Nucleic Acid Hybridization Enhanced Luminescence for Rapid and Sensitive RNA and DNA Based Diagnostics.

Long-lived emissive nucleic acid probes are widely used in biochemical analysis due to their programmable structures, high signal-to-background ratio, and high sensitivity. Homogeneous detection based on long-lived emissive nucleic acid probes is often achieved through Förster resonance energy transfer (FRET), which suffers from the limitation of a narrow effective distance range. Herein, a new strategy of accessing nucleic acid hybridization-responsive luminescent probes is presented. The photoluminescence (PL) of a Lumi4-Tb complex internally modified with DNA is switched on by nucleic acid hybridization, after which the PL is increased up to 20 times. PL lifetime analysis revealed a possible mechanism of luminescence enhancement. Due to the flexibility of single-stranded nucleic acid chains, the bases and phosphate groups can coordinate with the Tb(III), which reduces the stability of the Tb complex and results in weak PL. After hybridization, the rigid double helix structure suppresses the coordination between Tb(III) and the bases or phosphate groups, causing luminescence enhancement. As the DNA sequence can be freely designed, an array of probes for different DNA or RNA targets can be created with the same Tb complex. Moreover, the novel probe design can afford pM detection limits of DNA or RNA without any nucleic acid amplification and exhibits great potential for nucleic acid detection in clinical diagnosis.

Highly selective recognition of the Al(ClO4)3 molecule by a mono-pyrene substituted thiacalix[4]arene chemosensor.

A mono-pyrene substituted thiacalix[4]arene chemosensor (TCA-Py) was successfully synthesized in satisfactory yield. Fluorescence analysis revealed that TCA-Py exhibited a high recognition selectivity toward the Al(ClO4)3 molecule due to the synergy between the Al3+ cation and ClO4- anion. This unique ability to recognise an entire inorganic molecule broadens the field of molecular recognition.

A Genetically Encoded Bioluminescent System for Fast and Highly Sensitive Detection of Antibodies with a Bright Green Fluorescent Protein.

A method for fast and highly sensitive detection of antibodies in serum would greatly facilitate the early diagnosis of disease and infection and dose optimization of therapeutic antibody. Bioluminescence detection with LUMABS (renamed mNeonG-LUMABS, where mNeonG is short for mNeonGreen) sensors based on bioluminescence resonance energy transfer (BRET) between blue-emitting luciferase Nluc and green fluorescent protein (FP) mNeonGreen has been demonstrated to enable fast detection of antibodies directly in serum with reasonable sensitivity. However, some mNeonG-LUMABS sensors exhibit low sensitivity, and thus, sensitivity improvement remains imperative. Here, we report a bright green FP, Clover4, obtained by structure-guided mutagenesis of green FP Clover. Despite similar brightness and fluorescence spectra of Clover and mNeonGreen, Clover4-LUMABS sensors exhibit a largely increased dynamic range (maximum 20-fold) and much lower limit of detection (LOD) (maximum 5.6-fold), most likely because Clover4 is positioned in a more parallel orientation to Nluc in LUMABS. Due to modular design, Clover4-LUMABS offers a general BRET system for fast and highly sensitive antibody detection in serum.

A compact fiber-integrated optofluidic platform for highly specific microRNA Förster resonance energy transfer detection.

MicroRNAs (miRNAs) have attracted extensive interest as promising biomarkers for the profiling of diseases. However, quantitative measurement of miRNAs presents a significant challenge in biochemical studies. In this work, we developed an innovative optofluidic platform to perform a rapid, simple, quantitative and high-specificity miRNA assay using the Förster resonance energy transfer (FRET) principle. A novel three-way junction FRET probe was proposed to enable rapid and enzyme-free miRNA detection. Using this platform, we performed one-step, amplification-free miRNA detection with simple device operation and achieved miRNA identification at a low concentration. The detection system could achieve high specificity for discrimination of three-base mismatches, and the sample volume was significantly reduced, favorable for low-level miRNA detection in material-limited samples. The establishment of a compact, low-cost, highly sensitive and selective miRNA analysis platform provides a valuable tool for point-of-care diagnosis.

