Fluorophore-Promoted RNA Folding and Photostability Enables Imaging of Single Broccoli-Tagged mRNAs in Live Mammalian Cells

Spinach and Broccoli are fluorogenic RNA aptamers that bind DFHBI, a mimic of the chromophore in green fluorescent protein, and activate its fluorescence. Spinach/Broccoli-DFHBI complexes exhibit high fluorescence in vitro, but they exhibit lower fluorescence in mammalian cells. Here, computational screening was used to identify BI, a DFHBI derivative that binds Broccoli with higher affinity and leads to markedly higher fluorescence in cells compared to previous ligands. BI prevents thermal unfolding of Broccoli at 37 °C, leading to more folded Broccoli and thus more fluorescent Broccoli-BI complexes in cells. Broccoli-BI complexes are more photostable owing to impaired photoisomerization and rapid unbinding of photoisomerized cis-BI. These properties enable single mRNA containing 24 Broccoli aptamers to be imaged in live mammalian cells treated with BI. Small molecule ligands can thus promote RNA folding in cells, and thus allow single mRNA imaging with fluorogenic aptamers.     

In Situ Spatial Complementation of Aptamer‐Mediated Recognition Enables Live‐Cell Imaging of Native RNA Transcripts in Real Time

Direct cellular imaging of the localization and dynamics of biomolecules helps to understand their function and reveals novel mechanisms at the single‐cell resolution. In contrast to routine fluorescent‐protein‐based protein imaging, technology for RNA imaging remains less well explored because of the lack of enabling technology. Herein, we report the development of an aptamer‐initiated fluorescence complementation (AiFC) method for RNA imaging by engineering a green fluorescence protein (GFP)‐mimicking turn‐on RNA aptamer, Broccoli, into two split fragments that could tandemly bind to target mRNA. When genetically encoded in cells, endogenous mRNA molecules recruited Split‐Broccoli and brought the two fragments into spatial proximity, which formed a fluorophore‐binding site in situ and turned on fluorescence. Significantly, we demonstrated the use of AiFC for high‐contrast and real‐time imaging of endogenous RNA molecules in living mammalian cells. We envision wide application and practical utility of this enabling technology to in vivo single‐cell visualization and mechanistic analysis of macromolecular interactions.     

Genetically Encoded Ratiometric RNA‐Based Sensors for Quantitative Imaging of Small Molecules in Living Cells

Precisely determining the intracellular concentrations of metabolites and signaling molecules is critical in studying cell biology. Fluorogenic RNA‐based sensors have emerged to detect various targets in living cells. However, it is still challenging to apply these genetically encoded sensors to quantify the cellular concentrations and distributions of targets. Herein, using a pair of orthogonal fluorogenic RNA aptamers, DNB and Broccoli, we engineered a modular sensor system to apply the DNB‐to‐Broccoli fluorescence ratio to quantify the cell‐to‐cell variations of target concentrations. These ratiometric sensors can be broadly applied for live‐cell imaging and quantification of metabolites, signaling molecules, and other synthetic compounds.     

In Vivo Production of RNA Aptamers and Nanoparticles: Problems and Prospects

RNA aptamers are becoming increasingly attractive due to their superior properties. This review discusses the early stages of aptamer research, the main developments in this area, and the latest technologies being developed. The review also highlights the advantages of RNA aptamers in comparison to antibodies, considering the great potential of RNA aptamers and their applications in the near future. In addition, it is shown how RNA aptamers can form endless 3-D structures, giving rise to various structural and functional possibilities. Special attention is paid to the Mango, Spinach and Broccoli fluorescent RNA aptamers, and the advantages of split RNA aptamers are discussed. The review focuses on the importance of creating a platform for the synthesis of RNA nanoparticles in vivo and examines yeast, namely Saccharomyces cerevisiae, as a potential model organism for the production of RNA nanoparticles on a large scale.     

