Visualization of nonengineered single mRNAs in living cells using genetically encoded fluorescent probes

Single mRNA imaging in live cells is a useful technique to elucidate its precise localization and dynamics. We developed a method for visualizing endogenous mRNAs in living cells with single molecule sensitivity using genetically encoded probes. An RNA-binding protein of human PUMILIO1 (PUM-HD) was used for recognizing base sequences of a target mRNA, β-actin mRNA. Two PUM-HDs were modified by amino acid mutations to bind specifically to tandem 8-base sequences of the target mRNA. Because each PUM-HD was connected with amino- and carboxyl-terminal fragments of enhanced green fluorescent protein (EGFP), the probes emit fluorescence by reconstitution of EGFP fragments upon binding to β-actin mRNAs. The EGFP reconstituted on the mRNAs was monitored with a total internal reflection fluorescence microscope. Results show that each fluorescent spot in live cells represented a single β-actin mRNA and that distinct spatial and temporal movement of the individual β-actin mRNAs was visualized. We also estimated the average velocity of the movement of the single mRNAs along microtubules in live cells. This method is widely applicable to tracking various mRNAs of interest in the native state of living cells with single-mRNA sensitivity.     

Genetically encoded fluorescent indicators to visualize protein phosphorylation by extracellular signal-regulated kinase in single living cells

Extracellular signal-regulated kinase (ERK) is a serine/threonine protein kinase that regulates a wide variety of cell functions, such as cell growth and differentiation. To study the spatiotemporal dynamics of protein phosphor-ylation by activated ERK in living cells, we have developed genetically encoded fluorescent indicators for ERK. The present indicators are based on fluorescence resonance energy transfer (FRET) between two green fluorescent protein mutants. Phosphorylation of the indicators by activated ERK changes the FRET efficiency due to their conformational alterations. We visualized the cytosolic and nuclear activity of ERK using the present indicators. We thus found that the activation duration of ERK is considerably different between the cytosol and nucleus in living cells. The subcellular difference in the ERK activity may be fundamental to the regulation of cell functions by ERK. The present fluorescent indicators provide a powerful tool to reveal the spatiotemporal dynamics of protein phosphorylation by ERK in single living cells.     

Genetically encoded stress indicator for noninvasively imaging endogenous corticosterone in living mice

Physical and emotional stress is one of the major controllers of physiological reactions and homeostasis in living animals. A stress hormone, corticosterone, is secreted from the adrenal cortex into the blood vessels when animals sense the stress. The quantitative evaluation of corticosterone in living animals has been limited because of the unavailability of suitable methods in vivo. For a noninvasive molecular imaging of the stress, we developed a method for detecting physiological increases in the endogenous corticosterone caused by exo- and endogenous stress in living animals. We constructed a pair of genetically encoded indicators composed of cDNAs of glucocorticoid receptor (GR), split Renilla luciferase (RLuc), and a Synechocystis sp. DnaE intein. The GR fused with C-terminal halves of RLuc and DnaE is localized in the cytosol, whereas a fusion protein of N-terminal halves of RLuc and DnaE is localized in the nucleus. If corticosterone induces GR translocation into the nucleus, the C-terminal RLuc meets the N-terminal one in the nucleus, and full-length RLuc is reconstituted by protein splicing with DnaE. Cell-based methods provided a quantitative bioluminescence assay of the extent of GR translocation into the nucleus. We further demonstrated that the indicator enabled noninvasive imaging against two different types of imposed stress: a forced swimming and metabolic perturbation caused by 2-deoxy-D-glucose. This stress indicator should be valuable for screening pharmacological compounds and for tools to study the mechanism of physiological stress.     

