Binding-induced fluorescence turn-on assay using aptamer-functionalized silver nanocluster DNA probes

We present here a binding-induced fluorescence turn-on assay for protein detection. Key features of this assay include affinity binding-induced DNA hybridization and fluorescence enhancement of silver nanoclusters (Ag NCs) using guanine-rich DNA sequences. In an example of an assay for human α-thrombin, two aptamers (Apt15 and Apt29) were used and were modified by including additional sequence elements. A 12-nucleotide (nt) sequence was used to link the first aptamer with a nanocluster nucleation sequence at the 5'-end. The second aptamer was linked through a complementary sequence (12-nt) to a G-rich overhang at the 3'-end. Binding of the two aptamer probes to the target protein initiates hybridization between the complementary linker sequences attached to each aptamer and thereby bring the end of the G-rich overhang to close proximity to Ag NCs, resulting in a significant fluorescence enhancement. With this approach, a detection limit of 1 nM and a linear dynamic range of 5 nM-2 μM were achieved for human α-thrombin. This fluorescence assay is performed in a single tube, and it does not require washing or separation steps. The principle of the binding-induced DNA hybridization and fluorescence enhancement of Ag NCs can be extended to other homogeneous assay applications provided that two appropriate probes are available to bind with the same target molecule.     

Aptamer-mediated nanoparticle-based protein labeling platform for intracellular imaging and tracking endocytosis dynamics

Although nanoparticles have been widely used as optical contrasts for cell imaging, the complicated prefunctionalized steps and low labeling efficiency of nanoprobes greatly inhibit their applications in cellular protein imaging. In this study, we developed a novel and general strategy that employs an aptamer not only as a recognizer for protein recognition but also as a linker for nanoreporter targeting to specifically label membrane proteins of interest and track their endocytic pathway. With this strategy, three kinds of nanoparticles, including gold nanoparticles, silver nanoparticles, and quantum dots (QDs), have been successfully targeted to the membrane proteins of interest, such as nucleolin or prion protein (PrP(C)). The following investigations on the subcellular distribution with fluorescent immunocolocalization assay indicated that PrP(C)-aptamer-QD complexes most likely internalized into cytoplasm through a classical clathrin-dependent/receptor-mediated pathway. Further single-particle tracking and trajectory analysis demonstrated that PrP(C)-aptamer-QD complexes exhibited a complex dynamic process, which involved three types of movements, including membrane diffusion, vesicle transportation, and confined diffusion, and all types of these movements were associated with distinct phases of PrP(C) endocytosis. Compared with traditional multilayer methods, our proposed aptamer-mediated strategy is simple in procedure, avoiding any complicated probe premodification and purification. In particular, the new double-color labeling strategy is unique and significant due to its superior advantages of targeting two signal reporters simultaneously in a single protein using only one aptamer. What is more important, we have constructed a general and versatile aptamer-mediated protein labeling nanoplatform that has shown great promise for future biomedical labeling and intracellular protein dynamic analysis.     

Nucleic acid-based fluorescence sensors for detecting proteins

We report here development of a rapid, homogeneous, aptamer-based fluorescence assay ("molecular beacons") for detecting proteins. The assay involves protein-induced coassociation of two aptamers recognizing two distinct epitopes of the protein. The aptamers contain short fluorophore-labeled complementary "signaling" oligonucleotides attached to the aptamer by non-DNA linker. Coassociation of the two aptamers with the protein results in bringing the two "signaling" oligonucleotides into proximity, producing a large change of fluorescence resonance energy transfer between the fluorophores. We used thrombin as a model system to provide proof-of-principle evidence validating this molecular beacon design. Thrombin beacon was capable of detecting the protein with high selectivity (also in complex biological mixtures), picomolar sensitivity, and high signal-to-background ratio. This is a homogeneous assay requiring no sample manipulation. Since the design of molecular beacons described here is not limited to any specific protein, it will be possible to develop these beacons to detect a variety of target proteins of biomedical importance.     

