FRET-based polymer materials for detection of cellular microenvironments

Effective detection of cellular microenvironments and understanding of physiological activities in living cells remain a considerable challenge.In recent years,fluore scence(or Forster) resonance energy trans fe r(FRET) technology has emerged as a valuable method for real-time imaging of intracellular environment with high sensitivity,specificity and spatial resolution.Particularly,polymer-based imaging systems show enhanced stability,improved biodistribution,increased dye payloads,and amplified signal/noise ratio compared with small molecular sensors.This review summarizes the recent progress in FRET-based polymeric systems for probing the physiological environments in cells.     

A surface energy transfer nanoruler for measuring binding site distances on live cell surfaces

Measuring distances at molecular length scales in living systems is a significant challenge. Methods like Fo?rster resonance energy transfer (FRET) have limitations due to short detection distances and strict orientations. Recently, surface energy transfer (SET) has been used in bulk solutions; however, it cannot be applied to living systems. Here, we have developed an SET nanoruler, using aptamer-gold nanoparticle conjugates with different diameters, to monitor the distance between binding sites of a receptor on living cells. The nanoruler can measure separation distances well beyond the detection limit of FRET. Thus, for the first time, we have developed an effective SET nanoruler for live cells with long distance, easy construction, fast detection, and low background. This is also the first time that the distance between the aptamer and antibody binding sites in the membrane protein PTK7 was measured accurately. The SET nanoruler represents the next leap forward to monitor structural components within living cell membranes.     

β-cyclodextrin as the vehicle for forming ratiometric mercury ion sensor usable in aqueous media, biological fluids, and live cells

The selective and sensitive detection methods for toxic transition-metal ions, which are rapid, facile, and applicable to the environmental and biological milieus, are of great importance. In this study, we designed a β-CD-based ratiometric sensor for detecting mercury ions in aqueous media, some biological fluids, and live cells. In this sensing platform, the thiocarbamido-containing probe dye was covalently linked onto the hydrophilic β-CD rim, which is conducive to complexing with metal ion, while the donor dye was anchored inside hydrophobic β-CD cavity via the adamantyl moiety, which is good for avoiding self-aggregation and enhancing the quantum yield of the donor dye. Upon associating with mercury ion, the probe dye undergoes ring-opening process and serves as the energy acceptor and constitutes the FRET system with the donor dye; by this way ratiometric detection of mercury ion in water can be realized with the detection limit of 10 nM. The cyclodextrin plays a crucial role for the sensing system; it not only accommodates both the donor dye and the probe dye which can form FRET system upon addition of Hg(2+) but also makes the sensor water-soluble and cell membrane permeable. This nontoxic sensing platform can be used for mercury ion detection in aqueous medium, biological fluids, and live cells (L929 and Hela). We also found that, upon being taken up by L929 cells, the sensor exhibited no cytotoxicity, and the cell proliferation was not affected.     

Live‐Cell Protein Sulfonylation Based on Proximity‐driven N‐Sulfonyl Pyridone Chemistry

The development of bioorthogonal approaches for labeling of endogenous proteins under the multimolecular crowding conditions of live cells is highly desirable for the analysis and engineering of proteins without using genetic manipulation. N‐Sulfonyl pyridone (SP) is reported as a new reactive group for protein sulfonylation. The ligand‐directed SP chemistry was able to modify not only purified proteins in vitro, but also endogenous ones on the surface of and inside live cells selectively and rapidly, which allowed to convert endogenous proteins to FRET‐based biosensors in situ.     

