Dynamic kinetic capillary isoelectric focusing: a powerful tool for studying protein-DNA interactions

A new method called dynamic kinetic capillary isoelectric focusing (DK-CIEF) is presented for the study of protein-DNA interactions. The method is based on CIEF with laser-induced fluorescence-whole column imaging detection in which protein-DNA complexes are separated with spatial resolution while dissociations of the complexes are dynamically monitored using a CCD camera with temporal resolution. This method allows for the discrimination of different complexes and the measurement of the individual dissociation rate constants.     

A fluorescent indicator for detecting protein-protein interactions in vivo based on protein splicing

We describe a new method with general applicability for monitoring any protein-protein interaction in vivo. The principle is based on a protein splicing system, which involves a self-catalyzed excision of protein splicing elements, or inteins, from flanking polypeptide sequences, or exteins, leading to formation of a new protein in which the exteins are linked directly by a peptide bond. As the exteins, split N- and C-terminal halves of enhanced green fluorescent protein (EGFP) were used. When a single peptide consisting of an intein derived from Saccharomyces cerevisiae intervening the split EGFP was expressed in Escherichia coli, the two external regions of EGFP were ligated, thereby forming the EGFP corresponding fluorophore. Genetic alteration of the intein, which involved large deletion of the central region encoding 104 amino acids, was performed. In the expression of the residual N- and C-terminal intein fragments each fused to the split EGFP exteins, the splicing in trans did not proceed. However, upon coexpression of calmodulin and its target peptide M13, each connected to the N- and C-terminal inteins, fluorescence of EGFP was observed. These results demonstrate that interaction of calmodulin and M13 triggers the refolding of intein, which induces the protein splicing, thereby folding the ligated extein correctly for yielding the EGFP fluorophore. This method opens a new way not only to screen protein-protein interactions but also to visualize the interaction in vivo in transgenic animals.     

Fluorescence recovery assay for the detection of protein-DNA binding

We report a novel and straightforward fluorescence recovery assay which enables the detection of protein-DNA interactions and simultaneously determines relative binding affinities of sequence-specific DNA-binding proteins for a variety of DNA sequences in a multiplexed format. The detection of protein-DNA binding is accomplished by monitoring fluorescence recovery during exonuclease digestion of DNA sequences that are modified with fluorophore-quencher pairs. Retardation of fluorescence recovery occurs with binding of the protein to the putative DNA binding element, which arrests exonuclease digestion. The assay detects protein-DNA binding in a homogeneous solution simply, quickly, and reliably without using radioisotopes. Multiplexing is possible by labeling different DNA sequences with spectrally distinct dyes, allowing simultaneous analysis of experimental and control binding reactions in the same mixture.     

New approach for the detection of peptide- and protein-based radicals using a pre-fluorescent probe

A novel application for pre-fluorescent probes in the detection of peptide- and protein-based radicals is proposed. Pre-fluorescent probes combine a fluorescent moiety labeled with a paramagnetic nitroxide that acts as a fluorescence quencher. Trapping of a radical by the nitroxide group restores the fluorescence properties. The increase in fluorescence intensity with time reflects the formation and quenching of free radicals and can be employed for the quantitative evaluation of yields and kinetics. In this test system, the pre-fluorescent probe 4-(9-acridinecarbonate)-2,2,6,6-tetramethylpiperidinyl-1-oxyl radical (Ac-Tempo), in which an acridine moiety was labeled with 2,2,6,6-tetramethylpiperidinyl-1-oxy (Tempo), was employed to probe peptide- and protein-based radicals. Peptide-based radicals were generated through the reaction between horseradish peroxidase (HRP)/H(2)O(2) and a derivative of tyrosine. Protein-based radicals were generated through the reaction between myoglobin (Mb) and H(2)O(2). In both cases the Ac-Tempo was found, using a combination of high-performance liquid chromatography (HPLC) and mass spectrometry, to be converted into fluorescent acridine (Ac)-piperidine (4-(9-acridinecarbonate)-2,2,6,6-tetramethylpiperidine).     