Monitoring of chloride and activity of glycine receptor channels using genetically encoded fluorescent sensors

Genetically encoded probes have become powerful tools for non-invasive monitoring of ions, distributions of proteins and the migration and formation of cellular components. We describe the functional expression of two molecular probes for non-invasive fluorescent monitoring of intracellular Cl ([Cl]i) and the functioning of glycine receptor (GlyR) channels. The first probe is a recently developed cyan fluorescent protein-yellow fluorescent protein-based construct, termed Cl-Sensor, with relatively high sensitivity to Cl (Kapp approximately 30mM). In this study, we describe its expression in retina cells using in vivo electroporation and analyse changes in [Cl]i at depolarization and during the first three weeks of post-natal development. An application of 40mM K+ causes an elevation in [Cl]i of approximately 40mM. In photoreceptors from retina slices of a 6-day-old rat (P6 rat), the mean [Cl]i is approximately 50mM, and for P16 and P21 rats it is approximately 30-35mM. The second construct, termed BioSensor-GlyR, is a GlyR channel with Cl-Sensor incorporated into the cytoplasmic domain. This is the first molecular probe for spectroscopic monitoring of the functioning of receptor-operated channels. These types of probes offer a means of screening pharmacological agents and monitoring Cl under different physiological and pathological conditions and permit spectroscopic monitoring of the activity of GlyRs expressed in heterologous systems and neurons.     

Locating inositol 1,4,5-trisphosphate in the nucleus and neuronal dendrites with genetically encoded fluorescent indicators

Inositol 1,4,5-trisphosphate (InsP3) is a key second messenger in many cell types and also in distinct subcellular regions of single living cells; however, little is examined about the subcellular dynamics of InsP3 in a variety of cell types. We have developed fluorescent indicators to locate InsP3 dynamics in single living cells based on an intramolecular fluorescence resonance energy transfer. Our indicator has visualized InsP3 dynamics in the cytoplasm of cultured cells and even in single thin dendrites of hippocampal neurons, which has been unseen previously. We have further localized the present indicator in the nucleus and pinpointed nuclear InsP3 dynamics. The observation with our nuclear InsP3 indicator has solved a question on nuclear propagation of InsP3 from the cytoplasm and has drawn a conclusion that the nuclear InsP3 dynamics synchronously occurs with cytosolic InsP3 dynamics evoked by agonist stimulations. The present approach contributes to the understanding of when, where, and how InsP3 is generated and removed in a variety of living cells.     

Cell-based indicator to visualize picomolar dynamics of nitric oxide release from living cells

We report a novel cell-based indicator that is able to visualize picomolar dynamics of nitric oxide release from living cells. Cells from a pig kidney-derived cell line (PK15) endogenously express soluble guanylate cyclase (sGC), which is a receptor protein for the selective recognition of NO. Binding of NO by sGC causes the amplified generation of guanosine 3',5'-cyclic monophosphate (cGMP). To make the PK15 cells into NO indicators, the cells are transfected with a plasmid vector encoding a fluorescent indicator for cGMP and fluorescence resonance energy transfer is recorded at 480 +/- 15 and 535 +/- 12.5 nm upon excitation of the cells at 440 +/- 10 nm. The cell-based indicator exhibits exceptional sensitivity (detection limit of 20 pM), selectivity, reversibility, and reproducibility. The outstanding sensitivity of the present indicator has led us to uncover an oscillatory release of picomolar concentrations of NO from hippocampal neurons. We present evidence that Ca2+ oscillations in hippocampal neurons underlie the oscillatory NO release from the neurons during neurotransmission. We also have succeeded in visualizing the extent of diffusing NO from single vascular endothelial cells. The present cell-based indicator provides a powerful tool to uncover picomolar dynamics of NO that regulates a wide range of cell functions in biological systems.     

