On-chip transduction of nucleic acid hybridization using spatial profiles of immobilized quantum dots and fluorescence resonance energy transfer

The glass surface of a glass-polydimethylsiloxane (PDMS) microfluidic channel was modified to develop a solid-phase assay for quantitative determination of nucleic acids. Electroosmotic flow (EOF) within channels was used to deliver and immobilize semiconductor quantum dots (QDs), and electrophoresis was used to decorate the QDs with oligonucleotide probe sequences. These processes took only minutes to complete. The QDs served as energy donors in fluorescence resonance energy transfer (FRET) for transduction of nucleic acid hybridization. Electrokinetic injection of fluorescent dye (Cy3) labeled oligonucleotide target into a microfluidic channel and subsequent hybridization (within minutes) provided the proximity for FRET, with emission from Cy3 being the analytical signal. The quantification of target concentration was achieved by measurement of the spatial length of coverage by target along a channel. Detection of femtomole quantities of target was possible with a dynamic range spanning an order of magnitude. The assay provided excellent resistance to nonspecific interactions of DNA. Further selectivity of the assay was achieved using 20% formamide, which allowed discrimination between a fully complementary target and a 3 base pair mismatch target at a contrast ratio of 4:1.     

Identification of p53 gene by using CdSe/ZnS conjugation and hybridization

Recently Quantum Dots (QDs) have been of great interest due to their unique optical properties such as size-dependent, symmetric, narrow, and stable emissions, allowing for prolonged observation and multiplexing. We have prepared oligonucleotide conjugated to QD as a probe to detect p53 tumor suppressor gene related to hereditary cancer. QDs with carboxyl functional group have been conjugated to thiol-modified oligo nucleotides, which have been used as a hybridization probe for p53 gene. Target gene was added and hybridized with the QD bound probe. The conjugation of QD and thiolated oligonucleotide was stained by gel electrophoresis using Etrium Bromide (EtBr) as intercalating dye. Fluorescence resonance energy transfer (FRET) has been observed between QD and intercalating dye (Propidium Iodide) after hybridization of target and probe. FRET efficiency was increased with the increase of dye and DNA concentration. This shows the possibility of specific detection of low concentration of unlabeled complimentary DNA via quantum dots.     

The detection of p53 gene via fluorescence quenching of quantum dot in microfluidic chip

Recently, quantum dot (QD) has been used widely in the field of bio assay including cell imaging, biomarker, and fluorescence resonance energy transfer (FRET) sensor. The DNA assay without labeling process has several advantages including low cost, short time, and simplicity. Microbeads of agarose, glass, and polystyrene have been used as a solid support in microfluidic devices to trace molecules. The main advantages of microfluidics include high throughput, short analysis time, small sample volume, and high sensitivity. PDMS based microfluidic chips were prepared for the detection of p53 gene by using QD-DNA conjugate. The microfluidic chip has a weir in the channel to trap microbeads to which QD-DNA probes bind. Carboxylated CdSe/ZnS QDs (wavelength of emission: 605 nm) could bind to microbeads of polystyrene/divinyl benzene via EDC/NHS crosslinking reaction. The target gene and DNA intercalating dye (TOTO-3) were loaded into the micro-channel. Fluorescence quenching from QDs by intercalating dye was observed after hybridization of DNA at the weir in the channel of microfluidic chip. The fluorescence quenching from QDs by TOTO-3 was dependent on the concentration of target gene. This experiment shows the possibility of rapid detection of DNA via bead-QD complex on microfluidic chip.     

Ultrafast dynamics of excitons in semiconductor quantum dots on a plasmonically active nano-structured silver film

The excited state dynamics of core-shell type semiconductor quantum dots (QDs) of various sizes in close contact with a plasmonically active silver thin film has been demonstrated by using picosecond resolved fluorescence spectroscopy. The non-radiative energy transfer from the QDs to the metal surface is found to be of F?rster resonance energy transfer (FRET) type rather than the widely expected nano-surface energy transfer (NSET) type. The slower rate of energy transfer processes compared to that of the electron transfer from the excited QDs to an organic molecule benzoquinone reveals an insignificant possibility of charge migration from the QDs to the metallic film.     