Biarsenical-tetracysteine motif as a fluorescent tag for detection in capillary electrophoresis

Biarsenical dyes complexed to tetracysteine motifs have proven to be highly useful fluorescent dyes in labeling specific cellular proteins for microscopic imaging. Their many advantages include membrane permeability, relatively small size, stoichiometric labeling, high affinity, and an assortment of excitation/emission wavelengths. The goal of the current study was to determine whether the biarsenical labeling scheme could be extended to fluorescent detection of analytes in capillary electrophoresis. Recombinant protein or synthesized peptides containing the optimized tetracysteine motif "-C-C-P-G-C-C-" were labeled with biarsenical dyes and then analyzed by micellar electrokinetic capillary chromatography (MEKC). The biarsenical-tetracysteine complex was stable and remained fluorescent under standard MEKC conditions for peptide and protein separations. The detection limit following electrophoresis in a capillary was less than 3 x 10(-20) mol with a simple laser-induced fluorescence system. A mixture of multiple biarsenical-labeled peptides and a protein were easily resolved. Demonstrating that the label did not interfere with bioactivity, a peptide-based enzyme substrate conjugated to the tetracysteine motif and labeled with a biarsenical dye retained its ability to be phosphorylated by the parent kinase. The feasibility of using this label for chemical cytometry experiments was shown by intracellular labeling and subsequent analysis of a recombinant protein possessing the tetracysteine motif expressed in living cells. The extension of the biarsenical-tetracysteine tag to fluorescent labeling of peptides and proteins in chemical separations is a valuable addition to biochemical and cell-based investigations.     

Thermoresponsive copolymer containing a coumarin-spiropyran conjugate: reusable fluorescent sensor for cyanide anion detection in water

A simple copolymer consisting of N-isopropylacrylamide and coumarin-conjugated spiropyran (CS) units, poly(NIPAM-co-CS), has been synthesized. This polymer enables selective fluorometric detection of cyanide anion (CN(-)) in water at room temperature. The polymer itself shows almost no fluorescence, but shows a strong blue fluorescence in the presence of CN(-) under irradiation of UV light. The fluorescence enhancement occurs via a nucleophilic interaction between CN(-) and the photoformed merocyanine form of the CS unit, leading to a localization of π-electrons on the coumarin moiety. The polymer enables accurate determination of very low levels of CN(-) (>0.5 μM). The polymer can be recovered from water by simple centrifugation at high temperature (>40 °C), due to the heat-induced aggregation of the polymer. In addition, the polymer is regenerated by simple acid treatment, and the resulting polymer is successfully reused for further CN(-) sensing without loss of sensitivity.     

Immobilized fluorescent cyclodextrin on a cellulose membrane as a chemosensor for molecule detection

Dansylglycine-modified cyclodextrin (DnsC4-beta-CD) was prepared as a fluorescent host that is capable of being immobilized on a cellulose membrane (DnsC4-beta-CD membrane). DnsC4-beta-CD immobilized on the cellulose membrane decreased its fluorescence intensity with increasing concentration of guest molecules, indicating that the host changes the location of the dansyl group from inside to outside the cyclodextrin cavity upon guest accommodation, which is similar to DnsC4-beta-CD in solution; thereby, the DnsC4-beta-CD membrane is useful as a novel chemosensor for detecting molecules. This result demonstrates that the cellulose membrane is useful as a practical supporting material for various chromophore-modified cyclodextrins.     

Fabrication of histidine-tagged fusion protein arrays for surface plasmon resonance imaging studies of protein-protein and protein-DNA interactions

The creation and characterization of histidine-tagged fusion protein arrays using nitrilotriacetic acid (NTA) capture probes on gold thin films for the study of protein-protein and protein-DNA interactions is described. Self-assembled monolayers of 11-mercaptoundecylamine were reacted with the heterobifunctional linker N-succinimidyl S-acetylthiopropionate (SATP) to create reactive sulfhydryl-terminated surfaces. NTA capture agents were immobilized by reacting maleimide-NTA molecules with the sulfhydryl surface. The SATP and NTA attachment chemistry was confirmed with Fourier transform infrared reflection absorption spectroscopy. Oriented protein arrays were fabricated using a two-step process: (i) patterned NTA monolayers were first formed through a single serpentine poly(dimethylsiloxane) microchannel; (ii) a second set of parallel microchannels was then used to immobilize multiple His-tagged proteins onto this pattern at discrete locations. SPR imaging measurements were employed to characterize the immobilization and specificity of His-tagged fusion proteins to the NTA surface. SPR imaging measurements were also used with the His-tagged fusion protein arrays to study multiple antibody-antigen binding interactions and to monitor the sequence-specific interaction of double-stranded DNA with TATA box-binding protein. In addition, His-tagged fusion protein arrays created on gold surfaces were also used to monitor antibody binding with fluorescence microscopy in a sandwich assay format.     

