Facile Probe Design: Fluorescent Amphiphilic Nucleic Acid Probes without Quencher Providing Telomerase Activity Imaging Inside Living Cells

Precisely Detecting the Telomerase Activities by an AIEgen Probe with Dual Signal Outputs after Cell-Cycle Synchronization

By maintaining the telomere lengths, telomerase can make the tumor cells avoid the apoptosis, thus, achieving the cell immortalization. In the past, a series of telomerase detection systems have been developed through utilizing the unique characteristic of telomerase extended primer. However, fluctuation of telomerase activity, along with the cell cycle progression, leads to ambiguous detection results. Here, we reported a dual signal output detection strategy based on cell-cycle synchronization for precisely detecting telomerase activities by using a new AIEgen probe SSNB. Experimental and simulating calculation results demonstrated that positively charged SSNB could interact with DNA through the electrostatic interaction and π-π interaction, as well as the hydrogen bonds. The aggregation of SSNB caused by the extended template strand primer (TP) could be observed in tumor cells, thus, indicating the telomerase activity in various cell lines. Furthermore, after cell cycle synchronization, it was found that the telomerase activity in the S phase was the highest, no matter from the fluorescence intensity or the ROS generation situation. Dual signal outputs of SSNB verified the significance and necessity of cell-cycle synchronization detection for telomerase activity. This strategy could open a new window for the biotargets of which activity is variational in time dimension.

Engineered Aptamer-Organic Amphiphile Self-Assemblies for Biomedical Applications: Progress and Challenges

Currently, nucleic acid aptamers are exploited as robust targeting ligands in the biomedical field, due to their specific molecular recognition, little immunogenicity, low cost, ect. Thanks to the facile chemical modification and high hydrophilicity, aptamers can be site-specifically linked with hydrophobic moieties to prepare aptamer-organic amphiphiles (AOAs), which spontaneously assemble into aptamer-organic amphiphile self-assemblies (AOASs). These polyvalent self-assemblies feature with enhanced target-binding ability, increased resistance to nuclease, and efficient cargo-loading, making them powerful platforms for bioapplications, including targeted drug delivery, cell-based cancer therapy, biosensing, and bioimaging. Besides, the morphology of AOASs can be elaborately manipulated for smarter biomedical functions, by regulating the hydrophilicity/hydrophobicity ratio of AOAs. Benefiting from the boom in DNA synthesis technology and nanotechnology, various types of AOASs, including aptamer-polymer amphiphile self-assemblies, aptamer-lipid amphiphile self-assemblies, aptamer-cell self-assemblies, ect, have been constructed with great biomedical potential. Particularly, stimuli-responsive AOASs with transformable structure can realize site-specific drug release, enhanced tumor penetration, and specific target molecule detection. Herein, the general synthesis methods of oligonucleotide-organic amphiphiles are firstly summarized. Then recent progress in different types of AOASs for bioapplications and strategies for morphology control are systematically reviewed. The present challenges and future perspectives of this field are also discussed.

Live-Cell Sensing of Telomerase Activity by Using Hybridization-Sensitive Fluorescent Oligonucleotide Probes

Live-cell sensing of telomerase activity with simple and efficient strategies remains a challenging target. In this work, a strategy for telomerase sensing by using hybridization-sensitive fluorescent oligonucleotide probes is reported. In the presence of telomerase and dNTPs, the designed supporting strand was extended and generated the hairpin structure that catalyzed the next telomerase extending reaction. The special extension mechanism increased the local concentration of another supporting strand and telomerase, which resulted in enhanced telomerase activity. The hybridization-sensitive oligonucleotide probes bound to the hairpin catalyst and generated turn-on fluorescence. This method realized the sensing of telomerase activity in HeLa cell extract with a detection limit below 1.6×10^-6  IU μL^-1 . The real-time in situ observation of telomerase extension was achieved in living HeLa cells. This strategy has been applied to monitor the efficiency of telomerase-targeting anticancer drugs in situ.

Modular Design of Peptide- or DNA-Modified AIEgen Probes for Biosensing Applications