Quantitatively Switchable pH-Sensitive Photoluminescence of Carbon Nanodots.

pH sensing plays a key role in the life sciences as well as the environmental, industrial, and agricultural fields. Carbon nanodots (C-dots) with small size, low toxicity, and excellent stability hold great potential in pH sensing as nanoprobes due to their intrinsic pH-sensitive photoluminescence (PL). Nonetheless, the undesirable sensitivity and response range of C-dot PL toward pH cannot meet the requirements of practical applications, and the unclear pH-sensitive PL mechanism makes it difficult to control their pH sensitivity. Herein, the quantitative correlation of pH-sensitive PL with specific surface structures of C-dots is uncovered for the first time, to our best knowledge. The association of carboxylate and H+ increases the ratio of nonradiation to radiation decay of C-dots through excited-state proton transfer, resulting in the decrease of PL intensity. Meanwhile, the dissociation of α-H in ß-dicarbonyl forming enolate increases the extent of delocalization of the C-dots conjugated system, which induces the PL broadening to the red region and a decreasing intensity. Based on the understanding of the pH-sensitive PL mechanism, the pH-sensitive PL of C-dots can be switched by quantitative modulation of carboxyl and ß-dicarbonyl groups to achieve a desirable pH response range with high sensitivity. This work contributes to a better understanding of the pH-sensitive PL of C-dots and therefore presents an effective strategy for controllably tuning their pH sensitivity, facilitating the rational design of C-dot-based pH sensors.

Molecular Tweezers-like Calix[4]arene Based Alkaline Earth Metal Cation (Ca2+, Sr2+, and Ba2+) Chemosensor and Its Imaging in Living Cells and Zebrafish.

Although alkaline earth metal cations play an important role in our daily life, little attention has been paid to the field of fast quantitative analysis of their content due to a lack of satisfactory precision and a fast and convenient means of detection. In this study, we have designed a set of molecular tweezers based on the calix[4]arene chemosensor L, which was found to exhibit high selectivity and sensitivity toward Ca2+, Sr2+, and Ba2+ (by UV-vis and fluorescence methods) with low detection limits of the order of 10-7 to 10-8 M and high association constants (of the order of 106). More significantly, sensor L not only can recognize Ca2+, Sr2+, and Ba2+ but also can further discriminate between these three cations via the differing red shifts in their UV-vis spectra (560 nm for L·Ca2+, 570 nm for L·Sr2+, and 580 nm for L·Ba2+ complex) which is attributed to their different atomic radii. A rare synergistic effect for the recognition mechanism has been demonstrated by 1H NMR spectroscopic titration. Sensor L constructed a high shielding field by the cooperation of Tris with alkaline earth metal ion after complex. Additionally, the presence of acetoxymethyl group in sensor L results in enhancement of cell permeability, and as a consequence, sensor L exhibited excellent sensing and imaging (in vivo) in living cells and in zebrafish.

The Marriage of Protein and Lanthanide: Unveiling a Time-Resolved Fluorescence Sensor Array Regulated by pH toward High-Throughput Assay of Metal Ions in Biofluids.

A protein/lanthanide complex (BSA/Tb3+)-based sensor array in two different pH buffers has been designed for high-throughput recognition and time-resolved fluorescence (TRF) detection of metal ions in biofluids. BSA, which acted as an antenna ligand, can sensitize the fluorescence of Tb3+ (i.e., antenna effect), while the presence of metal ions would lead to the corresponding conformational change of BSA for altering the antenna effect accompanied by a substantial TRF performance of Tb3+. This principle has also been fully proved by both experimental characterizations and coarse-grained molecular dynamics (CG-MD) studies. By using Tris-HCl buffer with different pHs (at 7.4 and 8.5), 17 metal ions have been well-distinguished by using our proposed BSA/Tb3+ sensor array. Moreover, the sensor array has the potential to discriminate different concentrations of the same metal ions and a mixture of metal ions. Remarkably, the detection of metal ions in biofluids can be realized by utilizing the presented sensor array, verifying its practical applications. The platform avoids the synthesis of multiplex sensing receptors, providing a new method for the construction of convenient and feasible lanthanide complex-based TRF sensing arrays.

Manganese(II)-doped zinc/germanium oxide nanoparticles as a viable fluorescent probe for visual and time-resolved fluorometric determination of ascorbic acid and its oxidase.