Surface-modified CdS nanoparticles as a fluorescent probe for the selective detection of cysteine

We present a novel method for the selective detection of cysteine, a sulfur-containing amino acid, which plays a crucial role in many important biological functions such as protein folding. Surface-modified colloidal CdS nanoparticles have been used as a fluorescent probe to selectively detect cysteine in the presence of other amino acids in the micromolar concentration range. Cysteine quenches the emission of CdS in the 0.5-10?μM concentration range, whereas the other amino acids do not affect its emission. Among the other amino acids, histidine is most efficient in quenching the emission of the CdS nanoparticles. The sulfur atom of cysteine plays a crucial role in the quenching process in the 0.5-10?μM concentration range. Cysteine is believed to quench the emission of the CdS nanoparticles by binding to their surface via its negatively charged sulfur atom. This method can potentially be applied for its detection in biological samples.     

An evaluation of nanostructured zinc oxide as a fluorescent powder for fingerprint detection

Zinc oxide is evaluated as a fluorescent powder for the detection of fingermarks on non-porous surfaces. Pure and lithium-doped nanostructured zinc oxide powders were characterized using scanning electron microscopy, X-ray diffraction, and fluorescence spectroscopy. The zinc oxide powders were applied to fresh and aged fingermarks deposited on non-porous surfaces such as glass, polyethylene and aluminium foil. Zinc oxide was found to produce clear fluorescent impressions of the latent fingermarks when illuminated with long-wave UV light. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

荧光材料在爆炸物检测中的应用研究

近年来,全球恐怖事件呈现日益频发的趋势,各个国家与国际组织对安全的要求越来越高.使用各种技术检测爆炸物成为了当今安防领域研究的重点.其中,使用荧光猝灭材料检测爆炸物是一种既简单又快捷的方法.本文总结了国内外各类荧光传感器上所使用的荧光材料,并简要叙述了其在实际应用中的性能.     

High-affinity binding of cadmium ions by mouse metallothionein prompting the design of a reversed-displacement protein-based fluorescence biosensor for cadmium detection

Reported in this study are the experimental design and results of a protein-based biosensor for the detection of the cadmium in water using a reversed-displacement format. This reversed-displacement biosensor methodology has successfully measured cadmium in water by direct injection, eliminating the need for preconcentration or pretreatment of samples. A column containing Chelex resin saturated with Zn2+ and a rodhamine-labeled metallothionein (MT) comprised the assay reactive chamber. In fact, MT are small cysteine-rich proteins that bind heavy metals such as zinc, cadmium, copper, and mercury. Since the affinity for cadmium is higher than zinc and mercury, we used this intrinsic feature of MT to develop a fluorescence biosensor. The rodhamine-labeled MT was incubated with the Zn2+-saturated Chelex resin until binding equilibrium was reached. Under a constant flow, samples containing cadmium were introduced into the flow stream displacing the rodhamine-labeled MT. Limits of detection were lower than 0.5 microM for cadmium in water. Importantly, the addition of 1.0 microM Cu2+, 1.0 microM Zn2+, 1.0 microM Mg2+, or 1.0 microM Ca2+ did not cause the displacement of the rodhamine-labeled MT, indicating that the presence of these ions do not affect the specificity of the biosensor. Furthermore, we also demonstrated that the reversed-displacement format can be used to screen water samples containing cadmium, remains effective after dozens of cycles, and provides significant fluorescence response before regeneration is required.     

Nano-C(60) : a novel, effective, fluorescent sensing platform for biomolecular detection

Water-soluble nano-C(60) can serve as a novel, effective, fluorescent sensing platform for biomolecular detection with high sensitivity and selectivity. In this paper, fluorescent detection of DNA and thrombin via nano-C(60) is demonstrated for the first time. The principle of the assay lies in the fact that the adsorption of the fluorescently labeled single-stranded DNA (ssDNA) probe by nano-C(60) leads to substantial fluorescence quenching. In the presence of a target, the biomolecular mutual interaction suppresses this quenching, signaling the existence of the target. This sensing system rivals graphene oxide but is superior to other carbon-structure-based systems. The present method can also achieve multiplex DNA detection and withstand the interference from human blood serum.     