Fluorescence Lifetime Imaging and FRET‐Induced Intracellular Redistribution of Tat‐Conjugated Quantum Dot Nanoparticles through Interaction with a Phthalocyanine Photosensitiser

The interaction of Tat‐conjugated PEGylated CdSe/ZnS quantum dots (QD) with the amphiphilic disulfonated aluminium phthalocyanine photosensitiser is investigated in aqueous solution and in a human breast cancer cell line. In aqueous solution, the QDs and phthalocyanine form stable nanocomposites. Using steady‐state and time‐resolved fluorescence measurements combined with singlet oxygen detection, efficient Förster resonance energy transfer (FRET) is observed with the QDs acting as donors, and the phthalocyanine photosensitiser, which mediates production of singlet oxygen, as acceptors. In cells, the Tat‐conjugated QDs localise in lysosomes and the QD fluorescence lifetimes are close to values observed in aqueous solution. Strong FRET‐induced quenching of the QD lifetime is observed in cells incubated with the nanocomposites using fluorescence lifetime imaging microscopy (FLIM). Using excitation of the QDs at wavelengths where phthalocyanine absorption is negligible, FRET‐induced release of QDs from endo/lysosomes is confirmed using confocal imaging and FLIM, which is attributed to photooxidative damage to the endo/lysosomal membranes mediated by the phthalocyanine acceptor.     

基于量子点的分子灯塔探针的制备及其在DNA探针中的应用

根据荧光共振能量转移理论合成出一种新颖的分子灯塔探针.由于CdTe量子点（QD s）的荧光发射光谱与DABCYL的紫外-可见吸收光谱有很好的重叠性,所以此种探针采用CdTe量子点作为能量给体,DABCYL作为能量受体.通过水相法合成出直径为2.5 nm的CdTe量子点,并且在偶联剂1-乙基-3-（3-二甲基氨丙基）碳二亚氨盐酸盐（EDC）作用下,与5-′NH2-DNA-DABCYL连接得到了分子灯塔探针.实验发现探针的荧光强度相比CdTe-DNA有明显的下降,最大能量转移效率为68.3%,表明CdTe QD s和DABCYL之间发生了荧光共振能量转移.结果表明,此种探针体系对于互补DNA及其变种有着很好的特异性,且其检测极限为5.170×10^-9mol/L.     

Chemical Redox Modulation of the Surface Chemistry of CdTe Quantum Dots for Probing Ascorbic Acid in Biological Fluids

Most of the fluorescence resonance energy transfer (FRET)‐based sensors employing quantum dots (QDs) usually use organic fluorophores and gold nanoparticles as the quenchers. However, complex processes for the modification/immobilization of the QDs are always necessary, as the generation of FRET requires strict distance between the donor and acceptor. Herein, a simple chemical redox strategy for modulating the surface chemistry of the QDs to develop a QD‐based turn‐on fluorescent probe is reported. The principle of the strategy is demonstrated by employing CdTe QDs with KMnO₄ as the quencher and ascorbic acid as the target analyte. The fluorescence of CdTe QDs is quenched with a blue‐shift upon addition of KMnO₄ due to the oxidation of the Te atoms on the surface of the QDs. The quenched fluorescence of the QDs is then recovered upon addition of ascorbic acid due to the reduction of CdTeO₃/TeO₂ on the surface of the QDs to CdTe. The recovered fluorescence of the QDs increases linearly with the concentration of ascorbic acid from 0.3 to 10 µM . Thus, a novel QD‐based turn‐on fluorescent probe with a detection limit as low as 74 nM is developed for the sensitive and selective detection of ascorbic acid in biological fluids. The present approach avoids the complex modification/immobilization of the QDs involved in FRET‐based sensors, and opens a simple pathway to developing cost‐effective, sensitive, and selective QD‐based fluorescence turn‐on sensors/probes for biologically significant antioxidants.     

On the quenching of semiconductor quantum dot photoluminescence by proximal gold nanoparticles

Luminescent quantum dots (QDs) were proven to be very effective fluorescence resonance energy transfer donors with an array of organic dye acceptors, and several fluorescence resonance energy transfer based biosensing assemblies utilizing QDs have been demonstrated in the past few years. Conversely, gold nanoparticles (Au-NPs) are known for their capacity to induce strong fluorescence quenching of conventional dye donors. Using a rigid variable-length polypeptide as a bifunctional biological linker, we monitor the photoluminescence quenching of CdSe-ZnS QDs by Au-NP acceptors arrayed around the QD surface, where the center-to-center separation distance was varied over a broad range of values (approximately 50-200 Angstrom). We measure the Au-NP-induced quenching rates for such QD conjugates using steady-state and time-resolved fluorescence measurements and examine the results within the context of theoretical treatments based on the F?rster dipole-dipole resonance energy transfer, dipole-metal particle energy transfer, and nanosurface energy transfer. Our results indicate that nonradiative quenching of the QD emission by proximal Au-NPs is due to long-distance dipole-metal interactions that extend significantly beyond the classical F?rster range, in agreement with previous studies using organic dye-Au-NP donor-acceptor pairs.     

