Ratiometric optical probes for biosensing

Biosensing by optical probes is bringing about a revolution in our understanding of physiological and pathological states. Conventional optical probes for biosensing are prone to inaccurate detection results due to various analyte-independent factors that can lead to fluctuations in the absolute signal intensity. Ratiometric optical probes provide built-in self-calibration signal correction for more sensitive and reliable detection. Probes specifically developed for ratiometric optical detection have been shown to significantly improve the sensitivity and accuracy of biosensing. In this review, we focus on the advancements and sensing mechanism of ratiometric optical probes including photoacoustic (PA) probes, fluorescence (FL) probes, bioluminescence (BL) probes, chemiluminescence (CL) probes and afterglow probes. The versatile design strategies of these ratiometric optical probes are discussed along with a broad range of applications for biosensing such as sensing of pH, enzymes, reactive oxygen species (ROS), reactive nitrogen species (RNS), glutathione (GSH), metal ions, gas molecules and hypoxia factors, as well as the fluorescence resonance energy transfer (FRET)-based ratiometric probes for immunoassay biosensing. Finally, challenges and perspectives are discussed.

Nanoparticle-Based Liquid-Liquid Extraction for the Determination of Metal Ions

Traditional liquid phase extraction techniques that use optically responsive ligands provide benefits that enable cost-efficient and rapid measurements. However, these approaches have limitations in their excessive use of organic solvents and multistep procedures. Here, we developed a simple, nanoscale extraction approach by replacing the macroscopic organic phase with hydrophobic polymeric nanoparticles that are dispersed in an aqueous feed. The concentration of analytes in polymeric nanoparticle suspensions is governed by similar partition principles to liquid-liquid phase extraction techniques. By encasing optically responsive metal ligands inside polymeric nanoparticles, we introduce a one-step metal quantification assay based on traditional two-phase extraction methodologies. As an initial proof of concept, we encapsulated bathophenanthroline (BP) inside the particles to extract then quantify Fe2+ with colorimetry in a dissolved supplement tablet and creek water. These Fe2+ nanosensors are sensitive and selective and report out with fluorescence by adding a fluorophore (DiO) into the particle core. To show that this new rapid extraction assay is not exclusive to measuring Fe2+, we replaced BP with either 8-hydroxyquinoline or bathocuproine to measure Al3+ or Cu+, respectively, in water samples. Utilizing this nanoscale extraction approach will allow users to rapidly quantify metals of interest without the drawbacks of larger-scale phase extraction approaches while also allowing for the expansion of phase extraction methodologies into areas of biological research.

Recent Advances in Biomedical Photonic Sensors: A Focus on Optical-Fibre-Based Sensing

In this invited review, we provide an overview of the recent advances in biomedical photonic sensors within the last five years. This review is focused on works using optical-fibre technology, employing diverse optical fibres, sensing techniques, and configurations applied in several medical fields. We identified technical innovations and advancements with increased implementations of optical-fibre sensors, multiparameter sensors, and control systems in real applications. Examples of outstanding optical-fibre sensor performances for physical and biochemical parameters are covered, including diverse sensing strategies and fibre-optical probes for integration into medical instruments such as catheters, needles, or endoscopes.

Iron Oxide-Based Magneto-Optical Nanocomposites for In Vivo Biomedical Applications

Iron oxide nanoparticles (IONPs) have played a pivotal role in the development of nanomedicine owing to their versatile functions at the nanoscale, which facilitates targeted delivery, high contrast imaging, and on-demand therapy. Some biomedical inadequacies of IONPs on their own, such as the poor resolution of IONP-based Magnetic Resonance Imaging (MRI), can be overcome by co-incorporating optical probes onto them, which can be either molecule- or nanoparticulate-based. Optical probe incorporated IONPs, together with two prominent non-ionizing radiation sources (i.e., magnetic field and light), enable a myriad of biomedical applications from early detection to targeted treatment of various diseases. In this context, many research articles are in the public domain on magneto-optical nanoparticles; discussed in detail are fabrication strategies for their application in the biomedical field; however, lacking is a comprehensive review on real-life applications in vivo, their toxicity, and the prospect of bench-to-bedside clinical studies. Therefore, in this review, we focused on selecting such important nanocomposites where IONPs become the magnetic component, conjugated with various types of optical probes; we clearly classified them into class 1 to class 6 categories and present only in vivo studies. In addition, we briefly discuss the potential toxicity of such nanocomposites and their respective challenges for clinical translations.