Peptidyl fluorescent chemosensors for the detection of divalent copper

Fluorescent organic chemosensors for the detection of divalent copper with high selectivity and sensitivity are the subject of intense research in the recent years. Structurally, ionophore and fluorophore are two essential parts determining the resultant performance of the chemosensor. While much work has been focused on designing highly selective ligands, little attention has been paid to the possible influence of ionophore-fluorophore interaction on their properties in metal ion binding. We studied here fluorescent chemosensors based on the Gly-His peptidyl motif and found that the functionality of the chemosensors was greatly influenced by the spatial alignment of the fluorophore in the molecules. In Gly-His-Lys(Dns) (1), the dansyl group is on a side branch and does not interact with copper, while in Dpr(Dns)-His-Lys (2), the dansyl group is also on a side branch but the close placement allows it to directly participate in the binding with copper ions. Therefore, although dansyl can signal the binding event in both molecules, the mechanisms involved are quite different, and this difference resulted in different sensing performance, e.g., the selectivity. Even more strikingly, the dansyl group in Dns-Gly-His-Gly (3) exhibited a profound effect on the molecular complexation. The binding constant decreased, and binding mode was affected since only 1:1 binding was observed while in side-branch-labeled ligands, a 2:1 binding may also be involved. In contrast to those side-chain-labeled ligands, molecule 3 is extremely simple in structure and possesses superior detecting qualities such as selectivity, molecular sensitivity, and applicability in a wide range of pH.     

Combined fluorescent and interferometric detection of protein on a BioCD

We perform simultaneous interferometric and fluorescent detection of molecular protein layers on a BioCD. The 488 nm excitation wavelength of fluorescein also provides the interferometric detection channel that operates in a common-path in-line configuration in the condition of phase quadrature set by a thermal oxide on silicon. The simultaneous acquisition of both channels enables a direct correlation between bound mass and fluorescent surface density, which we compare in forward- and reverse-phase immunoassays. Scaling mass sensitivities for immunoassays measured in the interferometric and fluorescent channels are 15 pg/mm and 1.5 pg/mm, respectively, when applied to gel-printed periodic antibody patterns detected in the frequency domain from the spinning disc. These sensitivities are limited by the inhomogeneities of the print. While fluorescence is subject to bleaching, the interferometry signal is robust under long-term laser illumination.     

Zinc oxide-coated plasmonic chip modified with a bispecific antibody for sensitive detection of a fluorescent labeled-antigen

A plasmonic biosensor chip of silver-coated PMMA grating with a zinc oxide (ZnO) overlayer is fabricated for surface plasmon field-enhanced fluorescence (SPF) detection of Cy5-labeled green fluorescent protein (GFP). A bispecific antibody (anti-GFP x anti-ZnO antibody) prepared in our lab is densely immobilized on the sensor chip for GFP detection. The sensitivity of the plasmonic biosensors is improved due to densely packed antibodies and ZnO-coating that suppresses nonspecific protein adsorption and fluorescent quenching. With the ZnO-coated plasmonic chip, Cy5-labeled GFP of 10 pM can be detected through SPF. This sensitivity is 100 higher compared with the normal fluorescent detection on a ZnO-coated glass slide.     

UV fluorescence lifetime imaging microscopy: a label-free method for detection and quantification of protein interactions

Due to the ability to detect multiple parameters simultaneously, protein microarrays have found widespread applications from basic biological research to diagnosis of diseases. Generally, readout of protein microarrays is performed by fluorescence detection using either dye-labeled detector antibodies or direct labeling of the target proteins. We developed a method for the label-free detection and quantification of proteins based on time-gated, wide-field, camera-based UV fluorescence lifetime imaging microscopy to gain lifetime information from each pixel of a sensitive CCD camera. The method relies on differences in the native fluorescence lifetime of proteins and takes advantage of binding-induced lifetime changes for the unequivocal detection and quantification of target proteins. Since fitting of the fluorescence decay for every pixel in an image using a classical exponential decay model is time-consuming and unstable at very low fluorescence intensities, we used a new, very robust and fast alternative method to generate UV fluorescence lifetime images by calculating the average lifetime of the decay for each pixel in the image stack using a model-free average decay time algorithm.To validate the method, we demonstrate the detection and quantification of p53 antibodies, a tumor marker in cancer diagnosis. Using tryptophan-containing capture peptides, we achieved a detection sensitivity for monoclonal antibodies down to the picomolar concentration range. The obtained affinity constant, Ka, of (1.4 +/- 0.6) x 10(9) M(-1), represents a typical value for antigen/antibody binding and is in agreement with values determined by traditional binding assays.     

