and excited by evanescent-wave illumination. Fluorescence emitted from an SM fluorophore is split by a wide-range dichroic mirror (WR DM) in a dual-view optics and imaged as two SM fluorescence spots (SM spots) on an electron-multiplying charge-coupled device (EM-CCD) at 100 Hz. The transmittance of the WR DM changes gradually over the wavelength range of 500 to 700 nm so that the signal ratios of the two SM spots for the four fluorophore species differ. A method for classifying SM fluorophores into four species in accordance with their signal ratios was developed. It was used to classify 597 SM fluorophores at an accuracy of above 98% for all the species. This accuracy is comparable to that of a conventional four-color SM detection system. To classify four species, the conventional system disperses SM fluorescence with a prism and provides an elongated SM spot that uses more pixels of an EM-CCD chip than that of the developed system. The developed system can thus detect 1.5-fold more SM spots with the same-size EM-CCD chip, so it can achieve 1.5-fold higher throughput. Moreover, the developed system is based on a simple and practical approach, namely, replacing an ordinary dichroic mirror in a commercially available dual-view optics with a WR DM. This replacement transforms a dual-view imaging system for two-color detection into a system for four-color detection. The developed system is suitable for detection systems of next-generation DNA sequencers and DNA microarray-chip analyzers.     

One-step homogeneous protein detection based on aptamer probe and fluorescence cross-correlation spectroscopy

A new protein assay based on fluorescence cross-correlation spectroscopy (FCCS) and aptamer probe is developed. In this assay, two spectrally distinct fluorophores labeled aptamer probes are used to recognize and detect thrombin through a sandwich reaction. The sandwich complexes are diffused through a confocal detection volume. The cross-correlation signals can be observed only at the presence of the aptamer probes-protein sandwich complexes. Thrombin is selected as a target to validate the assay. The whole detection process can be completed within an hour with low-nanomolar sensitivity and high specificity. The novel aptamer-based FCCS detection offers a simple, rapid and sensitive method for protein analysis in a homogeneous format.     

Target‐Triggered Assembly of Nanogap Antennas to Enhance the Fluorescence of Single Molecules and Their Application in MicroRNA Detection

Nanogap antennas are plasmonic nanostructures with a strong electromagnetic field generated at the gap region of two neighboring particles owing to the coupling of the collective surface plasmon resonance. They have great potential for improving the optical properties of fluorophores. Herein, nanogap antennas are constructed using an aqueous solution‐based method to overcome the defects of weak fluorescence and photobleaching associated with traditional organic dyes, and a highly sensitive nanogap antenna‐based sensing strategy is presented for the detection of low‐abundance nucleic acid biomarkers via a target‐triggered strand displacement amplification (SDA) reaction between two DNA hairpins that are tagged to the tips of gold nanorods (Au NRs). In the presence of targets, end‐to‐end Au NR dimers gradually form, and the fluorophores quenched by the Au NRs exhibit a dramatic fluorescence enhancement due to the plasmon‐enhanced fluorescence effect of nanogap antennas. Meanwhile, the SDA reaction results in secondary amplification of fluorescence signals. Combined with single‐molecule counting, this method applied in miRNA‐21 detection can achieve a low detection limit of 97.2 × 10^?18 m . Moreover, accurate discrimination between different cells through miRNA‐21 imaging demonstrates the potential of this method in monitoring the expression level of low‐abundance nucleic acid biomarkers.     

Exploring feasibility of multicolored CdTe quantum dots for in vitro and in vivo fluorescent imaging

We report the use of novel multicolored CdTe quantum dots (QDs) as fluorophores for biological fluorescence imaging. The CdTe QDs were prepared to exhibit emission wavelengths in the green, yellow, and red range by using trifluoroacetic acid (TFA), L-cysteine and thioglycolic acid (TGA) as surface stabilizers, respectively. The particles have good water solubility and photostability. Fluorescence imaging potential was evaluated in vitro and in vivo using a multispectral Maestro CRI Fluorescence Imaging system. The results show that different colored CdTe QDs allow sensitive detection simultaneously or separately both in vitro and in vivo against background fluorescence. The studies indicate that CdTe QDs can provide alternative fluorescent probes for biological imaging.     