Sensitive detection of microRNA with isothermal amplification and a single-quantum-dot-based nanosensor

MicroRNAs (miRNAs) play important roles in a wide range of biological processes, and their aberrant expressions are associated with various diseases. Here we develop a rapid, highly sensitive, and specific miRNA assay based on the two-stage exponential amplification reaction (EXPAR) and a single-quantum-dot (QD)-based nanosensor. The two-stage EXPAR involves two templates and two-stage amplification reactions under isothermal conditions. The first template enables the amplification of miRNA, and the second template enables the conversion of miRNA to the reporter oligonucleotide. Importantly, different miRNAs can be converted to the same reporter oligonucleotides, which can hybridize with the same set of capture and reporter probes to form sandwich hybrids. These sandwich hybrids can be assembled on the surface of 605 nm emission QDs (605QDs) to form the 605QD/reporter oligonucleotide/Cy5 complexes, where the 605QD functions as both a fluorescence resonance energy transfer donor and a target concentrator. Upon excitation with a wavelength of 488 nm, distinct Cy5 signals can be observed in the presence of target miRNA. This assay is highly sensitive and specific with a detection limit of 0.1 aM and can even discriminate single-nucleotide differences between miRNA family members. Moreover, in combination with the specific templates, this method can be applied for multiplex miRNA assay by simply using the same set of capture and reporter probes. This highly sensitive and specific assay has potential to become a promising miRNA quantification method in biomedical research and clinical diagnosis.     

Dual-color fluorescence and homogeneous immunoassay for the determination of human enterovirus 71

We have developed a new fluorescent immune ensemble probe comprised of a conjugated lower toxic water-soluble CdTe:Zn(2+) quantum dots (QDs) and Ru(bpy)(2)(mcbpy-O-Su-ester)(PF(6))(2)- antibody complex (Ru-Ab) for the dual-color determination of human enterovirus 71 (EV71) in homogeneous solution. EV71 monoantibody was easily covalently conjugated with Ru(bpy)(2)(mcbpy-O-Su-ester)(PF(6))(2) to form a stable complex Ru-Ab, which acted both as an effective quencher of QDs fluorescence and the capture probe of virus antigen EV71. Herein, the target EV71 can break up the low fluorescent ionic ensemble by antigen-antibody combination to set free the fluorescent QDs and restore the fluorescence of QDs whereas the fluorescence intensity of Ru-Ab remains the same. Thus, the determination of EV71 by the complex Ru-Ab and QDs can be realized via the restoration of QDs fluorescence upon addition of EV71 and even can be directly evaluated by the ratio of green-colored QDs fluorescence intensity to Ru-Ab red-colored fluorescence intensity. The green-colored fluorescence of QDs was very sensitive to the change of EV71 concentration, and its fluorescence intensity increased with the increase of EV71 concentration between 1.8 ng/mL and 12 μg/mL. With this method, EV71 was detected at subnanogram per milliliter concentration in the presence of 160 μg/mL bovine serum albumin. More importantly, this strategy can be used as a universal method for any protein or virus by changing conjugated antibodies in disease early diagnosis providing a fast and promising clinical approach for virus determination. In a word, a simple, fast, sensitive, and highly selective assay for EV71 has been described. It could be applied in real sample analysis with a satisfactory result. It was notable that the sensor could not only achieve rapid and precise quantitative determination of protein/virus by fluorescent intensity but also could be applied in semiquantitative protein/virus determination by digital visualization.     

Mechanisms of prion disease progression: a chemical reaction network approach

Fatal neurodegenerative diseases such as bovine spongiform encephalopathy in cattle, scrapie in sheep and Creutzfeldt-Jakob disease in humans are caused by prions. Prion is a protein encoded by a normal cellular gene. The cellular form of the prion, namely PrP(C), is benign but can be converted into a disease-causing form (named scrapie), PrP(Sc), by a conformational change from -helix to -sheets. Prions replicate by this conformational change; that is, PrP(Sc) interacts with PrP(C) producing a new molecule of PrP(Sc). This kind of replication is modelled in this contribution as an autocatalytic process. The kinetic model accounts for two of the three epidemiological manifestations: sporadic and infectious. By assuming irreversibility of the PrP(Sc) replication and describing a first-order reaction for the degradation of cellular tissue, the authors explore dynamical scenarios for prion progression, such as oscillations and conditions for multiplicity of equilibria. Feinberg's chemical reaction network theory is exploited to identify multiple steady states and their associate kinetic constants.     