Genetically encoded optical probe for detecting release of proteins from mitochondria toward cytosol in living cells and mammals

We developed a genetically encoded bioluminescence indicator for monitoring the release of proteins from the mitochondria in living cells. The principle of this method is based on reconstitution of split Renilla reniformis luciferase (Rluc) fragments by protein splicing with an Ssp DnaE intein. A target mitochondrial protein connected with an N-terminal fragment of Rluc and an N-terminal fragment of DnaE is expressed in mammalian cells. If the target protein is released from the mitochondria toward the cytosol upon stimulation with a specific chemical, the N-terminal Rluc meets the C-terminal Rluc connected with C-terminal DnaE in the cytosol, and thereby, the full-length Rluc is reconstituted by protein splicing. The extent of release of the target fusion protein is evaluated by measuring activities of the reconstituted Rluc. To test the feasibility of this method, here we monitored the release of Smac/DIABLO protein from mitochondria during apoptosis in living cells and mice. The present method allowed high-throughput screening of an apoptosis-inducing reagent, staurosporine, and imaging of the Smac/DIABLO release in cells and in living mice. This rapid analysis can be used for screening and assaying chemicals that would increase or inhibit the release of mitochondrial proteins in living cells and animals.     

Quantum measurement and orientation tracking of fluorescent nanodiamonds inside living cells

Fluorescent particles are routinely used to probe biological processes. The quantum properties of single spins within fluorescent particles have been explored in the field of nanoscale magnetometry, but not yet in biological environments. Here, we demonstrate optically detected magnetic resonance of individual fluorescent nanodiamond nitrogen-vacancy centres inside living human HeLa cells, and measure their location, orientation, spin levels and spin coherence times with nanoscale precision. Quantum coherence was measured through Rabi and spin-echo sequences over long (>10 h) periods, and orientation was tracked with effective 1° angular precision over acquisition times of 89 ms. The quantum spin levels served as fingerprints, allowing individual centres with identical fluorescence to be identified and tracked simultaneously. Furthermore, monitoring decoherence rates in response to changes in the local environment may provide new information about intracellular processes. The experiments reported here demonstrate the viability of controlled single spin probes for nanomagnetometry in biological systems, opening up a host of new possibilities for quantum-based imaging in the life sciences.     

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

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

A novel clinically translatable fluorescent nanoparticle for targeted molecular imaging of tumors in living subjects

The use of quantum dots (QDs) in biomedical research has grown tremendously, yet successful examples of clinical applications are absent due to many clinical concerns. Here, we report on a new type of stable and biocompatible dendron-coated InP/ZnS core/shell QD as a clinically translatable nanoprobe for molecular imaging applications. The QDs (QD710-Dendron) were demonstrated to hold several significant features: near-infrared (NIR) emission, high stability in biological media, suitable size with possible renal clearance, and ability of extravasation. More importantly, a pilot mouse toxicity study confirmed that QD710-Dendron lacks significant toxicity at the doses tested. The acute tumor uptake of QD710-Dendron resulted in good contrast from the surrounding nontumorous tissues, indicating the possibility of passive targeting of the QDs. The highly specific targeting of QD710-Dendron-RGD(2) to integrin α(v)β(3)-positive tumor cells resulted in high tumor uptake and long retention of the nanoprobe at tumor sites. In summary, QD710-Dendron and RGD-modified nanoparticles demonstrate small size, high stability, biocompatibility, favorable in vivo pharmacokinetics, and successful tumor imaging properties. These features satisfy the requirements for clinical translation and should promote efforts to further investigate the possibility of using QD710-Dendron-based nanoprobes in the clinical setting in the near future.     

Digital switching of local arginine density in a genetically encoded self-assembled polypeptide nanoparticle controls cellular uptake

Cell-penetrating peptides (CPPs) are a class of molecules that enable efficient internalization of a wide variety of cargo in diverse cell types, making them desirable for delivery of anticancer drugs to solid tumors. For CPPs to be useful, it is important to be able to turn their function on in response to an external trigger that can be spatially localized in vivo. Here we describe an approach to turning on CPP function by modulation of the local density of arginine (Arg) residues by temperature-triggered micelle assembly of diblock copolymer elastin-like polypeptides (ELP(BC)s). A greater than 8-fold increase in cellular uptake occurs when Arg residues are presented on the corona of ELP(BC) micelles, as compared to the same ELP(BC) at a temperature in which it is a soluble unimer. This approach is the first to demonstrate digital 'off-on' control of CPP activity by an extrinsic thermal trigger in a clinically relevant temperature range by modulation of the interfacial density of Arg residues on the exterior of a nanoparticle.     