A method is described for the determination of ascorbic acid (AA) in complex biological fluids. It based on maganese(II)-doped zinc/germanium oxide nanoparticles (Mn@ZnGe NPs) with appealing time-resolved phosphorescence (TRP). TRP can provide a background-free reporter signal in analytical methods. The absorption of AA overlaps the excitation band of Mn@ZnGe NPs at 254 nm. This reduces the intensity of fluorescence via an inner filter effect (IFE) with increasing concentration of AA. Typical experimental conditions include an emission peak at 536 nm, a delay time of 50 µs and a counting time of 2 ms. This method can detect AA in a range of 5-500 µM with a 0.13 µM limit of detection. If AA is oxidized by the enzyme AA oxidase (AAOx), dehydroascorbic acid will be formed which doesn't absorb at 254 nm. Hence, the IFE cannot occur and fluorescence is not reduced. The strategy can be used to quantify AAOx in the activity range of 1-4 U·mL-1. By using a handheld UV lamp and a smart phone with a color-scanning feature, the feasibility for visual detection and real-time/onsite quantitative scanometric monitoring of AA and AAOx is demonstrated. Graphical abstract Schematic presentation of a fluorometric method for determination of ascorbic acid (AA) and ascorbic oxidase and a scanometric visual assay. It based on the use of maganese(II)-doped zinc/germanium oxide nanoparticles (Mn@ZnGe NPs) with appealing time-resolved phosphorescence (TRP) and the inner-filter effect (IFE) between AA and Mn@ZnGe NPs.

A rapid, ratiometric, enzyme-free, and sensitive single-step miRNA detection using three-way junction based FRET probes.

MicroRNAs (miRNAs) are single stranded endogenous molecules composed of only 18-24 nucleotides which are critical for gene expression regulating the translation of messenger RNAs. Conventional methods based on enzyme-assisted nucleic acid amplification techniques have many problems, such as easy contamination, high cost, susceptibility to false amplification, and tendency to have sequence mismatches. Here we report a rapid, ratiometric, enzyme-free, sensitive, and highly selective single-step miRNA detection using three-way junction assembled (or self-assembled) FRET probes. The developed strategy can be operated within the linear range from subnanomolar to hundred nanomolar concentrations of miRNAs. In comparison with the traditional approaches, our method showed high sensitivity for the miRNA detection and extreme selectivity for the efficient discrimination of single-base mismatches. The results reveal that the strategy paved a new avenue for the design of novel highly specific probes applicable in diagnostics and potentially in microscopic imaging of miRNAs in real biological environments.

Near infrared quantum dots in biomedical applications: current status and future perspective.

To address the requirements of biomedical applications including biosensing, bioimaging, and drug delivery, fluorescent nanomaterials served as efficient tools in many cases. Among them, near-infrared quantum dots (NIR QDs) have been used as novel fluorescent labels for their binary advantages of both QDs and NIR light. In this review, through collecting references in recent 10 years, we have introduced basic structures and properties of NIR QDs and summarized the classification and the related synthetic methods. This review also highlights the functionalization and surface bioconjugation of NIR QDs, and their biomedical applications in biosensing, bioimaging, and drug delivery. This article is categorized under: Diagnostic Tools > Diagnostic Nanodevices Diagnostic Tools > In Vitro Nanoparticle-Based Sensing Diagnostic Tools > In Vivo Nanodiagnostics and Imaging.

Highly selective recognition of Al3+ and I- ions using a bi-functional fluorescent probe.

A tripodal fluorescent probe L1 armed with Rhodamine B and 1-naphthaleneisothiocyanates was prepared in high yield. A study of the recognition properties revealed that probe L1 exhibited high sensitivity and selectivity towards Al3+ through a "FRET" fluorescence response and colorimetric response with low detection limits of the order of 10-8 M. Meanwhile, probe L1 also possessed high recognition ability for I- through fluorescence decay, which given there are comparatively few selective fluorescent probes for I-, is significant. Furthermore, the complexation mechanisms were fully investigated by spectral titrations, 1H NMR spectroscopic titrations and mass spectrometry. The utility of probe L1 as a biosensor in living cells (PC3 cells) towards Al3+ ions has also been demonstrated.

Multiplexed Nucleic Acid Hybridization Assays Using Single-FRET-Pair Distance-Tuning.