A Telomerase-Assisted Strategy for Regeneration of DNA Nanomachines in Living Cells

DNA nanomachines have been engineered into diverse personalized devices for diagnostic imaging of biomarkers; however, the regeneration of DNA nanomachines in living cells remains challenging. Here, we report an ingenious DNA nanomachine that can implement telomerase (TE)-activated regeneration in living cells. Upon apurinic/apyrimidinic endonuclease 1 (APE1)-responsive initiation of the nanomachine, the walker of the nanomachine moves along tracks regenerated by TE, generating multiply amplified signals through which APE1 can be imaged in situ. Additionally, augmentation of the signal due to the regeneration of the nanomachines could reveal differential expression of TE in different cell lines. To the best of our knowledge, this is the first proof-of-concept demonstration of the use of biomarkers to assist in the regeneration of nanomachines in living cells. This study offers a new paradigm for the development of more applicable and efficient DNA nanomachines.     

Cysteine‐Mediated Intracellular Building of Luciferin to Enhance Probe Retention and Fluorescence Turn‐On

The development of sensitive and selective small molecular probes that enable real‐time detection of endogenous cysteine (Cys) has become an attractive topic because of the essential roles played by Cys in controlling the cellular nitrogen balance and in maintaining biological redox homeostasis. Herein, we report a Cys‐specific probe, 2‐cyanobenzothiazol‐6‐yl acrylate (CBTOA), that shows not only fluorescence turn‐on for sensitive detection of endogenous Cys but also enhanced probe retention inside cells for real‐time monitoring of Cys levels upon external stimulation. Cys‐mediated intracellular formation of luciferin from CBTOA was the key strategy leading to this new type of fluorogenic probe. CBTOA showed fast response to Cys in living cells and liver tissue slices with high sensitivity and selectivity. By using CBTOA as a real‐time probe, we were able to monitor the change in Cys levels in living HeLa cells under ROS‐induced oxidative stress as well as in human mesenchymal stem cells during adipogenic differentiation.     

Spectral Förster resonance energy transfer detection of protein interactions in surface-supported bilayers

F?rster resonance energy transfer (FRET), a fluorescence detection technique, is often used for sensing molecular interactions in solution and in membranes. Here we show that (1) FRET spectra can be recorded in single bilayers, supported on a surface, and (2) the fluorescein/rhodamine dye pair is an adequate reporter of FRET when spectral detection is used. Thus, measurements pertaining to molecular interactions in membranes can be carried out in supported bilayers. Spectral FRET has advantages over imaging FRET, which monitors only signal amplitudes at certain wavelength. There are also advantages to performing spectral FRET measurements in supported bilayers as compared to free liposomes in suspension. However, the spectral properties of dyes can be altered in an unexpected manner in an ordered bilayer structure on a surface, such that fluorescence detection in surface-supported bilayers is not always trivial.     

A novel FRET approach for in situ investigation of cellulase–cellulose interaction

A novel real-time in situ detection method for the investigation of cellulase–cellulose interactions based on fluorescence resonance energy transfer (FRET) has been developed. FRET has been widely used in biological and biophysical fields for studies related to proteins, nucleic acids, and small biological molecules. Here, we report the efficient labeling of carboxymethyl cellulose (CMC) with donor dye 5-(aminomethyl)fluorescein and its use as a donor in a FRET assay together with an Alexa Fluor 594 (AF594, acceptor)–cellulase conjugate as acceptor. This methodology was successfully employed to investigate the temperature dependency of cellulase binding to cellulose at a molecular level by monitoring the fluorescence emission change of donor (or acceptor) in a homogeneous liquid environment. It also provides a sound base for ongoing cellulase–cellulose study using cellulosic fiber.     

Photo-pH dually modulated fluorescence switch based on DNA spatial nanodevice

In this paper, we describe our strategy on the design, construction, and characterization of a novel molecular device. By integrating a photoregulated fluorescent switch and a DNA-based nanomachine, the distance-dependent FRET process between fluorescein and photochromic moieties can be further modulated by the spatial output of a unique proton-driven DNA manomachine. This device could be reversibly switched in a reliable manner, and the fluorescence variation behavior, exhibited by this dually modulated fluorescence switch, can also mimic the function of a Boolean logic operation.     