Highly sensitive fluorescent analysis of dynamic glycan expression on living cells using glyconanoparticles and functionalized quantum dots

A double signal amplification strategy was designed for highly sensitive and selective in situ monitoring of carbohydrate on living cells. The double signal amplification included the multiplex sandwich binding of functionalized quantum dots (QDs) to both glycan groups on the cell surface and glyconanoparticles and a cadmium cation sensitized fluorescence emission of Rhod-5N. Using the sialic acid-phenylboronic acid recognition system as a model, the 3-aminophenylboronic acid functionalized QDs (APBA-QDs) were synthesized by covalently binding APBA to mercaptopropionic acid capped CdS QDs, and the glyconanoparticles, polysialic acid stabilized gold nanoparticles (PSA-AuNPs), were prepared by a one-pot procedure. The APBA-QDs first recognized the sialic acid (SA) groups on BGC-823 human gastric carcinoma (BGC) cells and then the PSA on AuNPs, which were further used to bind more APBA-QDs on the cell surface for signal amplification. After the bound QDs were dissolved to release the Cd(2+), a Cd(2+)-sensitized fluorescence method was developed for the detection of BGC cells in a linear range from 5.0 × 10(2) to 1.0 × 10(7) cells mL(-1) with a limit of detection down to 210 cells mL(-1) (8 cells in 40 μL of solution) and the dynamic monitoring of SA expression variation on the cell surface. The monitoring result was identical with that from flow cytometric analysis. This approach showed high specificity and acceptable reproducibility. This strategy provided a promising platform for highly sensitive cytosensing and cytobiologic study.     

Subcellular tracking of drug release from carbon nanotube vehicles in living cells

The direct observation of drug release from carbon nanotube vehicles in living cells is realized through a unique two-dye labeling approach. Single-walled carbon nanotubes (SWNTs) are firstly marked with fluorescein isothiocyanate (FITC) to track their location and movement inside the cell. Then a fluorescent anticancer drug doxorubicin (DOX) is attached by means of π-stacking onto SWNTs. Delivered by SWNTs into cells, DOX will detach from the vehicle in an acidic environment due to the pH-dependent π-π stacking interaction between DOX and SWNTs. From observation of the two different kinds of fluorescence (green and red) that respectively represent the carrier SWNTs and drug DOX, the process of drug release inside the living cell can be monitored under a confocal microscope. Results show that the drug DOX detaches from SWNTs inside the lysosomes to yield free molecules and escape into the cytoplasm and finally into the nucleus, while the vehicle SWNTs are trapped inside the lysosomes, without entering the nucleus. The current observations confirm previously proposed mechanisms for drug/DOX release inside cells. The experimental establishment of drug-release mechanisms in living cells here might provide important insights for future design of new drug-delivery and release systems.     

Green fluorescent protein in the design of a living biosensing system for L-arabinose

Analysis of monosaccharides is typically performed using analytical systems that involve a separation step followed by a detection step. The separation step is usually necessary because of the high degree of structural similarity between different monosaccharides. A novel sensing system for monosaccharides is described here in which living bacteria were designed to detect a model monosaccharide, L-arabinose, without the need for a separation step. In such sensing systems, analytes are detected by employing the selective recognition properties found in certain bacterial proteins. These systems are designed so that a reporter protein is expressed by the bacteria in response to the analyte. The concentration of the analyte can be related to the signal generated by the reporter protein. In the sensing system described here, the green fluorescent protein (GFP) was used as the reporter protein. L-Arabinose concentrations can be determined by monitoring the fluorescence emitted by the bacteria at 509 nm after excitation of GFP at 395 nm. The system can detect L-arabinose at concentrations as low as 5 x 10(-7) M and is selective over D-arabinose, the stereoisomer of the analyte, as well as over a variety of pentose and hexose sugars.     