Live-cell RNA imaging using the CRISPR-dCas13 system with modified sgRNAs appended with fluorescent RNA aptamers

The development of RNA imaging strategies in live cells is essential to improve our understanding of their role in various cellular functions. We report an efficient RNA imaging method based on the CRISPR-dPspCas13b system with fluorescent RNA aptamers in sgRNA (CasFAS) in live cells. Using modified sgRNA attached to fluorescent RNA aptamers that showed reduced background fluorescence, this approach provides a simple, sensitive way to image and track endogenous RNA with high accuracy and efficiency. In addition, color switching can be easily achieved by changing the fluorogenic dye analogues in living cells through user-friendly washing and restaining operations. CasFAS is compatible with orthogonal fluorescent aptamers, such as Broccoli and Pepper, enabling multiple colors RNA labeling or intracellular RNA–RNA interaction imaging. Finally, the visualization of severe fever with thrombocytopenia syndrome virus (SFTSV) was achieved by CasFAS, which may facilitate further studies on this virus.

The development of RNA imaging strategies in live cells is essential to improve our understanding of their role in various cellular functions.     

Supramolecular Fluorescence Resonance Energy Transfer in Nucleobase‐Modified Fluorogenic RNA Aptamers

RNA aptamers form compact tertiary structures and bind their ligands in specific binding sites. Fluorescence‐based strategies reveal information on structure and dynamics of RNA aptamers. Herein, we report the incorporation of the universal emissive nucleobase analog 4‐cyanoindole into the fluorogenic RNA aptamer Chili, and its application as a donor for supramolecular FRET to the bound ligands DMHBI⁺ or DMHBO⁺. The photophysical properties of the new nucleobase–ligand‐FRET pair revealed structural restraints for the overall RNA aptamer organization and identified nucleotide positions suitable for FRET‐based readout of ligand binding. This strategy is generally suitable for binding‐site mapping and may also be applied for responsive aptamer devices.     

Synthesis and structures of photoactive manganese–carbonyl complexes derived from 2‐(pyridin‐2‐yl)‐1,3‐benzothiazole and 2‐(quinolin‐2‐yl)‐1,3‐benzothiazole

PhotoCORMs (photo‐active CO‐releasing molecules) have emerged as a class of CO donors where the CO release process can be triggered upon illumination with light of appropriate wavelength. We have recently reported an Mn‐based photoCORM, namely [MnBr(pbt)(CO)₃] [pbt is 2‐(pyridin‐2‐yl)‐1,3‐benzothiazole], where the CO release event can be tracked within cellular milieu by virtue of the emergence of strong blue fluorescence. In pursuit of developing more such trackable photoCORMs, we report herein the syntheses and structural characterization of two Mn^I–carbonyl complexes, namely fac‐tricarbonylchlorido[2‐(pyridin‐2‐yl)‐1,3‐benzothiazole‐κ²N ,N ′]manganese(I), [MnCl(C₁₂H₈N₂S)(CO)₃], (1), and fac‐tricarbonylchlorido[2‐(quinolin‐2‐yl)‐1,3‐benzothiazole‐κ²N ,N ′]manganese(I), [MnCl(C₁₆H₁₀N₂S)(CO)₃], (2). In both complexes, the Mn^I center resides in a distorted octahedral coordination environment. Weak intermolecular C—H…Cl contacts in complex (1) and Cl…S contacts in complex (2) consolidate their extended structures. These complexes also exhibit CO release upon exposure to low‐power broadband visible light. The apparent CO release rates for the two complexes have been measured to compare their CO donating capacity. The fluorogenic 2‐(pyridin‐2‐yl)‐1,3‐benzothiazole and 2‐(quinolin‐2‐yl)‐1,3‐benzothiazole ligands provide a convenient way to track the CO release event through the `turn‐ON' fluorescence which results upon de‐ligation of the ligands from their respective metal centers following CO photorelease.     

Detection of LacZ‐Positive Cells in Living Tissue with Single‐Cell Resolution

The LacZ gene, which encodes Escherichia coli β‐galactosidase, is widely used as a marker for cells with targeted gene expression or disruption. However, it has been difficult to detect lacZ‐positive cells in living organisms or tissues at single‐cell resolution, limiting the utility of existing lacZ reporters. Herein we present a newly developed fluorogenic β‐galactosidase substrate suitable for labeling live cells in culture, as well as in living tissues. This precisely functionalized fluorescent probe exhibited dramatic activation of fluorescence upon reaction with the enzyme, remained inside cells by anchoring itself to intracellular proteins, and provided single‐cell resolution. Neurons labeled with this probe preserved spontaneous firing, which was enhanced by application of ligands of receptors expressed in the cells, suggesting that this probe would be applicable to investigate functions of targeted cells in living tissues and organisms.     