Tuning the Intensity of Metal‐Enhanced Fluorescence by Engineering Silver Nanoparticle Arrays

It is demonstrated that silver nanoparticle (SNP) arrays fabricated by combining nanoimprint lithography and electrochemical deposition methods can be used as substrates for metal‐enhanced fluorescence, which is widely used in optics, sensitive detection, and bioimaging. The method presented here is simple and efficient at controlling the nanoparticle density and interparticle distance within one array. Furthermore, it is found that the fluorescence intensity can be tuned by engineering the feature size of the SNP arrays. This is due to the different coupling efficiency between the emission of the fluorophores and surface plasmon resonance band of the metallic nanostructures.     

The Microemulsion Synthesis of Hydrophobic and Hydrophilic Silicon Nanocrystals

Silicon nanocrystals, also called quantum dots, have unique optical properties when in the quantum‐confinement regime. These optical properties make silicon nanocrystals promising materials for a wide variety of applications ranging from optoelectronic devices to fluorophores in biological imaging. A liquid‐phase synthetic approach is reported using surfactant molecules to control particle growth, producing highly monodisperse silicon particles. The surface of the nanocrystals are capped by functional organic molecules that passivate and protect the silicon particles from oxidation, enabling the particles to be used in hydrophobic and hydrophilic applications. The use of hydrophilic silicon quantum dots as optical probes is illustrated by the imaging of Vero cells.     

Tandem dye acceptor used to enhance upconversion fluorescence resonance energy transfer in homogeneous assays

In fluorescence resonance energy transfer (FRET)-based assays, spectral separation of acceptor emission from donor emission is a common problem affecting the assay sensitivity. The challenge derives from small Stokes shifts characteristic to conventional fluorescent dyes resulting in leakage of donor emission to the measurement window intended only to collect the acceptor emission. We have studied a FRET-based homogeneous bioaffinity assay utilizing a tandem dye acceptor with a large pseudo-Stokes shift (139 nm). The tandem dye was constructed using B-phycoerythrin as an absorber and multiple Alexa Fluor 680 dyes as emitters. As a donor, we employed upconverting phosphor particles, which uniquely emit at visible wavelengths under low-energy infrared excitation enabling the fluorescence measurements free from autofluorescence even without time-resolved detection. With the tandem dye, it was possible to achieve four times higher signal from a single binding event compared to the conventional Alexa Fluor 680 dye alone. Tandem dyes are widely used in cytometry and other multiplex purposes, but their applications can be expanded to fluorescence-based homogeneous assays. Both the optimal excitation and emission wavelengths of tandem dye can be tuned to a desired region by choosing appropriate fluorophores enabling specifically designed acceptor dyes with large Stokes shift.     

Photonic-Plasmonic Coupling Enhanced Fluorescence Enabling Digital-Resolution Ultrasensitive Protein Detection

Assays utilizing fluorophores are common throughout life science research and diagnostics, although detection limits are generally limited by weak emission intensity, thus requiring many labeled target molecules to combine their output to achieve higher signal-to-noise. We describe how the synergistic coupling of plasmonic and photonic modes can significantly boost the emission from fluorophores. By optimally matching the resonant modes of a plasmonic fluor (PF) nanoparticle and a photonic crystal (PC) with the absorption and emission spectrum of the fluorescent dye, a 52-fold improvement in signal intensity is observed, enabling individual PFs to be observed and digitally counted, where one PF tag represents one detected target molecule. The amplification can be attributed to the strong near-field enhancement due to the cavity-induced activation of the PF, PC band structure-mediated improvement in collection efficiency, and increased rate of spontaneous emission. The applicability of the method by dose-response characterization of a sandwich immunoassay for human interleukin-6, a biomarker used to assist diagnosis of cancer, inflammation, sepsis, and autoimmune disease is demonstrated. A limit of detection of 10 fg mL⁻¹ and 100 fg mL⁻¹ in buffer and human plasma respectively, is achieved, representing a capability nearly three orders of magnitude lower than standard immunoassays.     