8-aminoquinoline functionalized silica nanoparticles: a fluorescent nanosensor for detection of divalent zinc in aqueous and in yeast cell suspension

Zinc is one of the most important transition metal of physiological importance, existing primarily as a divalent cation. A number of sensors have been developed for Zn(II) detection. Here, we present a novel fluorescent nanosensor for Zn(II) detection using a derivative of 8-aminoquinoline (N-(quinolin-8-yl)-2-(3 (triethoxysilyl)propylamino)acetamide (QTEPA) grafted on silica nanoparticles (SiNPs). These functionalized SiNPs were used to demonstrate specific detection of Zn(II) in tris-HCl buffer (pH 7.22), in yeast cell (Saccharomyces cerevisiae) suspension, and in tap water. The silane QTEPA, SiNPs and final product were characterized using solution and solid state nuclear magnetic resonance, Fourier transform infrared, ultraviolet-visible absorption spectroscopy, transmission electron microscopy, elemental analysis, thermogravimetric techniques, and fluorescence spectroscopy. The nanosensor shows almost 2.8-fold fluorescence emission enhancement and about 55 nm red-shift upon excitation with 330 ± 5 nm wavelength in presence of 1 μM Zn(II) ions in tris-HCl (pH 7.22). The presence of other metal ions has no observable effect on the sensitivity and selectivity of nanosensor. This sensor selectively detects Zn(II) ions with submicromolar detection to a limit of 0.1 μM. The sensor shows good applicability in the determination of Zn(II) in tris-HCl buffer and yeast cell environment. Further, it shows enhancement in fluorescence intensity in tap water samples.     

Microspotting streptavidin and double-stranded DNA arrays on gold for high-throughput studies of protein-DNA interactions by surface plasmon resonance microscopy

We present two strategies for microspotting 10 x 12 arrays of double-stranded DNAs (dsDNAs) onto a gold-coated glass slide for high-throughput studies of protein-DNA interactions by surface plasmon resonance (SPR) microscopy. Both methods use streptavidin (SA) as a linker layer between a biotin-containing mixed self-assembled monolayer (SAM) and biotinylated dsDNAs to produce arrays with high packing density. The primary mixed SAM is produced from biotin- and oligo(ethylene glycol)-terminated thiols bonded as thiolates onto the gold surface. In the first method, a robotic microspotter is used to deliver nanoliter droplets of dsDNA solution onto a uniform layer of this SA ( approximately 2 x 10(12) SA/cm(2)). SPR microscopy shows a density of (5-6) x 10(11) dsDNA/cm(2) (0.2-0.3 dsDNA/SA) in the array elements. The second method uses instead a microspotted array of this SA linker layer, onto which the microspots of dsDNA are added with spatial registry. SPR microscopy before addition of the dsDNA shows a SA coverage of 2 x 10(12) SA/cm(2) within the spots and a dsDNA density of 8.5 +/- 3.5 x 10(11) dsDNA/cm(2) (0.3-0.7 dsDNA/SA, depending on the length of dsDNA) after dsDNA spotting. We demonstrate the ability to simultaneously monitor protein binding with the SPR microscope in many 200-microm spots with 1-s time resolution and sensitivity to <1 pg of protein.     

Highly fluorescent silver nanoclusters stabilized by glutathione: a promising fluorescent label for bioimaging

A panel of silver nanoclusters (Ag NCs) protected by glutathione has been produced by collecting them on a plastic surface during an interfacial etching process. Blue-green, yellow and red emitting Ag NCs with size smaller than 2 nm exhibited distinct fluorescence properties (both emission and lifetime). In particular, the yellow emitting Ag NCs were found to reach a very high quantum yield of over 60% with a monoexponential fluorescence lifetime. These labels show no bleaching and high photostability over time and a high stability for a wide range of pH values. Cytotoxicity tests demonstrated the viability in the presence of of these luminescent probes even at high concentration (1 mg/mL). Cell studies confirmed the uptake of Ag NCs in epithelial lung cancer cells by an endocytotic process. These results show the high potential of fluorescent noble metal nanoclusters for biolabeling and imaging as alternatives to the standard fluorescent probes such as quantum dots or organic dyes.