Assessing The Key Photophysical Properties of Triangulenium Dyes for DNA Binding by Alteration of the Fluorescent Core

Four-stranded G-quadruplex (G4) DNA is a non-canonical DNA topology that has been proposed to form in cells and play key roles in how the genome is read and used by the cellular machinery. Previously, a fluorescent triangulenium probe (DAOTA-M2) was used to visualise G4s in cellulo, thanks to its distinct fluorescence lifetimes when bound to different DNA topologies. Herein, the library of available triangulenium probes is expanded to explore how modifications to the fluorescent core of the molecule affect its photophysical characteristics, interaction with DNA and cellular localisation. The benzo-bridged and isopropyl-bridged diazatriangulenium dyes, BDATA-M2 and CDATA-M2 respectively, featuring ethyl-morpholino substituents, were synthesised and characterised. The interactions of these molecules with different DNA topologies were studied to determine their binding affinity, fluorescence enhancement and fluorescence lifetime response. Finally, the cellular uptake and localisation of these optical probes were investigated. Whilst structural modifications to the triangulenium core only slightly alter the binding affinity to DNA, BDATA-M2 and CDATA-M2 cannot distinguish between DNA topologies through their fluorescence lifetime. It is argued theoretically and experimentally that this is due to reduced effectiveness of photoinduced electron transfer (PET) quenching. This work presents valuable new evidence into the critical role of PET quenching when using the fluorescence lifetime of triangulenium dyes to discriminate G4 DNA from duplex DNA, highlighting the importance of fine tuning redox and spectral properties when developing new triangulenium-based G4 probes.

Site-Specific Incorporation of a Photoactivatable Fluorescent Amino Acid

Photoactivatable fluorophores are emerging optical probes for biological applications. Most photoactivatable fluorophores are relatively large in size and need to be activated by ultraviolet light; this dramatically limits their applications. To introduce photoactivatable fluorophores into proteins, recent investigations have explored several protein-labeling technologies, including fluorescein arsenical hairpin (FlAsH) Tag, HaloTag labeling, SNAPTag labeling, and other bioorthogonal chemistry-based methods. However, these technologies require a multistep labeling process. Here, by using genetic code expansion and a single sulfur-for-oxygen atom replacement within an existing fluorescent amino acid, we have site-specifically incorporated the photoactivatable fluorescent amino acid thioacridonylalanine (SAcd) into proteins in a single step. Moreover, upon exposure to visible light, SAcd can be efficiently desulfurized to its oxo derivatives, thus restoring the strong fluorescence of labeled proteins.

Fluoro-Photoacoustic Polymeric Renal Reporter for Real-Time Dual Imaging of Acute Kidney Injury

Photoacoustic (PA) imaging agents detect disease tissues and biomarkers with increased penetration depth and enhanced spatial resolution relative to traditional optical imaging, and thus hold great promise for clinical applications. However, existing PA imaging agents often encounter the issues of slow body excretion and low-signal specificity, which compromise their capability for in vivo detection. Herein, a fluoro-photoacoustic polymeric renal reporter (FPRR) is synthesized for real-time imaging of drug-induced acute kidney injury (AKI). FPRR simultaneously turns on both near-infrared fluorescence (NIRF) and PA signals in response to an AKI biomarker (γ-glutamyl transferase) with high sensitivity and specificity. In association with its high renal clearance efficiency (78% at 24 h post-injection), FPRR can detect cisplatin-induced AKI at 24 h post-drug treatment through both real-time imaging and optical urinalysis, which is 48 h earlier than serum biomarker elevation and histological changes. More importantly, the deep-tissue penetration capability of PA imaging results in a signal-to-background ratio that is 2.3-fold higher than NIRF imaging. Thus, the study not only demonstrates the first activatable PA probe for real-time sensitive imaging of kidney function at molecular level, but also highlights the polymeric probe structure with high renal clearance.

Microwave-Assisted Synthesis and Characterization of Poly(L-lysine)-Based Polymer/Carbon Quantum Dot Nanomaterials for Biomedical Purposes

Carbon nanomaterials in the form of quantum dots have a high potential due to their luminescent properties and low cytotoxicity which allows their use in optical probes for use in bioimaging and biodetection. In this article, we present a novel type of nanomaterials and their obtainment method under microwave-assisted conditions using poly(L-lysine) as a raw material. The ready products were characterized over their chemical structure, pH-dependent fluorescence properties and cytotoxicity on human dermal fibroblasts. Moreover, their antioxidant activity as well as ability to biologically active molecules (vitamins) and heavy metal ions detection was evaluated. The results confirmed the obtainment of biocompatible nanomaterials with advanced properties and good water solubility according to sustained development principles.