Multiplexed photoluminescence (PL) detection plays an important role in chemical and biological sensing. Here, it is shown that time-gated (TG) detection of a single terbium-donor-based Förster resonance energy transfer (FRET) pair can be used to selectively quantify low nanomolar concentrations of multiple DNAs or microRNAs in a single sample. This study demonstrates the applicability of single-TG-FRET-pair multiplexing for molecular (Tb-to-dye) and nanoparticle (Tb-to-quantum-dot) biosensing. Both systems use acceptor-sensitization and donor-quenching for quantifying biomolecular recognition and modification of the donor-acceptor distance for tuning the PL decays. TG intensity detection provides extremely low background noise and a quick and simple one-step assay format. Single-TG-FRET-pair multiplexing can be combined with spectral and spatial resolution, paving the way for biosensing with unprecedented high-order multiplexing capabilities.

A Rapid, Amplification-Free, and Sensitive Diagnostic Assay for Single-Step Multiplexed Fluorescence Detection of MicroRNA.

The importance of microRNA (miRNA) dysregulation for the development and progression of diseases and the discovery of stable miRNAs in peripheral blood have made these short-sequence nucleic acids next-generation biomarkers. Here we present a fully homogeneous multiplexed miRNA FRET assay that combines careful biophotonic design with various RNA hybridization and ligation steps. The single-step, single-temperature, and amplification-free assay provides a unique combination of performance parameters compared to state-of-the-art miRNA detection technologies. Precise multiplexed quantification of miRNA-20a, -20b, and -21 at concentrations between 0.05 and 0.5 nM in a single 150 µL sample and detection limits between 0.2 and 0.9 nM in 7.5 µL serum samples demonstrate the feasibility of both high-throughput and point-of-care clinical diagnostics.

Size-controlled construction of magnetic nanoparticle clusters using DNA-binding zinc finger protein.

Nanoparticle clusters (NPCs) have attracted significant interest owing to their unique characteristics arising from their collective individual properties. Nonetheless, the construction of NPCs in a structurally well-defined and size-controllable manner remains a challenge. Here we demonstrate a strategy to construct size-controlled NPCs using the DNA-binding zinc finger (ZnF) protein. Biotinylated ZnF was conjugated to DNA templates with different lengths, followed by incubation with neutravidin-conjugated nanoparticles. The sequence specificity of ZnF and programmable DNA templates enabled a size-controlled construction of NPCs, resulting in a homogeneous size distribution. We demonstrated the utility of magnetic NPCs by showing a three-fold increase in the spin-spin relaxivity in MRI compared with Feridex. Furthermore, folate-conjugated magnetic NPCs exhibited a specific targeting ability for HeLa cells. The present approach can be applicable to other nanoparticles, finding wide applications in many areas such as disease diagnosis, imaging, and delivery of drugs and genes.

Nanobodies and nanocrystals: highly sensitive quantum dot-based homogeneous FRET immunoassay for serum-based EGFR detection.

Semiconductor quantum dot nanocrystals (QDs) for optical biosensing applications often contain thick polyethylene glycol (PEG)-based coatings in order to retain the advantageous QD properties in biological media such as blood, serum or plasma. On the other hand, the application of QDs in Förster resonance energy transfer (FRET) immunoassays, one of the most sensitive and most common fluorescence-based techniques for non-competitive homogeneous biomarker diagnostics, is limited by such thick coatings due to the increased donor-acceptor distance. In particular, the combination with large IgG antibodies usually leads to distances well beyond the common FRET range of approximately 1 to 10 nm. Herein, time-gated detection of Tb-to-QD FRET for background suppression and an increased FRET range is combined with single domain antibodies (or nanobodies) for a reduced distance in order to realize highly sensitive QD-based FRET immunoassays. The "(nano)(2) " immunoassay (combination of nanocrystals and nanobodies) is performed on a commercial clinical fluorescence plate reader and provides sub-nanomolar (few ng/mL) detection limits of soluble epidermal growth factor receptor (EGFR) in 50 µL buffer or serum samples. Apart from the first demonstration of using nanobodies for FRET-based immunoassays, the extremely low and clinically relevant detection limits of EGFR demonstrate the direct applicability of the (nano)(2-) assay to fast and sensitive biomarker detection in clinical diagnostics.

Quantum-dot-basedFörster resonance energy transfer immunoassay for sensitive clinical diagnostics of low-volume serum samples.