Cytotoxicity tests of water soluble ZnS and CdS quantum dots

Cytotoxicity tests of zinc sulfide (ZnS) and cadmium sulfide (CdS) quantum dots (QDs) synthesized via all-aqueous process with various surface conditions were carried out with human endothelial cells (EA hy926) using two independent viability assays, i.e., by cell counting following Trypan blue staining and by measuring Alamar Blue (AB) fluorescence. The ZnS QDs with all four distinct types of surface conditions were nontoxic at both 1 microM and 10 microM concentrations for at least 6 days. On the other hand, the CdS QDs were nontoxic only at 1 microM, and showed significant cytotoxicity at 10 microM after 3 days in the cell counting assay and after 4 days in the AB fluorescence assay. The CdS QDs with (3-mercaptopropyl)trimethoxysilane (MPS)-replacement plus silica capping were less cytotoxic than those with 3-mercaptopropionic acid (MPA) capping and those with MPS-replacement capping. Comparing the results of ZnS and CdS QDs with the same particle size, surface condition and concentration, it is indicated that the cytotoxicity of CdS QDs and the lack of it in ZnS QDs were probably due to the presence and absence of the toxic Cd element, respectively. The nontoxicity of the aqueous ZnS QDs makes them favorable for in vivo imaging applications.     

Capillary electrophoresis-based noncompetitive immunoassay for the prion protein using fluorescein-labeled protein A as a fluorescent probe

A novel CE-based noncompetitive immunoassay for prion protein (PrP) was established. Fluorescein isothiocyanate (FITC)-labeled protein A (FITC-PrA) was used as a fluorescent probe to tag monoclonal antibody through noncovalent binding of FITC-PrA to the Fc region of the antibody. The FITC-PrA-Ab was incubated with the analyte, prion protein, under optimized condition, forming the immunocomplex FITC-PrA-Ab-PrP. The complex was separated and analyzed by capillary zone electrophoresis. The addition of carboxymethyl-beta-cyclodextrin in the running buffer as dynamical coating reagent improved the reproducibility and the resolution. The complex was isolated in less than 1 min with theoretical plates of 3.8 x 10(4). Relative standard deviations of peak height and migration time for the complex were 3.46 and 1.48%, respectively. A linear relationship was established for the bovine recombinant prion protein (rPrP) concentration in the range from 0.2 to 2.0 mug/mL and the peak height. The correlation factor was r2 = 0.9969. The estimated detection limit for rPrP was approximately 6 ng/mL, which is 3 times the signal-to-noise ratio. The method was successfully applied for testing blood samples from scrapie-infected sheep.     

Simulations of biomolecules: Characterization of the early steps in the pH-induced conformational conversion of the hamster,bovine and human forms of the prion protein

As computer power increases, so too does the range of interesting biomolecular phenomena and properties that can be simulated. It is now possible to simulate complicated protein conformational changes at ambient or physiological temperatures. In this regard, we are attempting to map the conformational transitions of the normal, cellular prion protein (PrP(C)) to its infectious scrapie isoform (PrP(Sc)), which causes neurodegenerative diseases in many mammals. These two forms have identical sequences and are conformational isomers, with heightened formation of beta-sheet structure in the scrapie form. Conversion can be triggered by lowering the pH, but thus far it has been impossible to characterize the conformational change at high resolution using experimental methods. Therefore, to investigate the effect of acidic pH on PrP conformation, we have performed molecular-dynamics simulations of hamster, human and bovine forms of the prion protein in water at neutral and low pH. In all cases the core of the protein is well maintained at neutral pH. At low pH, however, the protein is more dynamic, and the sheet-like structure increases both by lengthening of the native beta-sheet and by addition of a portion of the N-terminus to widen the sheet by another 2-3 strands.     