In Situ Self-Assembly of Fluorogenic RNA Nanozipper Enables Real-Time Imaging of Single Viral mRNA Translation

Real-time visualization of individual viral mRNA translation activities in live cells is essential to obtain critical details of viral mRNA dynamics and to detect its transient responses to environmental stress. Fluorogenic RNA aptamers are powerful tools for real-time imaging of mRNA in live cells, but monitoring the translation activity of individual mRNAs remains a challenge due to their intrinsic photophysical properties. Here, we develop a genetically encoded turn-on 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI)-binding RNA nanozipper with superior brightness and high photostability by in situ self-assembly of multiple nanozippers along single mRNAs. The nanozipper enables real-time imaging of the mobility and dynamic translation of individual viral mRNAs in live cells, providing information on the spatial dynamics and translational elongation rate of viral mRNAs.     

Multi‐Use NBD‐Based Tetra‐amino Macrocycle: Fluorescent Probe for Metals and Anions and Live Cell Marker

Ligand L (4‐(7‐nitrobenzo[1,2,5]oxadiazole‐4‐yl)‐1,7‐dimethyl‐1,4,7,10‐tetra‐azacyclododecane) is a versatile fluorescent sensor useful for Cu^II, Zn^II and Cd^II metal detection, as a building block of fluorescent metallo‐receptor for halide detection, and as an organelle marker inside live cells. Ligand L undergoes a chelation‐enhanced fluorescence (CHEF) effect upon metal coordination in acetonitrile solution. In all three complexes investigated the metal cation is coordinatively unsaturated; thus, it can bind secondary ligands as anionic species. The crystal structure of [Zn L Cl](ClO₄) is discussed. Cu^II and Zn^II complexes are quenched upon halide interaction, whereas the [Cd L ]²⁺ species behaves as an OFF–ON sensor for halide anions in acetonitrile solution. The mechanism of the fluorescence response in the presence of the anion depends on the nature of the metal ion employed and has been studied by spectroscopic methods, such as NMR spectroscopy, UV/Vis and fluorescence techniques and by computational methods. Subcellular localization experiments performed on HeLa cells show that L mainly localizes in spot‐like structures in a polarized portion of the cytosol that is occupied by the Golgi apparatus to give a green fluorescence signal.     

New 3‐(Heteroaryl)‐2‐iminocoumarin‐based Borate Complexes: Synthesis,Photophysical Properties,and Rational Functionalization for Biosensing/Biolabeling Applications

Members of a series of boron difluoride complexes with 3‐(heteroaryl)‐2‐iminocoumarin ligands bearing both a phenolic hydroxyl group (acting as a fluorogenic center) and an N‐aryl substituent (acting as a stabilizing moiety) have been synthesized in good yields by applying a straightforward two‐step method. These novel fluorogenic dyes belong to the family of “Boricos” (D. Frath et al., Chem. Commun.­ 2013 , 49, 4908–4910) and are the first examples of phenol‐based fluorophores of which the photophysical properties in the green‐yellow spectral range are dramatically improved by N,N‐chelation of a boron atom. Modulation of their fluorescence properties through reversible chemical modification of their phenol moieties has been demonstrated by the preparation of the corresponding 2,4‐dinitrophenyl (DNP) ethers, which led to a dramatic “OFF‐ON” fluorescence response upon reaction with thiols. Additionally, to expand the scope of these “7‐hydroxy‐Borico” derivatives, particularly in biolabeling, amine or carboxylic acid functionalities amenable to (bio)conjugation have been introduced within their scaffold. Their utility has been demonstrated in the preparation of fluorescent bovine serum albumin (BSA) conjugates and “Borico”‐DOTA‐like scaffolds in an effort to design novel monomolecular multimodal fluorescence‐ radioisotope imaging agents.     