A myriad of quantum dot (QD) biosensor examples have emerged from the literature over the past decade, but despite their photophysical advantages, QDs have yet to find acceptance as standard fluorescent reagents in clinical diagnostics. Lack of reproducible, stable, and robust immunoassays using easily prepared QD-antibody conjugates has historically plagued this field, preventing researchers from advancing the deeper issues concerning assay sensitivity and clinically relevant detection limits on low-volume serum samples. Here we demonstrate a ratiometric multiplexable FRET immunoassay using Tb donors and QD acceptors, which overcomes all the aforementioned limitations toward application in clinical diagnostics. We demonstrate the determination of prostate specific antigen (PSA) in 50 µL serum samples with subnanomolar (1.6 ng/mL) detection limits using time-gated detection and two different QD colors. This concentration is well below the clinical cutoff value of PSA, which demonstrates the possibility of direct integration into real-life in vitro diagnostics. The application of IgG, F(ab')2, and F(ab) antibodies makes our homogeneous immunoassay highly flexible and ready-to-use for the sensitive and specific homogeneous detection of many different biomarkers.

Semiconductor quantum dots for in vitro diagnostics and cellular imaging.

The need for companion diagnostics, point-of-care testing (POCT) and high-throughput screening in clinical diagnostics and personalized medicine has pushed the need for more biological information from a single sample at extremely low concentrations and volumes. Optical biosensors based on semiconductor quantum dots (QDs) can answer these requirements because their unique photophysical properties are ideally suited for highly sensitive multiplexed detection. Many different biological systems have been successfully scrutinized with a large variety of QDs over the past decade but their future as widely applied commercial biosensors is still open. In this review, we highlight recent in vitro diagnostic and cellular imaging applications of QDs and discuss milestones and obstacles on their way toward integration into real-life diagnostic and medical applications.

Controlled and oriented immobilization of protein by site-specific incorporation of unnatural amino acid.

Immobilization of proteins in a functionally active form and proper orientation is crucial for effective surface-based analysis of proteins. Here we present a general method for controlled and oriented immobilization of protein by site-specific incorporation of unnatural amino acid and click chemistry. The utility and potential of this method was demonstrated by applying it to the analysis of interaction between a pathogenic protein DrrA of Legionella pneumophila and its binding partner Rab1 of human. Kinetic analysis of Rab1 binding onto the DrrA-immobilized surfaces using surface plasmon resonance revealed that immobilization of site-specifically biotinylated DrrA results in about 10-fold higher sensitivity in binding assay than the conventional immobilization of DrrA with random orientation. The present method is expected to find wide applications in the fields of the surface-based studies of protein-protein (or ligand) interactions, drug screening, biochip, and single molecule analysis.

Sensitive and high-fidelity electrochemical immunoassay using carbon nanotubes coated with enzymes and magnetic nanoparticles.

We demonstrate a highly sensitive electrochemical immunosensor based on the combined use of substrate recycling and carbon nanotubes (CNTs) coated with tyrosinase (TYR) and magnetic nanoparticles (MNP). Both TYR and MNP were immobilized on the surface of CNTs by covalent attachment, followed by additional cross-linking via glutaraldehyde treatment to construct multi-layered cross-linked TYR-MNP aggregates (M-EC-CNT). Magnetically capturable, highly active and stable M-EC-CNT were further conjugated with primary antibody against a target analyte of hIgG, and used for a sandwich-type immunoassay with a secondary antibody conjugated with alkaline phosphatase (ALP). In the presence of a target analyte, a sensing assembly of M-EC-CNT and ALP-conjugated antibody was attracted onto a gold electrode using a magnet. On an electrode, ALP-catalyzed hydrolysis of phenyl phosphate generated phenol, and successive TYR-catalyzed oxidation of phenol produced electrochemically measurable o-quinone that was converted to catechol in a scheme of substrate recycling. Combination of highly active M-EC-CNT and substrate recycling for the detection of hIgG resulted in a sensitivity of 27.6 nA ng(-1) mL(-1) and a detection limit of 0.19 ng mL(-1) (1.2 pM), respectively, representing better performance than any other electrochemical immunosensors relying on the substrate recycling with the TYR-ALP combination. The present immunosensing system also displayed a long-term stability by showing a negligible loss of electrochemical detection signal even after reagents were stored in an aqueous buffer at 4°C for more than 6 months.