Prion protein detection using nanomechanical resonator arrays and secondary mass labeling

Nanomechanical resonators have shown potential application for mass sensing and have been used to detect a variety of biomolecules. In this study, a dynamic resonance-based technique was used to detect prion proteins (PrP), which in conformationally altered forms are known to cause neurodegenerative diseases in animals as well as humans. Antibodies and nanoparticles were used as mass labels to increase the mass shift and thus amplify the frequency shift signal used in PrP detection. A sandwich assay was used to immobilize PrP between two monoclonal antibodies, one of which was conjugated to the resonator's surface while the other was either used alone or linked to the nanoparticles as a mass label. Without additional mass labeling, PrP was not detected at concentrations below 20 microg/mL. In the presence of secondary antibodies the analytical sensitivity was improved to 2 microg/mL. With the use of functionalized nanoparticles, the sensitivity improved an additional 3 orders of magnitude to 2 ng/mL.     

Label-free fluorescent detection of protein kinase activity based on the aggregation behavior of unmodified quantum dots

Herein, we present a novel label-free fluorescent assay for monitoring the activity and inhibition of protein kinases based on the aggregation behavior of unmodified CdTe quantum dots (QDs). In this assay, cationic substrate peptides induce the selective aggregation of unmodified QDs with anionic surface charge, whereas phosphorylated peptides do not. Phosphorylation by kinase alters the net charge of peptides and subsequently inhibits the aggregation of unmodified QDs, causing an enhanced fluorescence with a 45 nm blue-shift in emission and a yellow-to-green emission color change. Hence the fluorescence response allows this QD-based method to easily probe kinase activity by a spectrometer or even by the naked eye. The feasibility of the method has been demonstrated by sensitive measurement of the activity of cAMP-dependent protein kinase (PKA) with a low detection limit (0.47 mU μL(-1)). On the basis of the fluorescence response of QDs on the concentration of PKA inhibitor H-89, the IC(50) value, the half maximal inhibitory concentration, was estimated, which was in agreement with the literature value. Moreover, the system can be applicable to detect the Forskolin/3-isobutyl-1-methylxantine (IBMX)-stimulated activation of PKA in cell lysate. Unlike the existing QD-based enzyme activity assays in which the modification process of QDs is essential, this method relies on unmodified QDs without the requirement of peptide labeling and QDs' modification, presenting a promising candidate for cost-effective kinase activity and inhibitor screening assays.     

鲈鱼蛋白质感染因子蛋白基因的克隆和结构分析

采用RT-PCR方法分离了鲈鱼蛋白质感染因子蛋白编码基因序列,并进行了结构分析。研究证明,该感染因子蛋白由507个氨基酸组成,与红鳍东方、大西洋鲑蛋白质感染因子蛋白的平均相似性为67．9％,预测分子量约54kD,具有信号肽、短肽顺接重复、疏水区、糖基化位点、二硫键、糖基缩醛磷肌醇锚定位点等蛋白质感染因子蛋白的主要特征结构域。鲈鱼蛋白质感染因子蛋白编码基因序列的分离,为蛋白质感染因子的进化、功能研究以及可能存在的鱼类传染性海绵样脑病研究奠定了基础。     

Conjugation of quantum dots and JT95 IgM monoclonal antibody for thyroid carcinoma without abolishing the specificity and activity of the antibody

Among the immunoglobulins, IgM class-antibodies are now considered to be potent immunological reagents for anticancer remedies. However, only a few reports are available about the effective labeling of IgM with enzymes, fluorescence, or other bioreactive reagents. Here, we report an effective application of luminescent semiconductive nanoparticles, quantum dots (QDs), as a labeling material of the IgM antibody. The CdSe carboxyl QDs were reacted with 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride and N-hydroxysulfo- succinimide in 2-(morpholino) ethanesulfonic acid. The reacted QDs were then coupled to JT95 IgM antibody, which recognizes thyroid carcinoma associated antigen. The specificity and activity of the conjugates were tested by immunoblot, immunoquantitive assay and immunohistological imaging. The QDs were firmly conjugated with JT95 IgM monoclonal antibody. In immunoblot assay, QD-JT95 conjugates directly detected the target molecules without obstructing the binding site. In immunoquantitive assay, the conjugates could quantify the antigen in the range of 1.56-100 μg/mL. Also, QDs-labeled antibody detected the antigen on plasma membrane. Our results demonstrate that labeling of JT95 and other IgM class antibodies with QDs is feasible. This approach may be an important method for the medical application of IgM in the diagnosis and treatment of cancers.     