Fabrication of fluorescent holographic micropatterns based on the rare earth complexes using azobenzene‐containing poly(aryl ether)s as macromolecular ligands

In this work, on the basis of photoinduced surface relief gratings (SRGs) with the rare earth complexes using azo‐polymers as macromolecular ligands, a series of novel materials for fabricating rewritable fluorescent two‐dimensional micropatterns, whose color can be easily adjusted by changing the species of the rare earth ions, are demonstrated. The rare earth complexes are prepared using a series of poly(aryl ether)s containing azobenzene chromophores and carboxyl group as macromolecular ligands and 1,10‐phenanthroline as co‐ligands. The fluorescence properties of the rare earth complexes and the influence of the contents of azobenzene chromophores on the fluorescent intensity are investigated by means of fluorescence excitation and emission spectroscopy. By exposing the films of the rare earth complexes to an interference pattern laser beam, SRGs can be formed on the films. Under the excitation, fluorescent patterns of the SRGs can be observed by the measurement of fluorescence microscopy. © 2015 Wiley Periodicals, Inc. J. Polym. Sci. Part A: Polym. Chem. 2015 , 53, 936–943     

Multifunctional G‐Quadruplex Aptamers and Their Application to Protein Detection

Two significant G‐quadruplex aptamers named AGRO100 and T30695 are identified as multifunctional aptamers that can bind the protein ligands nucleolin or HIV‐1 integrase and hemin. Besides their strong binding to target proteins, both AGRO100 and T30695 exhibit high hemin‐binding affinities comparable to that of the known aptamer (termed PS2M) selected by the in vitro evolution process. Most importantly, their corresponding hemin–DNA complexes reveal excellent peroxidase‐like activities, higher than that of the reported hemin–PS2M DNAzyme. This enables these multifunctional aptamers to be applied to the sensitive detection of proteins, which is demonstrated by applying AGRO100 to the chemiluminescence detection of nucleolin expressed at the surface of HeLa cells. Based on the specific AGRO100–nucleolin interaction, the surface‐expressed nucleolin of HeLa cells is labeled in situ with the hemin–AGRO100 DNAzyme, and then determined in the luminol–H₂O₂ system. Through this approach, the sensitive detection of total nucleolin expressed at the surface of about 6000 HeLa cells is accomplished. Our results suggest that exploiting new functions of existing aptamers will help to extend their potential applications in the biochemical field.     

In vivo Fluorescence Imaging of Tumors using Molecular Aptamers Generated by Cell‐SELEX

Poor sensitivity and low specificity of current molecular imaging probes limit their application in clinical settings. To address these challenges, we used a process known as cell‐SELEX to develop unique molecular probes termed aptamers with the high binding affinity, sensitivity, and specificity needed for in vivo molecular imaging inside living animals. Importantly, aptamers can be selected by cell‐SELEX to recognize target cells, or even surface membrane proteins, without requiring prior molecular signature information. As a result, we are able to present the first report of aptamers molecularly engineered with signaling molecules and optimized for the fluorescence imaging of specific tumor cells inside a mouse. Using a Cy5‐labeled aptamer TD05 (Cy5‐TD05) as the probe, the in vivo efficacy of aptamer‐based molecular imaging in Ramos (B‐cell lymphoma) xenograft nude mice was tested. After intravenous injection of Cy5‐TD05 into mice bearing grafted tumors, noninvasive, whole‐body fluorescence imaging then allowed the spatial and temporal distribution to be directly monitored. Our results demonstrate that the aptamers could effectively recognize tumors with high sensitivity and specificity, thus establishing the efficacy of these fluorescent aptamers for diagnostic applications and in vivo studies requiring real‐time molecular imaging.     

Ultrafluorogenic Coumarin–Tetrazine Probes for Real‐Time Biological Imaging

We have developed a series of new ultrafluorogenic probes in the blue‐green region of the visible‐light spectrum that display fluorescence enhancement exceeding 11 000‐fold. These fluorogenic dyes integrate a coumarin fluorochrome with the bioorthogonal trans‐cyclooctene(TCO)–tetrazine chemistry platform. By exploiting highly efficient through‐bond energy transfer (TBET), these probes exhibit the highest brightness enhancements reported for any bioorthogonal fluorogenic dyes. No‐wash, fluorogenic imaging of diverse targets including cell‐surface receptors in cancer cells, mitochondria, and the actin cytoskeleton is possible within seconds, with minimal background signal and no appreciable nonspecific binding, opening the possibility for in vivo sensing.     