Rational Engineering of a Dynamic,Entropy-Driven DNA Nanomachine for Intracellular MicroRNA Imaging

We rationally engineered an elegant entropy-driven DNA nanomachine with three-dimensional track and applied it for intracellular miRNAs imaging. The proposed nanomachine is activated by target miRNA binding to drive a walking leg tethered to gold nanoparticle with a high density of DNA substrates. The autonomous and progressive walk on the DNA track via the entropy-driven catalytic reaction of intramolecular toehold-mediated strand migration leads to continuous disassembly of DNA substrates, accompanied by the recovery of fluorescence signal due to the specific release of a dye-labeled substrate from DNA track. Our nanomachine outperforms the conventional intermolecular reaction-based gold nanoparticle design in the context of an improved sensitivity and kinetics, attributed to the enhanced local effective concentrations of working DNA components from the proximity-induced intramolecular reaction. Moreover, the nanomachine was applied for miRNA imaging inside living cells.     

DNA‐Templated Assembly of a Heterobivalent Quantum Dot Nanoprobe For Extra‐ and Intracellular Dual‐Targeting and Imaging of Live Cancer Cells

Quantum dots (QDs) hold great promise for the molecular imaging of cancer because of their superior optical properties. Although cell‐surface biomarkers can be readily imaged with QDs, non‐invasive live‐cell imaging of critical intracellular cancer markers with QDs is a great challenge because of the difficulties in the automatic delivery of QD probes to the cytosol and the ambiguity of intracellular targeting signals. Herein, we report a new type of DNA‐templated heterobivalent QD nanoprobes with the ability to target and image two spatially isolated cancer markers (nucleolin and mRNA) present on the cell surface and in the cell cytosol. Bypassing endolysosomal sequestration, this type of QD nanoprobes undergo macropinocytosis following the nucleolin targeting and then translocate to the cytosol for mRNA targeting. Fluorescence resonance energy transfer (FRET) based confocal microscopy enables unambiguous signal deconvolution of mRNA‐targeted QD nanoprobes inside cancer cells.     

Rational Engineering of a Dynamic,Entropy‐Driven DNA Nanomachine for Intracellular MicroRNA Imaging

We rationally engineered an elegant entropy‐driven DNA nanomachine with three‐dimensional track and applied it for intracellular miRNAs imaging. The proposed nanomachine is activated by target miRNA binding to drive a walking leg tethered to gold nanoparticle with a high density of DNA substrates. The autonomous and progressive walk on the DNA track via the entropy‐driven catalytic reaction of intramolecular toehold‐mediated strand migration leads to continuous disassembly of DNA substrates, accompanied by the recovery of fluorescence signal due to the specific release of a dye‐labeled substrate from DNA track. Our nanomachine outperforms the conventional intermolecular reaction‐based gold nanoparticle design in the context of an improved sensitivity and kinetics, attributed to the enhanced local effective concentrations of working DNA components from the proximity‐induced intramolecular reaction. Moreover, the nanomachine was applied for miRNA imaging inside living cells.     

Direct energy transfer from conjugated polymer to DNA intercalated dye: label-free fluorescent DNA detection

The development of methods for DNA detection is of importance in disease diagnosis, gene-targeted drug discovery and molecular biology field. In this paper, we synthesize a new cationic water-soluble CP containing fluorene moiety and flexible ethylenic moiety in the backbone (PFV) for label-free DNA detection. The conformational freedom of PFV provides stronger interactions with double-stranded DNA (dsDNA) and optimizes the orientation of transition moments between PFV and ethidium bromide (EB) intercalated in dsDNA. The efficient FRET from PFV (donor) to EB (acceptor) intercalated in dsDNA is observed and the emission of EB is amplified by the good light-harvesting ability of conjugated polymers. The interactions between PFV and DNA can also be probed by measuring the FRET ratio between PFV and EB intercalated in DNA. In comparison to other DNA detection assays based on FRET and conjugated polymers, synthesis of dye-labeled DNA probe is avoided in our method, which significantly reduces the cost and the synthetic complexity. The PFV/dsDNA/EB system provides promising applications on DNA detection with a simply, fast and label-free manner.     