Fluorophore probes are widely used for bioimaging in cells, tissues, and animals as well as for monitoring of multiple biological processes in complex environments. Such imaging properties allow scientists to make direct visualizations of pathological events and cellular targets. Conventional fluorescent molecules have been developed for several decades and achieved great successes, but their emissions are often weakened or quenched at high concentrations that might suffer from the aggregation-caused quenching (ACQ) effect, which reduces the efficiencies of their applications. In contrast to the ACQ effect, aggregation-induced emission (AIE) luminogens (AIEgens) display much higher fluorescence in aggregated states and possess various advantages such as low background, long-term tracking ability, and strong resistance to photobleaching. Therefore, AIEgens are employed as unique fluorescence molecules and building blocks for biosensing applications in the fields of ions, amino acids, carbohydrates, DNAs/RNAs, peptides/proteins, cellular organelles, cancer cells, bacteria, and so on. Quite a few of the above biosensing missions are accomplished by modular peptide-modified AIEgen probes (MPAPs) or modular DNA-modified AIEgen probes (MDAPs) because of the multiple capabilities of peptide and DNA modules, including solubility, biocompatibility, and recognition. Meanwhile, both electrostatic interactions and coupling reactions could provide efficient methods to construct different MPAPs and MDAPs, finally resulting in a large variety of biosensing probes. Those probes exhibit leading features of detecting nucleic acids or proteins and imaging mass biomolecules. For example, under modular design, peptide modules possessing versatile recognition abilities enable MPAPs to detect numerous targets, such as integrin α_vβ₃, aminopeptidase N, MMP-2, MPO, H₂O₂, and so forth; MDAP could allow the imaging of mRNA in cells and tissue chips, suggesting the diagnostic functions of MDAP in clinical samples. Modular design offers a novel strategy to generate AIEgen-based probes and expedites functional biomacromolecules research. In this vein, here we review the progress on MPAPs and MDAPs in the most recent 10 years and highlight the modular design strategy as well as their advanced biosensing applications including briefly two aspects: (1) detection and (2) imaging. By the use of MPAPs/MDAPs, multiple bioanalytes can be efficiently analyzed at low concentrations and directly visualized through high-contrast and luminous imaging. Compared with MPAPs, the quantities of MDAPs are limited because of the difficult synthesis of long-length DNA strands. In future work, multifunctional of DNA sequences are needed to explore varieties of MDAPs for diverse biosensing purposes. At the end of this Account, some deficiencies and challenges are mentioned for briging more attention to accelerate the development of AIEgen-based probes.

AIEgens/Nucleic Acid Nanostructures for Bioanalytical Applications

DNA occupies significant roles in life processes, which include encoding the sequences of proteins and accurately transferring genetic information from generation to generation. Recent discoveries have demonstrated that a variety of biological functions are correlated with DNA's conformational transitions. The non-B form has attained great attention among the diverse forms of DNA over the past several years. The main reason for this is that a large number of studies have shown that the non-B form of DNA is associated with gross deletions, inversions, duplications, translocations as well as simple repeating sequences, which therefore causes human diseases. Consequently, the conformational transition of DNA between the B-form and the non-B form is important for biology. Conventional fluorescence probes based on the conformational transitions of DNA usually need a fluorophore and a quencher group, which suffers from the complex design of the structure and tedious synthetic procedures. Moreover, conventional fluorescence probes are subject to the aggregation-caused quenching (ACQ) effect, which limits their application toward imaging and analyte detection. Fluorogens exhibiting aggregation-induced emission (AIE) have attracted tremendous attention over the past decade. By taking advantage of this unique behavior, plenty of fluorescent switch-on probes without the incorporation of fluorescent quenchers/fluorophore pairs have been widely developed as biosensors for imaging a variety of analytes. Herein, the recent progress in bioanalytical applications on the basis of aggregation-induced emission luminogens (AIEgens)/nucleic acid nanostructures are presented and discussed.

Multivalent Self-Assembled DNA Polymer for Tumor-Targeted Delivery and Live Cell Imaging of Telomerase Activity

The efficient detection and in situ monitoring of telomerase activity is of great importance for cancer diagnosis and biomedical research. Here we report for the first time that the development of a novel multivalent self-assembled DNA polymer, constructed through telomerase primer sequence (ITS) triggered hybridization chain assembly using two functional hairpin probes (tumor-trageting aptamer modified H1 and signal probe modified H2), for sensitive detection and imaging of telomerase activity in living cells. After internalizing into the tumor cells by multivalent aptamer targeting, the ITS on DNA polymers can be elongated by intracellular telomerase to generate telomere repeat sequences that are complementary with the signal probe, which can proceed along the DNA polymers, and gradually light up the whole DNA polymers, leading to an enhanced fluorescence signal directly correlated with the activity of telomerase. Our results demonstrated that the developed DNA polymer show excellent performance for specifically detecting telomerase activity in cancer cells, dynamically monitoring the activity change of telomerase in response to telomerase-based drugs, and efficiently distinguishing cancer cells from normal cells. The proposed strategy may afford a valuable tool for the monitoring of telomerase activity in living cells and have great implications for biological and diagnostic applications.

Redefining Molecular Amphipathicity in Reversing the "Coffee-Ring Effect": Implications for Single Base Mutation Detection

The "coffee ring effect" is a natural phenomenon wherein sessile drops leave ring-shaped structures on the solid surfaces upon drying. It drives a nonuniform deposition of suspended compounds on the substrates, which adversely affects many processes, including surface-assisted biosensing and molecular self-assembly. In this study, we describe how the coffee ring effect can be eliminated by controlling the amphipathicity of the suspended compounds, for example, DNA modified with hydrophobic dye. Specifically, nuclease digestion of the hydrophilic DNA end converts the dye-labeled molecule into an amphipathic molecule (one with comparably weighted hydrophobic and hydrophilic ends) and reverses the coffee ring effect and results in a uniform disk-shaped feature deposition of the dye. The amphipathic product decreases the surface tension of the sessile drops and induces the Marangoni flow, which drives the uniform distribution of the amphipathic dye-labeled product in the drops. As a proof of concept, this strategy was used in a novel enzymatic amplification method for biosensing to eliminate the coffee ring effect on a nitrocellulose membrane and increase assay reliability and sensitivity. Importantly, the reported strategy for eliminating the coffee ring effect can be extended to other sessile drop systems for potentially improving assay reliability and sensitivity.