Construction of lanthanide complexes supported by 2,3‐dimethoxybenzoic acid and 5,5’‐dimethy‐2,2’‐bipyridine: crystal structures,thermoanalysis, magnetic and fluorescence properties

A series of novel trivalent lanthanide complexes, [Ln(2,3‐DMOBA)3(5,5′‐DM‐2,2′‐bipy)]2·C2H5OH (Ln = Eu(1), Sm(2), Gd(3), Ho(4) Er(5), Pr(6), Nd(7)) (2,3‐DMOBA = 2,3‐dimethoxybenzoate, 5,5′‐DM‐2,2′‐bipy = 5,5′‐dimethy‐2,2′‐bipyridine), have been successfully synthesized and structurally validated by single crystal diffraction. All complexes discussed herein feature a binuclear structure, and contain only one free ethanol molecule, which is interesting in the lanthanide complexes. The coordination number of center Ln3+ ions is nine, showing a distorted monocapped square anti‐prismatic coordination geometry. Through a pair of alternating identical C‐H···O hydrogen bonding interactions between two 2,3‐DMOBA ligands on the same lanthanum binuclear unit with 5,5′‐DM‐2,2′‐bipy ligands on two neighboring units, the binuclear complexes can form one‐ The thermal analysis of these complexes are investigated by TG‐DSC/FTIR, the result show that the decomposition process of complexes are mainly divided into four stages with the formation of the respective oxides. The visible light emission experiment of complex 1 is carried out, and the characteristic luminescence behavior of intense red light is exhibited. What'more, fluorescence lifetimes as well as the fluorescent quantum yield of complex 1 is calculated. And the magnetic properties of complexes 3–5 are also studied.     

In Situ Synthesis of an Aptamer‐Based Polyvalent Antibody Mimic on the Cell Surface for Enhanced Interactions between Immune and Cancer Cells

An ability to promote therapeutic immune cells to recognize cancer cells is important for the success of cell‐based cancer immunotherapy. We present a synthetic method for functionalizing the surface of natural killer (NK) cells with a supramolecular aptamer‐based polyvalent antibody mimic (PAM). The PAM is synthesized on the cell surface through nucleic acid assembly and hybridization. The data show that PAM has superiority over its monovalent counterpart in powering NKs to bind to cancer cells, and that PAM‐engineered NK cells exhibit the capability of killing cancer cells more effectively. Notably, aptamers can, in principle, be discovered against any cell receptors; moreover, the aptamers can be replaced by any other ligands when developing a PAM. Thus, this work has successfully demonstrated a technology platform for promoting interactions between immune and cancer cells.     

Acridine‐containing RuII,OsII, RhIII and IrIII Half‐Sandwich Complexes: Synthesis,Structure and Antiproliferative Activity

Research aimed at enhancing the efficacy of organometallic complexes against cancer, has shown that attaching bio‐active molecules to (metallo)drugs often enhances their biological properties. New salicylaldimine and 2‐pyridylimine ligands ( L2 and L3 ), containing a bio‐active acridine scaffold, were synthesized and complexed to Rh(III), Ir(III), Ru(II) and Os(II) metal ion centers. The resulting acridine‐containing half‐sandwich complexes have been characterized fully by elemental analysis, FT‐IR and NMR spectroscopy, HR‐ESI mass spectrometry as well as single crystal X‐ray diffraction, for the Rh(III) N^N bidentate complex [RhCp*Cl( L3 )][BPh₄]. The antiproliferative activity of the ligands ( L2 and L3 ) and complexes ( C1 to C9 ) were evaluated in vitro against human promyelocytic leukemia cells (HL60) and normal skin fibroblast cells (FG0). The compounds exhibit good activities against HL60 cells and are consistently selective towards cancerous cells over non‐tumorous cells. This study demonstrates the potential of such hybrid compounds to target cancer cells specifically. The most active complex, [RhCp*Cl( L2 )], exhibited binding to DNA model guanosine‐5’‐monophosphate (5’‐GMP) which suggests a mode of action involving interaction of the complex with 5’‐GMP found on DNA backbone.