Charge-driven selective localization of fluorescent nanoparticles in live cells

Covalent grafting of amino groups onto the carboxylic acid functionalities, naturally covering the surface of fluorescent nanoparticles produced from silicon carbide (SiC NPs), allowed tuning of their surface charge from negative to highly positive. Incubating 3T3-L1 fibroblast cells with differently charged SiC NPs demonstrates the crucial role of the charge in cell fluorescent targeting. Negatively charged SiC NPs concentrate inside the cell nuclei. Close to neutrally charged SiC NPs are present in both cytoplasm and nuclei while positively charged SiC NPs are present only in the cytoplasm and are not able to move inside the nuclei. This effect opens the door for the use of SiC NPs for easy and fast visualization of long-lasting biological processes taking place in the cell cytosol or nucleus as well as providing a new long-term cell imaging tool. Moreover, here we have shown that the interaction between charged NPs and nuclear pore complex plays an essential role in their penetration into the nuclei.     

Particle tracking microrheology of cancer cells in living subjects

Cumulative evidence shows that microenvironmental conditions play a significant role in the regulation of cell functions, and how cells respond to these conditions are of central importance to regenerative medicine and cancer cell response to therapeutics. Here, we develop a new method to examine cell mechanical properties by analyzing the motion of nanoparticles in living in mice, combining particle tracking with intravital microscopy. This method directly examines the mechanical response of breast carcinoma cells and normal breast epithelial cells under intravital microenvironments. Our results show both carcinoma and normal cells display significantly reduced compliance (less deformability) in vivo compared to the same cells cultured in 2D, in both sparse and confluent conditions. While the compliance of the normal cells remains steady over time, the compliance of carcinoma cells decreases further as they form tumor-like architectures. Integrating the cancer cells into spheroids embedded in 3D collagen matrices in part redirected the mechanical response to a state closer to the in vivo setting. Overall, our study demonstrates that the microenvironment is a crucial regulator of cell mechanics and the intravital particle tracking method can provide novel insights into the role of cell mechanics in vivo.     

Serial immunoassays in parallel on a microfluidic chip for monitoring hormone secretion from living cells

A microfluidic chip that allows for the continuous monitoring of cellular secretions from multiple independent living samples was developed. Performance of the device was characterized through the analysis of insulin secretion from islets of Langerhans. The chip contained four individual channel networks, each capable of performing electrophoresis-based immunoassays of the perfusate from islets. In the networks, islets were housed in a chamber that was continuously perfused with pressure-driven biological media at 0.6 microL min-1. Electroosmosis was used to pull perfusate containing secreted insulin into 4-cm-long reaction channels where it mixed with fluorescein isothiocyanate-labeled insulin and anti-insulin antibody for 60 s. The reaction streams were sampled at 6.25-s intervals and analyzed in parallel using an on-chip capillary electrophoresis separation with laser-induced fluorescence detection by a scanning confocal microscope. The limit of detection for insulin was 10 nM. The device was used to complete over 1450 immunoassays of biological samples in less than 40 min, allowing the parallel monitoring of insulin release from four islets every 6.25 s.     

Single particle tracking of fluorescent nanodiamonds in cells and organisms

Ever since the discovery of fullerenes in 1985, nanocarbon has demonstrated a wide range of applications in various areas of science and engineering. Compared with metal, oxide, and semiconductor nanoparticles, the carbon-based nanomaterials have distinct advantages in both biotechnological and biomedical applications due to their inherent biocompatibility. Fluorescent nanodiamond (FND) joined the nanocarbon family in 2005. It was initially developed as a contrast agent for bioimaging because it can emit bright red photoluminescence from negatively charged nitrogen-vacancy centers built in the diamond matrix. A notable application of this technology is to study the cytoplasmic dynamics of living cells by tracking single bioconjugated FNDs in intracellular medium. This article provides a critical review on recent advances and developments of such single particle tracking (SPT) research. It summarizes SPT and related studies of FNDs in cells (such as cancer cell lines) and organisms (including zebrafish embryos, fruit fly embryos, whole nematodes, and mice) using assorted imaging techniques.