Hyaluronic Acid-Based Optical Probe for the Diagnosis of Human Osteoarthritic Cartilage

Osteoarthritis is typically caused by cartilage injury, followed by localized inflammatory responses and tissue deterioration. Early treatment of osteoarthritis is often impossible due to the lack of diagnostic options. Recent studies have supported that different imaging probes can be used for arthritis detection in mice. However, none of these diagnostic tools have been tested on human articular cartilage. To fill this gap, an optical imaging probe was developed to target activated macrophages and the accumulation of imaging probes on tissue was used to assess the severity of human osteoarthritis. Methods: The probe was fabricated using hyaluronic acid (HA) particles conjugated with near-infrared dye and folic acid (FA). The ability of the FA-HA probes to detect activated macrophages and quantify cartilage injury was evaluated using a cell culture model in vitro and human osteoarthritic cartilage explants ex vivo. Results: Our cell study results supported that the FA-HA probes are cell compatible (up to 0.5mg/mL) and can detect activated macrophages in 30 minutes. Using human articular cartilage, we verified the existence of activated macrophages on osteoarthritic cartilage with highly up-regulated expression of folate receptors (~13 folds by comparison with healthy control). In addition, we found that FA-HA probes had higher binding amounts (~3 folds) to osteoarthritic tissue than healthy ones. Histological analyses confirmed that there was a strong linear relationship (R=0.933) between the fluorescent intensity of tissue-associated probe and the extent of folate receptors on osteoarthritic cartilage. Finally, the co-localization of the imaging probe, folate receptors and cartilage degeneration on the tissue sections indicated the extraordinary accuracy and efficiency of this osteoarthritis diagnostic probe. Conclusions: Our results support the probe as an effective diagnostic tool to detect the area and severity of osteoarthritic human articular cartilage.

Development of novel long noncoding RNA MALAT1 near-infrared optical probes for in vivo tumour imaging

With the advent of next-generation sequencing technology, there is rapidly increasing interest in long noncoding RNAs (lncRNAs). The objectives of this study were to develop a novel lncRNA MALAT1 near-infrared optical probe, to evaluate the characteristics of this optical imaging probe in vitro and to determine whether it can be used for imaging MALAT1 expression in malignant tumours in vivo. Conjugation of Cy5.5 to MALAT1 ASO was accomplished using standard NHS (N-hydroxysuccinimide) ester procedures, and the labelled MALAT1 ASO was purified with a Glen-Pak DNA Purification Cartridge and reversed-phase high performance liquid chromatography (HPLC). The in vitro cellular uptake results showed that the percentage of cell binding increased with an increasing final concentration and increased with increasing incubation time for the MHCC-LM3 tumour cell flow cytometry analyses. in vivo optical imaging exhibited 5' (Cy5.5)-MALAT1 ASO uptake in the tumour with a maximum at 30 min p.i. that slowly washed out over time. High contrast to normal tissue was gradually observed from 4 h to 48 h p.i. Tumour-to-normal ratios of fluorescence intensities were plotted as a function of time. The in vivo competition assay showed little uptake of the probe into the tumours at any time point, indicating effective competition, selectivity of probe binding and retention by tumours in vivo. Our proposed Cy5.5 labelling of MALAT1 ASO can serve as a potent optical probe for in vivo imaging of tumour expressing MALAT1. Importantly, the successful development of optical probes provides a basis for specific molecular diagnoses in the field of lncRNAs.

NMR Structure of a Triangulenium-Based Long-Lived Fluorescence Probe Bound to a G-Quadruplex

An NMR structural study of the interaction between a small-molecule optical probe (DAOTA-M2) and a G-quadruplex from the promoter region of the c-myc oncogene revealed that they interact at 1:2 binding stoichiometry. NMR-restrained structural calculations show that binding of DAOTA-M2 occurs mainly through π-π stacking between the polyaromatic core of the ligand and guanine residues of the outer G-quartets. Interestingly, the binding affinities of DAOTA-M2 differ by a factor of two for the outer G-quartets of the unimolecular parallel G-quadruplex under study. Unrestrained MD calculations indicate that DAOTA-M2 displays significant dynamic behavior when stacked on a G-quartet plane. These studies provide molecular guidelines for the design of triangulenium derivatives that can be used as optical probes for G-quadruplexes.