An Acidic‐Microenvironment‐Driven DNA Nanomachine Enables Specific ATP Imaging in the Extracellular Milieu of Tumor

Extracellular ATP is an emerging target for cancer treatment because it is a key messenger for shaping the tumor microenvironment (TME) and regulating tumor progression. However, it remains a great challenge to design biochemical probes for targeted imaging of extracellular ATP in the TME. A TME‐driven DNA nanomachine (Apt‐LIP) that permits spatially controlled imaging of ATP in the extracellular milieu of tumors with ultrahigh signal‐to‐background ratio is reported. It operates in response to the mild acidity in the TME with the pH (low) insertion peptide (pHLIP) module, thus allowing the specific anchoring of the structure‐switching signaling aptamer unit to the membrane of tumor cells for “off–on” fluorescence imaging of the extracellular ATP. Apt‐LIP allows for acidity driven visualization of different extracellular concentrations of exogenous ATP, as well as the monitoring of endogenous ATP release from cells. Furthermore, it is demonstrated that Apt‐LIP represents a promising platform for the specific imaging of the extracellular ATP in both primary and metastatic tumors. Ultimately, since diverse aptamers are obtained through in vitro selection, this design strategy can be further applied for precise detection of various extracellular targets in the TME.     

Single-molecule colocalization studies shed light on the idea of fully emitting versus dark single quantum dots

In this report the correlation between the solution photoluminescence (PL) quantum yield and the fluorescence emission of individual semiconductor quantum dots (QDs) is investigated. This is done by taking advantage of previously reported enhancement in the macroscopic quantum yield of water-soluble QDs capped with dihydrolipoic acid (DHLA) when self-assembled with polyhistidine-appended proteins, and by using fluorescence coincidence analysis (FCA) to detect the presence of "bright" and "dark" single QDs in solution. This allows for changes in the fraction of the two QD species to be tracked as the PL yield of the solution is progressively altered. The results clearly indicate that in a dispersion of luminescent nanocrystals, "bright" (intermittently emitting) single QDs coexist with "permanently dark" (non-emitting) QDs. Furthermore, the increase in the fraction of emitting QDs accompanies the increase in the PL quantum yield of the solution. These findings support the idea that a dispersion of QDs consists of two optically distinct populations of nanocrystals--one is "bright" while the other is "dark;" and that the relative fraction of these two populations defines the overall PL yield.     

Molecular aptamer for real-time oncoprotein platelet-derived growth factor monitoring by fluorescence anisotropy.

Monitoring proteins in real time and in homogeneous solution has always been a difficult task. We have applied a fluorophore-labeled molecular probe based on a high-affinity platelet-derived growth factor (PDGF) aptamer for the ultrasensitive detection of PDGF in homogeneous solutions. The aptamer is labeled with fluorescein to specifically bind with the PDGF protein. Fluorescence anisotropy is used for the real-time monitoring of the binding between the aptamer and the protein. When the labeled aptamer is bound with its target protein, the rotational motion of the fluorophore attached to the complex becomes much slower because of an increased molecular weight after binding, resulting in a significant fluorescence anisotropy change. Using the anisotropy change, we are able to detect the binding events between the aptamer and the protein in real time and in homogeneous solutions (detection without separation). This assay is highly selective and ultrasensitive. It can detect PDGF in the subnanomolar range. The new method for protein detection is simple and inherits all of the advantages of molecular aptamers. Efficient oncoprotein detection using aptamer-based fluorescence anisotropy measurement will find wide applications in protein monitoring, in cancer diagnosis as well as other studies in which protein analysis is important.     

Bioactivity of the conjugation of green-emitting CdTe quantum dots with a carborane complex

In this report, we describe the effect of conjugating o-carborane-C(1)C(2)-dicarboxylic acid (o-C2B10H10-C2O4H2, denoted as Cbac2) to cadmium telluride quantum dots (CdTe QDs) capped with cysteamine on the photophysics and cytotoxicity of the QDs. Cbac2 quenches the fluorescence intensity and induces a red shift of the fluorescence emission peak. Meanwhile, studies with a real time cell electronic sensing (RT-CES) system and the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl (MTT) assay indicate that the combination of the carborane carboxylic acid derivative Cbac2 with relevant QDs can efficiently improve the inhibition efficiency for target cancer cells when compared with a single ligand or the CdTe QDs alone. This study raises the possibility for the labeling of the important pharmacophore with QDs and the design of new promising anticancer agents containing the carborane pharmacophores for cancer therapy.     