A Lipid-Nanopillar-Array-Based Immunosorbent Assay

Since infectious diseases, particularly viral infections, have threatened human health and caused huge economical losses globally, a rapid, sensitive, and selective virus detection platform is highly demanded. Enzyme-linked immunosorbent assay (ELISA) with flat solid substrates has been dominantly used in detecting whole viruses for its straightforwardness and simplicity in assay protocols, but it often suffers from limited sensitivity, poor quantification range, and a time-consuming assay procedure. Here, a lipid-nanopillar-array-based immunosorbent assay (LNAIA) is developed with a nanopillar-supported lipid bilayer substrate with fluorophore-modified antibodies for rapid, sensitive, and quantitative detection of viruses. 3D nanopillar array structures and fluid antibodies with fluorophores facilitate faster and efficient target binding and rapid fluorophore localization for quick, reliable analysis on binding events with a conventional fluorescence microscopy setup. LNAIA enables quantification of H1N1 virus that targets down to 150 virus particles with 5-orders-of-magnitude dynamic range within 25 min, which cannot be achieved with conventional ELISA platforms.     

Ultrasensitive coincidence fluorescence detection of single DNA molecules

We have detected individual DNA molecules labeled with two different fluorophores in solution by using two-color excitation and detection of coincidence fluorescence bursts. The confocal volumes of the two excitation lasers were carefully matched so that the volume overlap was 30% of the total confocal volume illuminated. This method greatly reduces the level of background fluorescence and, hence, extends the sensitivity of single molecule detection down to 50 fM. At these concentrations, the dual-labeled DNA is detectable in the presence of a 1000-fold excess of single-fluorophore-labeled DNA. We demonstrate that we can detect 100 fM dual-labeled DNA diluted in 1 microM unlabeled DNA, which was not possible with single color detection. This method can be used to detect rare molecules in complex mixtures.     

Fluorescent diffuse photon density waves in homogeneous and heterogeneous turbid media: analytic solutions and applications

We present analytic solutions for fluorescent diffuse photon density waves originating from fluorophores distributed in thick turbid media. Solutions are derived for a homogeneous turbid medium containing a uniform distribution of fluorophores and for a system that is homogeneous except for the presence of a single spherical inhomogeneity Generally the inhomogeneity has fluorophore concentration, and lifetime and optical properties that differ from those of the background. The analytic solutions are verified by numerical calculations and are used to determine the fluorophore lifetime and concentration changes required for the accurate detection of inhomogeneities in biologically relevant systems. The relative sensitivities of absorption and fluorescence methods are compared.     

Resonance energy transfer-amplifying fluorescence quenching at the surface of silica nanoparticles toward ultrasensitive detection of TNT

This paper reports a resonance energy transfer-amplifying fluorescence quenching at the surface of silica nanoparticles for the ultrasensitive detection of 2,4,6-trinitrotoluene (TNT) in solution and vapor environments. Fluorescence dye and organic amine were covalently modified onto the surface of silica nanoparticles to form a hybrid monolayer of dye fluorophores and amine ligands. The fluorescent silica particles can specifically bind TNT species by the charge-transfer complexing interaction between electron-rich amine ligands and electron-deficient aromatic rings. The resultant TNT-amine complexes bound at the silica surface can strongly suppress the fluorescence emission of the chosen dye by the fluorescence resonance energy transfer (FRET) from dye donor to the irradiative TNT-amine acceptor through intermolecular polar-polar interactions at spatial proximity. The quenching efficiency of the hybrid nanoparticles with TNT is greatly amplified by at least 10-fold that of the corresponding pure dye. The nanoparticle-assembled arrays on silicon wafer can sensitively detect down to approximately 1 nM TNT with the use of only 10 microL of solution (approximately 2 pg TNT) and several ppb of TNT vapor in air. The simple FRET-based nanoparticle sensors reported here exhibit a high and stable fluorescence brightness, strong analyte affinity, and good assembly flexibility and can thus find many applications in the detection of ultratrace analytes.     

Imaging single fluorescent molecules at the interface of an optical fiber probe by evanescent wave excitation

We have developed a new fluorescent method for single-molecule detection (SMD) and imaging using an optical fiber probe. The fluorophores were excited by the evanescent wave field produced on the core surface of the optical fiber. This was achieved by exposing a section of the core of the optical fiber probe to the fluorophore solution. Both cylindrical and square optical fiber probes were used for SMD. The fluorescent signals were detected by an intensified charge-coupled device. Single rhodamine 6G molecules have been detected. The number of rhodamine 6G molecules imaged by the optical fiber probe showed an excellent linear relationship with the concentrations of the fluorophores. The SMD scheme was also applied to the imaging of biomolecules, such as molecular beacon DNA molecules, labeled with tetramethylrhodamine. Our results have shown that using an optical fiber is an easy yet effective approach to SMD. It represents a simpler fluorescent method for the detection of single-molecules in solution and at an interface.     