Trianguleniums as Optical Probes for G-Quadruplexes: A Photophysical, Electrochemical, and Computational Study

Nucleic acids can adopt non-duplex topologies, such as G-quadruplexes in vitro. Yet it has been challenging to establish their existence and function in vivo due to a lack of suitable tools. Recently, we identified the triangulenium compound DAOTA-M2 as a unique fluorescence probe for such studies. This probe's emission lifetime is highly dependent on the topology of the DNA it interacts with opening up the possibility of carrying out live-cell imaging studies. Herein, we describe the origin of its fluorescence selectivity for G-quadruplexes. Cyclic voltammetry predicts that the appended morpholino groups can act as intra- molecular photo-induced electron transfer (PET) quenchers. Photophysical studies show that a delicate balance between this effect and inter-molecular PET with nucleobases is key to the overall fluorescence enhancement observed upon nucleic acid binding. We utilised computational modelling to demonstrate a conformational dependence of intra-molecular PET. Finally, we performed orthogonal studies with a triangulenium compound, in which the morpholino groups were removed, and demonstrated that this change inverts triangulenium fluorescence selectivity from G-quadruplex to duplex DNA, thus highlighting the importance of fine tuning the molecular structure not only for target affinity, but also for fluorescence response.

Imaging chemical neurotransmission with genetically encoded fluorescent sensors

A major challenge in neuroscience is to decipher the logic of neural circuitry and to link it to learning, memory, and behavior. Synaptic transmission is a critical event underlying information processing within neural circuitry. In the extracellular space, the concentrations and distributions of excitatory, inhibitory, and modulatory neurotransmitters impact signal integration, which in turn shapes and refines the function of neural networks. Thus, the determination of the spatiotemporal relationships between these chemical signals with synaptic resolution in the intact brain is essential to decipher the codes for transferring information across circuitry and systems. Here, we review approaches and probes that have been employed to determine the spatial and temporal extent of neurotransmitter dynamics in the brain. We specifically focus on the design, screening, characterization, and application of genetically encoded indicators directly probing glutamate, the most abundant excitatory neurotransmitter. These indicators provide synaptic resolution of glutamate dynamics with cell-type specificity. We also discuss strategies for developing a suite of genetically encoded probes for a variety of neurotransmitters and neuromodulators.

Real-time noninvasive monitoring of in vivo inflammatory responses using a pH ratiometric fluorescence imaging probe

It is often difficult to continuously monitor and quantify inflammatory responses in vivo. These dynamic responses however are often accompanied by specific pH changes. A new ratiometric optical pH probe is developed by combining pH-sensitive (CypHer5E) and pH-insensitive (Oyster800) fluorescent dyes into nanoparticles for in vivo optical imaging. By taking the ratio of fluorescence intensities at different wavelengths, these nanosized sensors provide excellent measurement capabilities, and unique mapping, of the continuous in vivo pH changes for three different inflammation models. In each model a strong positive correlation is found between ratiometric pH changes and the corresponding inflammatory response measured by histological analyses. These results indicate that ratiometric imaging can provide a noninvasive, rapid, and highly sensitive optical readout for the pH-ratio changes in vivo. Furthermore this technique may be used to monitor the real-time dynamics of inflammatory processes.

Application of FRET probes in the analysis of neuronal plasticity

Breakthroughs in imaging techniques and optical probes in recent years have revolutionized the field of life sciences in ways that traditional methods could never match. The spatial and temporal regulation of molecular events can now be studied with great precision. There have been several key discoveries that have made this possible. Since green fluorescent protein (GFP) was cloned in 1992, it has become the dominant tracer of proteins in living cells. Then the evolution of color variants of GFP opened the door to the application of Förster resonance energy transfer (FRET), which is now widely recognized as a powerful tool to study complicated signal transduction events and interactions between molecules. Employment of fluorescent lifetime imaging microscopy (FLIM) allows the precise detection of FRET in small subcellular structures such as dendritic spines. In this review, we provide an overview of the basic and practical aspects of FRET imaging and discuss how different FRET probes have revealed insights into the molecular mechanisms of synaptic plasticity and enabled visualization of neuronal network activity both in vitro and in vivo.

An optical probe possessing upconversion luminescence and Hg(2+)-sensing properties

A Hg(2+)-selective chromophoric upconversion nanosystem is achieved by covalently grafting Rhodamine B hydrazide (RB-hydrazide) onto upconversion luminescent nanorod core-shell structures. The prepared β-NaYF4 nanorods are coated with silica and characterized by X-ray diffraction (XRD), transmission electron microscopy (TEM), scanning electron microscopy (SEM), energy-dispersive X-ray analysis (EDAX), Fourier-transform infrared spectroscopy (FTIR), and photoluminescence spectra. Under 980 nm excitation, the upconversion luminescence is sensitive towards Hg(2+) because RB-hydrazide-Hg can efficiently absorb green upconversion emission. The prepared nanocomposites exhibit high sensitivity and selectivity towards Hg(2+) over other metal ions. These results indicate that this nanosystem could be developed as a promising fluorescence probe for detecting Hg(2+) ions.