Fluorescence energy transfer between fluorescein label and DNA intercalators to detect nucleic acids hybridization in homogeneous media

A general approach to detecting nucleic acid sequences in homogeneous media by means of steady-state fluorescence measurements is proposed. The methodology combines the use of a fluorescence-labeled single-strand DNA model probe, the complementary single-strand DNA target, and a DNA intercalator. The probe was fluorescein labeled to a spacer arm at the N4 position of the cytosine amino groups in polyribocytidylic acid (5'), poly(C), which acts as a model DNA probe. The complementary strand was polyriboinosinic acid (5'), poly(I), as a model of the target, and the energy transfer acceptor was an intercalator, either ethidium bromide or ethidium homodimer. In previous papers we have shown that the fluorescence intensity of the fluorescein label decreases when labeled poly(C) hybridizes with poly(I), and this fluorescence quenching can be used to detect DNA hybridization or renaturation in homogeneous media. In this paper we demonstrate that fluorescence resonance energy transfer (FRET) between fluorescein labeled to poly(C) and an intercalator agent takes place when single-stranded poly(C) hybridizes with poly(I), and we show how the fluorescence energy transfer further decreases the steady-state fluorescence intensity of the label, thus increasing the detection limit of the method. The main aim of this work was to develop a truly homogeneous detection system for specific nucleic acid hybridization in solution using steady-state fluorescence and FRET, but with the advantage of only having to label the probe with the energy donor since the energy acceptor is intercalated spontaneously. Moreover, the site label is not critical and can be labeled randomly in the DNA strand. Thus, the method is simpler than those published previously based on FRET. The experiments were carried out in both direct and competitive formats.     

Visualizing resonance energy transfer in supramolecular surface patterns of β-CD-functionalized quantum dot hosts and organic dye guests by fluorescence lifetime imaging

Detection of an analyte via supramolecular host-guest binding and quantum dot (QD)-based fluorescence resonance energy transfer (FRET) signal transduction mechanism is demonstrated. Surface patterns consisting of CdSe/ZnS QDs functionalized at their periphery with β-cyclodextrin (β-CD) were obtained by immobilization of the QDs from solution onto glass substrates patterned with adamantyl-terminated poly(propylene imine) dendrimeric "glue." Subsequent formation of host-guest complexes between vacant β-CD on the QD surface and an adamantyl-functionalized lissamine rhodamine resulting in FRET was confirmed by fluorescence microscopy, spectroscopy, and fluorescence lifetime imaging microscopy (FLIM).     

Energy transfer between lead sulfide quantum dots in the liquid phase

Förster resonant energy transfer (FRET) from smaller sized PbS Quantum Dots (QDs) to larger sized ones occurs in the liquid phase when adjacent QDs are brought in close proximity by the bridging action of the two SH groups in aromatic or aliphatic dithiols. Signatures of FRET were observed by the lowering of the fluorescence peak corresponding to the smaller particle group and intensification of the peak corresponding to the larger particle group in a mixture of the two in the liquid phase. The suspensions of the two QDs size distributions were mixed in a ratio such that total surface area of the smaller QDs was equal to that of the larger QDs. A 10–13% size deviation in each PbS QDs group also allows this phenomenon to be observed in these samples and is manifested by red-shift and broadening of the fluorescence peak. The ratio of the absorption peak intensity corresponding to the two groups of PbS QDs in the mixture remains the same.     

Single-quantum-dot-based DNA nanosensor

Rapid and highly sensitive detection of DNA is critical in diagnosing genetic diseases. Conventional approaches often rely on cumbersome, semi-quantitative amplification of target DNA to improve detection sensitivity. In addition, most DNA detection systems (microarrays, for example), regardless of their need for target amplification, require separation of unhybridized DNA strands from hybridized stands immobilized on a solid substrate, and are thereby complicated by solution-surface binding kinetics. Here, we report an ultrasensitive nanosensor based on fluorescence resonance energy transfer (FRET) capable of detecting low concentrations of DNA in a separation-free format. This system uses quantum dots (QDs) linked to DNA probes to capture DNA targets. The target strand binds to a dye-labelled reporter strand thus forming a FRET donor-acceptor ensemble. The QD also functions as a concentrator that amplifies the target signal by confining several targets in a nanoscale domain. Unbound nanosensors produce near-zero background fluorescence, but on binding to even a small amount of target DNA (approximately 50 copies or less) they generate a very distinct FRET signal. A nanosensor-based oligonucleotide ligation assay has been demonstrated to successfully detect a point mutation typical of some ovarian tumours in clinical samples.     