A duplex–triplex nucleic acid nanomachine that probes pH changes inside living cells during apoptosis

A duplex–triplex switchable DNA nanomachine was fabricated and has been applied for the demonstration of intracellular acidification and apoptosis of Ramos cells, with graphene oxide (GO) not only as transporter but also as fluorescence quencher. The machine constructed with triplex-forming oligonucleotide exhibited duplex–triplex transition at different pH conditions. By virtue of the remarkable difference in affinity of GO with single-stranded DNA and triplex DNA, and the super fluorescence quenching efficiency of GO, the nanomachine functions as a pH sensor based on fluorescence resonance energy transfer. Moreover, taking advantage of the excellent transporter property of GO, the duplex–triplex/GO nanomachine was used to sense pH changes inside Ramos cells during apoptosis. Fluorescence images showed different results between living and apoptotic cells, illustrating the potential of DNA scaffolds responsive to more complex pH triggers in living systems.

Porphyrin FRET acceptors for apoptosis induction and monitoring

Photodynamic therapy (PDT) stands to benefit from improved approaches to real-time treatment monitoring. One method is to use activatable photosensitizers that can both induce cell death (via singlet oxygen) and monitor it (via caspase detection). Here, we report porphyrins as caspase-responsive Forster Resonance Energy Transfer (FRET) acceptors to organic fluorophore donors. Compared to porphyrin FRET donor constructs, singlet oxygen generation was unquenched prior to caspase activation, resulting in more efficient photosensitization in HT-29 cancer cells. The donor 5-Carboxy-X-Rhodamine (Rox) formed a robust FRET pair with the pyropheophorbide (Pyro) acceptor. The large dynamic range of the construct enabled ratiometric imaging (with Rox excitation) of caspase activation in live, single cells following induction of cell death (with Pyro excitation) using a single agent. Quantitative, unquenched activatable photosensitizers (QUaPS) hold potential for new feedback-oriented PDT approaches.     

DNA tetrahedron-based split aptamer probes for reliable imaging of ATP in living cells

Accurate detection and imaging of adenosine triphosphate(ATP) expression levels in living cells is of great value for understanding cell metabolism, physiological activities, and pathologic mechanisms. Here, we developed a DNA tetrahedron-based split aptamer probe(TD probe) for ratiometric fluorescence imaging of ATP in living cells. The TD probe is constructed by hybridizing two split ATP aptamer probes(Apt-a and Apt-b) to a DNA tetrahedron assembled by four DNA oligonucleotides(T1, T2, T3 and ...     

Aggregation-Induced Synergism by Hydrophobic-Driven Self-Assembly of Amphiphilic Oligonucleotides

The evident contradiction between high local-concentration-based substrate reactivity and free-diffusion-based high reaction efficiency remains one of the important challenges in chemistry. Herein, we propose an efficient aggregation-induced synergism through the hydrophobic-driven self-assembly of amphiphilic oligonucleotides to generate high local concentration whereas retaining high reaction efficiency through hydrophobic-based aggregation, which is important for constructing efficient DNA nanomachines for ultrasensitive applications. MicroRNA-155, used as a model, triggered strand displacement amplification of the DNA monomers on the periphery of the 3D DNA nanomachine and generated an amplified fluorescent response for its sensitive assay. The local concentration of substrates was increased by a factor of at least 9.0×10⁵ through hydrophobic-interaction-based self-assembly in comparison with the traditional homogeneous reaction system, achieving high local-concentration-based reactivity and free-diffusion-based enhanced reaction efficiency. As expected, the aggregation-induced synergism by hydrophobic-driven self-assembly of amphiphilic oligonucleotides created excellent properties to generate a 3D DNA nanomachine with potential as an assay for microRNA-155 in cells. Most importantly, this approach can be easily expanded for the bioassay of various biomarkers, such as nucleotides, proteins, and cells, offering a new avenue for simple and efficient applications in bioanalysis and clinical diagnosis.     