Molecular imaging probe development: a chemistry perspective

Molecular imaging is an attractive modality that has been widely employed in many aspects of biomedical research; especially those aimed at the early detection of diseases such as cancer, inflammation and neurodegenerative disorders. The field emerged in response to a new research paradigm in healthcare that seeks to integrate detection capabilities for the prediction and prevention of diseases. This approach made a distinct impact in biomedical research as it enabled researchers to leverage the capabilities of molecular imaging probes to visualize a targeted molecular event non-invasively, repeatedly and continuously in a living system. In addition, since such probes are inherently compact, robust, and amenable to high-throughput production, these probes could potentially facilitate screening of preclinical drug discovery, therapeutic assessment and validation of disease biomarkers. They could also be useful in drug discovery and safety evaluations. In this review, major trends in the chemical synthesis and development of positron emission tomography (PET), optical and magnetic resonance imaging (MRI) probes are discussed.

Exploration of fluorescent protein voltage probes based on circularly permuted fluorescent proteins

Genetically encoded fluorescent protein (FP) voltage sensors are promising tools for optical monitoring of the electrical activity of cells. Over the last decade, several designs of fusion proteins have been explored and some of them have proven to be sensitive enough to record membrane voltage transients from single mammalian cells. Most prominent are the families of voltage sensitive fluorescent proteins (VSFPs) that utilize the voltage sensor domain (VSD) of Ciona intestinalis voltage sensor-containing phosphatase (Ci-VSP). The voltage sensitivity of the fluorescence readout of these previously reported membrane potential indicators is achieved either via a change in the efficiency of fluorescence resonance energy transfer between two FP spectral variants or via modulation in the fluorescence intensity of a single FP. Here, we report our exploration on a third VSFP design principle based on circularly permuted fluorescent protein (cpFP) variants. Using circularly permuted EGFP derived from GCaMP2 and two newly generated circularly permuted variants of the far-red emitting protein named mKate, we generated and characterized a series of voltage-sensitive probes wherein the cpFPs were fused to the VSD of Ci-VSP. The most promising variants were based on circularly permuted mKate with new N- and C-termini given by residues 180 and 182. Even so their voltage sensitivity was relatively modest, they constitute a proof of principle for this novel protein design.

Clathrin-mediated endocytosis near active zones in snake motor boutons

We have used the activity-dependent probe FM1-43 with electron microscopy (EM) to examine endocytosis at the vertebrate nerve-muscle synapse. Preparations were fixed after very brief neural stimulation at reduced temperature, and internalized FM1-43 was photoconverted into an electron-dense reaction product. To locate the reaction product, we reconstructed computer renderings of individual terminal boutons from serial EM sections. Most of the reaction product was seen in 40-60 nm vesicles. All of the labeled vesicles were clathrin-coated, and 92% of them were located within 300 nm of the plasma membrane, suggesting that they had undergone little processing after retrieval from their endocytic sites. The vesicles (and by inference the sites) were not dispersed randomly near the plane of the membrane but instead were clustered significantly near active zones. Additional reaction product was found within putative macropinosomes; these appeared to form from deep membrane invaginations near active zones. Thus two mechanisms of endocytosis were evident after brief stimulation. Endocytosis near active zones is consistent with the existence of local exo/endocytic cycling pools. This mechanism also might serve to maintain alignment of active zones with postsynaptic folds during periods of activity when vesicular and plasma membranes are interchanged.

Endocytic active zones: hot spots for endocytosis in vertebrate neuromuscular terminals

We have used a sensitive activity-dependent probe, sulforhodamine 101 (SR101), to view endocytic events within snake motor nerve terminals. After very brief neural stimulation at reduced temperature, SR101 is visualized exclusively at punctate sites located just inside the presynaptic membrane of each terminal bouton. The number of sites (approximately 26 sites/bouton) and their location (in register with postsynaptic folds) are similar to the number and location of active zones in snake motor terminals, suggesting a spatial association between exocytosis and endocytosis under these stimulus conditions. With more prolonged stimulation, larger SR101-containing structures appear at the bouton margins. Thus endocytosis occurs initially at distinct sites, which we call "endocytic active zones," whereas further stimulation recruits a second endocytic paradigm.