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.     

Fluorescence Quenching Nanoprobes Dedicated to In Vivo Photoacoustic Imaging and High‐Efficient Tumor Therapy in Deep‐Seated Tissue

Photoacoustic imaging (PAI) and photoacoustic (PA) therapy have promising applications for treating tumors. It is known that the utilization of high‐absorption‐coefficient probes can selectively enhance the PAI target contrast and PA tumor therapy efficiency in deep‐seated tissue. Here, the design of a probe with the highest availability of optical‐thermo conversion by using graphene oxide (GO) and dyes via π–π stacking interactions is reported. The GO serves as a base material for loading dyes and quenching dye fluorescence via fluorescence resonance energy transfer (FRET), with the one purpose of maximum of PA efficiency. Experiments verify that the designed fluorescence quenching nanoprobes can produce stronger PA signals than the sum of the separate signals generated in the dye and the GO. Potential applications of the fluorescence quenching nanoprobes are demonstrated, dedicating to enhance PA contrast of targets in deep‐seated tissues and tumors in living mice. PA therapy efficiency both in vitro and in vivo by using the fluorescence quenching nanoprobes is found to be higher than with the commonly used PA therapy agents. Taken together, quenching dye fluorescence via FRET will provide a valid means for developing high‐efficiency PA probes. Fluorescence quenching nanoprobes are likely to become a promising candidate for deep‐seated tumor imaging and therapy.     

Energy transfer: Visualizing Resonance Energy Transfer in Supramolecular Surface Patterns of β‐CD‐Functionalized Quantum Dot Hosts and Organic Dye Guests by Fluorescence Lifetime Imaging (Small 24/2010)

Detection of an analyte via supramolecular host–guest binding and quantum dot (QD)‐based fluorescence resonance energy transfer (FRET) signal transduction mechanism is demonstrated. Surface patterns consisting of CdSe/ZnS QDs functionalized at their periphery with β‐cyclodextrin (β‐CD) were obtained by immobilization of the QDs from solution onto glass substrates patterned with adamantyl‐terminated poly(propylene imine) dendrimeric “glue.” Subsequent formation of host–guest complexes between vacant β‐CD on the QD surface and an adamantyl‐functionalized lissamine rhodamine resulting in FRET was confirmed by fluorescence microscopy, spectroscopy, and fluorescence lifetime imaging microscopy (FLIM).     

Optical protein modulation via quantum dot coupling and use of a hybrid sensor protein

Harnessing the energy transfer interactions between the optical protein bacteriorhodopsin (bR) and CdSe/ZnS quantum dots (QDs) could provide a novel bio-nano electronics substrate with a variety of applications. In the present study, a polydimethyldiallyammonium chloride based I-SAM technique has been utilized to produce bilayers, trilayers and multilayers of alternating monolayers of bR, PDAC and QD's on a conductive ITO substrate. The construction of multilayer systems was directly monitored by measuring the unique A570 nm absorbance of bR, as well as QD fluorescence emission. Both of these parameters displayed a linear relationship to the number of monolayers present on the ITO substrate. The photovoltaic response of bilayers of bR/PDAC was observed over a range of 3 to 12 bilayers and the ability to efficiently create an electrically active multilayered substrate composed of bR and QDs has been demonstrated for the first time. Evaluation of QD fluorescence emission in the multilayer system strongly suggests that FRET coupling is occurring and, since the I-SAM technique provide a means to control the bR/QD separation distance on the nanometer scale, this technique may prove highly valuable for optimizing the distance dependent energy transfer effects for maximum sensitivity to target molecule binding by a biosensor. Finally, preliminary studies on the production of a sensor protein/bR hybrid gene construct are presented. It is proposed that the energy associated with target molecule binding to a hybrid sensor protein would provide a means to directly modulate the electrical output from a sensor protein/bR biosensor platform.     