One-pot aqueous synthesis PbS quantum dots and their Hg2+ sensitive properties

In this study, we report the synthesis and stability of PbS quantum dots (QDs) using an aqueous route with L-Cysteine (L-Cys) as the capping molecule. The as-synthesized L-Cys-capped PbS QDs were characterized by high resolution transmission electron microscopy (HRTEM), and X-ray diffraction (XRD), the results indicated that the QDs were about 4 nm in size and dispersed well with a rock salt crystalline structure, and there was L-Cys on the surface of QDs, which was confirmed by Fourier transform infrared (FT-IR) spectrometry. The influence of various experimental variables, including amounts of capping ligand, pH value and refluxing time, on the luminescent properties of the obtained QDs have been systematically investigated. The QDs exhibited optimal PL intensity when Pb: L-Cys: S = 1:2.2:0.3. In addition, the as-prepared QDs could be used as fluorescence probes to detect Hg2+ ions in aqueous media. The response of QDs fluorescence probes was linearly proportional to the concentration of Hg2+ ions ranging from 8 x 10(-9) to 2 x 10(-6) mol x L(-1) with a limit of detection of 2 x 10(-9) mol x L(-1). Furthermore, the method was successfully applied to the determine Hg2+ ions in different real samples.     

Quantum dot as a drug tracer in vivo

Quantum dots (QDs) have been applied to a wide range of biological studies by taking advantage of their fluorescence properties. There is almost no method to trace small molecules including medicine. Here, we used QDs for fluorescent tracers for medicine and analyzed their kinetics and dynamics. We conjugated QDs with captopril, anti-hypertensive medicine, by an exchange reaction while retaining the medicinal properties. We investigated the medicinal effect of QD-conjugated captopril (QD-cap) in vitro and in vivo. We also evaluated the concentration and the distribution of the QD-cap in the blood and the organs with their fluorescence. We demonstrate that the QD-cap inhibits the activity of ACE in vitro. The QD-cap reduced the blood pressure of hypertensive model rats. The concentration of the QD-cap in the blood was measured by using the standard curve of the fluorescence intensity. The blood concentration of the QD-cap decrease exponentially and QD-cap has approximately the same half-life as that of captopril. In addition, the fluorescence of the QDs revealed that QD-cap accumulates in the liver, lungs, and spleen. We succeeded in analyzing the dynamics and kinetics of small molecules using fluorescence of QDs     

Preferential binding of a novel polyhistidine peptide dendrimer ligand on quantum dots probed by capillary electrophoresis

Fluorescence detection coupled to capillary electrophoresis (CE-FL) effectively separates molecules in solution and at the same time allows monitoring of the fluorescence spectrum of each individual species. The integration of separation and fluorescence detection results in a powerful method superior to the ensemble in-cuvette fluorescence measurement, in probing the binding interaction between ligands and quantum dots (QDs) in complex solutions. Fo?rster resonance energy transfer (FRET) between fluorescent ligands and QDs could be readily detected by CE-FL, which together with the migration times of the fluorescent peaks provides an indication of the binding interaction between ligands and QDs. In the present study, the binding interaction between a multivalent ligand, polyhistidine peptide denderimer (PHPD), and CdSe-ZnS QDs was probed by CE-FL using the monovalent hexahistidine peptide as a control. Cy5 labeled PHPD assembles on glutathione capped QDs, showing a higher FRET signal than that of the assembly between Cy5 labeled hexahistidine peptide and QDs. Capillary electrophoresis further revealed that PHPD outcompetes other QD binding small molecules, peptides, and proteins in cell lysate. Our study demonstrates the power of CE-FL in analyzing the binding interaction between ligands and QDs in a complex binding solution. It also shows that clustering surface binding motifs yields multivalent ligands that can preferentially assemble with nanoparticles.