A core–brush 3D DNA nanostructure: the next generation of DNA nanomachine for ultrasensitive sensing and imaging of intracellular microRNA with rapid kinetics

A highly loaded and integrated core–brush three-dimensional (3D) DNA nanostructure is constructed by programmatically assembling a locked DNA walking arm (DA) and hairpin substrate (HS) into a repetitive array along a well-designed DNA track generated by rolling circle amplification (RCA) and is applied as a 3D DNA nanomachine for rapid and sensitive intracellular microRNA (miRNA) imaging and sensing. Impressively, the homogeneous distribution of the DA and HS at a ratio of 1 : 3 on the DNA track provides a specific walking range for the DA to avoid invalid and random self-walking and notably improve the executive ability of the core–brush 3D DNA nanomachine, which easily solves the major technical challenges of traditional Au-based 3D DNA nanomachines: low loading capacity and low executive efficiency. As a proof of concept, the interaction of miRNA with the 3D DNA nanomachine could initiate the autonomous and progressive operation of the DA to cleave the HS for ultrasensitive ECL detection of target miRNA-21 with a detection limit as low as 3.57 aM and rapid imaging in living cells within 15 min. Therefore, the proposed core–brush 3D DNA nanomachine could not only provide convincing evidence for sensitive detection and rapid visual imaging of biomarkers with tiny change, but also assist researchers in investigating the formation mechanism of tumors, improving their recovery rates and reducing correlative complications. This strategy might enrich the method to design a new generation of 3D DNA nanomachine and promote the development of clinical diagnosis, targeted therapy and prognosis monitoring.

This study designed a highly loaded and integrated core–brush 3D DNA nanomachine for miRNA imaging and sensing, which easily solves the major technical challenges of traditional Au-based 3D nanomachines: low loading capacity and low executive efficiency.     

High-throughput examination of fluorescence resonance energy transfer-detected metal-ion response in mammalian cells

Fluorescence resonance energy transfer (FRET)-based genetically encoded metal-ion sensors are important tools for studying metal-ion dynamics in live cells. We present a time-resolved microfluidic flow cytometer capable of characterizing the FRET-based dynamic response of metal-ion sensors in mammalian cells at a throughput of 15 cells/s with a time window encompassing a few milliseconds to a few seconds after mixing of cells with exogenous ligands. We have used the instrument to examine the cellular heterogeneity of Zn(2+) and Ca(2+) sensor FRET response amplitudes and demonstrated that the cluster maps of the Zn(2+) sensor FRET changes resolve multiple subpopulations. We have also measured the in vivo sensor response kinetics induced by changes in Zn(2+) and Ca(2+) concentrations. We observed an ～30 fold difference between the extracellular and intracellular sensors.     

Visualization of Protein‐Specific Glycosylation inside Living Cells

Protein glycosylation is a ubiquitous post‐translational modification that is involved in the regulation of many aspects of protein function. In order to uncover the biological roles of this modification, imaging the glycosylation state of specific proteins within living cells would be of fundamental importance. To date, however, this has not been achieved. Herein, we demonstrate protein‐specific detection of the glycosylation of the intracellular proteins OGT, Foxo1, p53, and Akt1 in living cells. Our generally applicable approach relies on Diels–Alder chemistry to fluorescently label intracellular carbohydrates through metabolic engineering. The target proteins are tagged with enhanced green fluorescent protein (EGFP). Förster resonance energy transfer (FRET) between the EGFP and the glycan‐anchored fluorophore is detected with high contrast even in presence of a large excess of acceptor fluorophores by fluorescence lifetime imaging microscopy (FLIM).