Ligase detection reaction generation of reverse molecular beacons for near real-time analysis of bacterial pathogens using single-pair fluorescence resonance energy transfer and a cyclic olefin copolymer microfluidic chip

Detection of pathogenic bacteria and viruses require strategies that can signal the presence of these targets in near real-time due to the potential threats created by rapid dissemination into water and/or food supplies. In this paper, we report an innovative strategy that can rapidly detect bacterial pathogens using reporter sequences found in their genome without requiring polymerase chain reaction (PCR). A pair of strain-specific primers was designed based on the 16S rRNA gene and were end-labeled with a donor (Cy5) or acceptor (Cy5.5) dye. In the presence of the target bacterium, the primers were joined using a ligase detection reaction (LDR) only when the primers were completely complementary to the target sequence to form a reverse molecular beacon (rMB), thus bringing Cy5 (donor) and Cy5.5 (acceptor) into close proximity to allow fluorescence resonance energy transfer (FRET) to occur. These rMBs were subsequently analyzed using single-molecule detection of the FRET pairs (single-pair FRET; spFRET). The LDR was performed using a continuous flow thermal cycling process configured in a cyclic olefin copolymer (COC) microfluidic device using either 2 or 20 thermal cycles. Single-molecule photon bursts from the resulting rMBs were detected on-chip and registered using a simple laser-induced fluorescence (LIF) instrument. The spFRET signatures from the target pathogens were reported in as little as 2.6 min using spFRET.     

Ligand replacement-induced fluorescence switch of quantum dots for ultrasensitive detection of organophosphorothioate pesticides

The development of a simple and on-site assay for the detection of organophosphorus pesticed residues is very important for food safety and exosystem protection. This paper reports the surface coordination-originated fluorescence resonance energy transfer (FRET) of CdTe quantum dots (QDs) and a simple ligand-replacement turn-on mechanism for the highly sensitive and selective detection of organophosphorothioate pesticides. It has been demonstrated that coordination of dithizone at the surface of CdTe QDs in basic media can strongly quench the green emission of CdTe QDs by a FRET mechanism. Upon the addition of organophosphorothioate pesticides, the dithizone ligands at the CdTe QD surface are replaced by the hydrolyzate of the organophosphorothioate, and hence the fluorescence is turned on. The fluorescence turn on is immediate, and the limit of detection for chlorpyrifos is as low as ～0.1 nM. Two consecutive linear ranges allow a wide determination of chlorpyrifos concentrations from 0.1 nM to 10 μM. Importantly, the fluorescence turn-on chemosensor can directly detect chlorpyrifos residues in apples at a limit of 5.5 ppb, which is under the maximum residue limit allowed by the U.S. Environmental Protection Agency. The very simple strategy reported here should facilitate the development of fluorescence turn-on chemosensors for chemo/biodetection.     

核壳型量子点-纳米金颗粒组装体高效检测神经性毒剂模拟剂

实验设计制备了一种由12层硫化锌包覆硒化镉的核壳型量子点(CdSe/12ZnS QDs)和纳米金颗粒(Au NPs)自组装形成的CdSe/12ZnS QDs/Au NPs复合结构, 并将其应用于神经性毒剂模拟剂氰基磷酸二乙酯(Diethyl Cyanophosphonate, DCNP)的高效检测。QDs由于与Au NPs存在荧光共振能量转移作用(Fluorescence Resonance Energy Transfer, FRET)而发生荧光猝灭, 乙酰胆碱酯酶(AChE)水解氯化硫代乙酰胆碱(ATC)生成的硫胆碱能够将量子点取代而使量子点荧光恢复。当QDs与Au NPs的摩尔浓度比为20 : 1时, QDs荧光猝灭效果最佳, AChE浓度为1.0×10 ^-3 U/L时, QDs荧光恢复效果最好。DCNP的存在会抑制AChE的活性, 减少硫胆碱的生成并降低QDs的荧光恢复效率, 通过对QDs荧光恢复效率测定能够检测DCNP。在最优条件下对DCNP的检测结果表明, 量子点的荧光恢复效率与DCNP浓度的对数在5.0×10 ^-9~5.0×10 ^-4mol/L的范围内存在良好的线性关系, 检出限达5.0×10 ^-9mol/L。     

Quantum dot-fluorescent protein pairs as novel fluorescence resonance energy transfer probes

Fluorescence resonance energy transfer (FRET) characteristics, including the efficiency, donor-acceptor distance, and binding strength of six fluorescent protein (FP)-quantum dot (QD) pairs were quantified, demonstrating that FPs are efficient acceptors for QD donors with up to 90% quenching of QD fluorescence and that polyhistidine coordination to QD core-shell surface is a straightforward and effective means of conjugating proteins to commercially available QDs. This provides a novel approach to developing QD-based FRET probes for biomedical applications.