Three-dimensional autofluorescence spectroscopy of rat skeletal muscle tissue under two-photon excitation

We report on three-dimensional autofluorescence spectroscopy obtained from rat skeletal muscle tissue under two-photon excitation by an ultrashort pulsed-laser beam. It is demonstrated that two types of fluorophores within the skeletal muscle tissue can be simultaneously excited with the laser beam at a wavelength of 800 nm. The two fluorophores exhibited unique fluorescence spectral peaks at wavelengths of 450 and 550 nm. These spectroscopic signals can be used to form a three-dimensional image, giving the information about the biochemical makeup of the skeletal muscle tissue.     

Recovery of photoinduced reversible dark States utilized for molecular diffusion measurements

For a spatially restricted excitation volume, the effective modulation of the excitation in time is influenced by the passage times of the molecules through the excitation volume. By applying an additional time-modulated excitation, the buildup of photoinduced reversible dark states in fluorescent molecules can be made to vary significantly with their passage times through the excitation volume. The variations in the dark state populations are reflected by the time-averaged fluorescence intensity, which thus can be used to characterize the mobilities of the molecules. The concept was experimentally verified by measuring the fluorescence response of freely diffusing cyanine fluorophores (Cy5), undergoing trans-cis isomerization when subject to time-modulated excitation in a focused laser beam. From the fluorescence response, and by applying a simple photodynamic model, the transition times of the Cy5 molecules could be well reproduced when applying different laminar flow speeds through the detection volume. The presented approach puts no constraints on sample concentration, no requirements for high time resolution or sensitivity in the detection, nor requires a high fluorescence brightness of the characterized molecules. This can make the concept useful for a broad range of biomolecular mobility studies.     

Highly efficient multiphoton-absorption-induced luminescence from gold nanoparticles

We demonstrate that highly efficient photoluminescence is generated from gold nanoparticles as small as a few nanometers in diameter upon irradiation with sub-100-fs pulses of 790-nm light. Strong emission is observed at excitation intensities comparable to or less than those typically used for multiphoton imaging of fluorescently labeled biological samples. The particles have polarized emission, can radiate more efficiently than single molecules, do not exhibit significant blinking, and are photostable under hours of continuous excitation. These observations suggest that metal nanoparticles are a viable alternative to fluorophores or semiconductor nanoparticles for biological labeling and imaging.     

新型化学功能材料——瓜环与荧光化合物的主客体自组装研究进展

瓜环作为第四代超分子主体,两端由羰基氧原子环绕而成,内部为疏水性的空腔,具有刚性结构,微溶于水,不溶于有机溶剂。能与瓜环组成配合物的荧光类客体种类较多,通过荧光光谱的变化可以检测出主-客体相互作用,这一特性拓展了瓜环在生物化学领域的应用,包括医药载体、核酸检测、分子识别、pH探针等方面。未来研究中可以尝试以不同的发色母体取代不同的位点,这将为新型荧光试剂的设计与开发提供重要思路。     

A single-molecule Förster resonance energy transfer analysis of fluorescent DNA-protein conjugates for nanobiotechnology

The development of nanobiotechnological devices requires the ability to build various components with nanometer accuracy. DNA is a well-established nanoscale building block that self assembles due to specific interactions that are encoded in its sequence. Recently, it has become possible to couple proteins to DNA, thereby expanding the capabilities of DNA for use with molecular photonics and bioelectronics. Here, we present the design and characterization of a supramolecular F?rster resonance energy transfer (FRET) system by using a fluorescent protein bound to single-stranded DNA (ssDNA), a fluorophore attached to a second ssDNA molecule, and a complementary strand for hybridizing the two fluorophores together. The FRET efficiency was studied by using both ensemble and single-pair FRET measurements. The distance between the two fluorophores was determined from the single-pair FRET efficiency and could be described by a simple cylindrical model for the DNA. Hence, DNA can be used as a scaffold for positioning fluorescent proteins, as well as traditional fluorophores, with nanometer accuracy and shows great potential for use in the future of nanobiotechnology.