Probing DNA Hybridization Equilibrium by Cationic Conjugated Polymer for Highly Selective Detection and Imaging of Single-Nucleotide Mutation

Hybridization-based probes emerge as a promising tool for nucleic acid target detection and imaging. However, the single-nucleotide selectivity is still challenging because the specificity of hybridization reaction is typically low at room temperature. We disclose an effective and simple method for highly selective detection and in situ imaging of single-nucleotide mutation (SNM) by taking the advantages of the specific hybridization of short duplex and the signal amplifying effect of cationic conjugated polymer (CCP). Excellent discrimination of the nucleic acid strands only differing by single nucleotide was achieved enabling the sensitive detection of SNM at the abundance as low as 0.1%. Single-molecule fluorescence resonance energy transfer (smFRET) study reveals that the presence of CCP enhances the perfect matched duplex and the mismatched duplex to a different extent, which can be an explanation for the high single-nucleotide selectivity. Due to the simple design of the probe and the stable brightness of CCP, highly selective mRNA in situ imaging was achieved in fixed cells. Melanoma cell line A375 with BRAF V600E point mutation exhibits higher FRET efficiency than liver cancer cell line HegG2 that was not reported having the mutation at this point.

Determination of the activity of telomerase in cancer cells by using BSA-protected gold nanoclusters as a fluorescent probe

Gold nanoclusters (AuNCs) protected with a bovine serum albumin (BSA) coating are known to emit red fluorescence (peaking at 650 nm) on photoexcitation with ultraviolet light (365 nm). On addition of Cu(II) ions, fluorescence is quenched because Cu(II) complexes certain amino acid units in the BSA chain. Fluorescence is, however, restored if pyrophosphate (PPi) is added because it will chelate Cu(II) and remove it from the BSA coating on the AuNCs. Because PPi is involved in the function of telomerase, the BSA@AuNCs loaded with Cu(II) can act as a fluorescent probe for determination of the activity of telomerase. A fluorescent assay was worked out for telomerase that is highly sensitive and has a wide linear range (10 nU to 10 fM per mL). The fluorescent probe was applied to the determination of telomerase activity in cervix carcinoma cells via imaging. It is shown that tumor cells can be well distinguished from normal cells by monitoring the differences in intracellular telomerase activity. Graphical abstract Gold nanoclusters (AuNCs) protected by bovine serum albumin (BSA) and displaying red photoluminescence were prepared as fluorescent probe for the determination of telomerase activity and used for imaging of cervix carcinoma (HeLa) cells.

A Smart DNA Tweezer for Detection of Human Telomerase Activity

Reliable and accurate detection of telomerase activity is crucial to better understand its role in cancer cells and to further explore its function in cancer diagnosis and treatment. Here, we construct a smart DNA tweezer (DT) for detection of telomerase activity. The DT is assembled by three specially designed single-stranded oligonucleotides: a central strand dually labeled with donor/acceptor fluorophores and two arm strands containing overhangs complementary to telomerase reaction products (TRPs). It can get closed through hybridization with TRPs and get reopen through strand displacement reaction by TRPs' complementary sequences. First, under the action of telomerase, telomerase binding substrates (TS) are elongated to generate TRPs ended with telomeric repeats (TTAGGG) _n. TRPs hybridize with the two arm overhangs cooperatively and strain DT to closed state, inducing an increased fluorescence resonance energy transfer (FRET) efficiency, which is utilized for telomerase activity detection. Second, upon introduction of a removal strand (RS) complementary to TRPs, the closed DT is relaxed to open state via the toehold-mediated strand displacement, inducing a decreased FRET efficiency, which is utilized for determination of TRP length distribution. The detection limit of telomerase activity is equivalent to 141 cells/μL for HeLa cells, and telomerase-active cellular extracts can be differentiated from telomerase-inactive cellular extracts. Furthermore, TRPs owning 1, 2, 3, 4, and ≥5 telomeric repeats are identified to account for 25.6%, 20.5%, 15.7%, 12.5%, and 25.7%, respectively. The proposed strategy will offer a new approach for reliable, accurate detection of telomerase activity and product length distribution for deeper studying its role and function in cancer.

Highly sensitive fluorescence quantification of intracellular telomerase activity by repeat G-rich DNA enhanced silver nanoclusters

As an important biomarker for early cancer diagnosis and a valuable therapeutic target, the detection and monitoring of telomerase activity has attracted extensive attention.

A robust fluorescent probe for detection of telomerase activityin vitroand imaging in living cellsviatelomerase-triggering primer extension to desorb DNA from graphene oxide

A novel strategy for telomerase imaging was developed based on telomerase-triggering primer extension to desorb fluorophore labeled DNA from graphene oxide.

A highly sensitive and selective fluorescent probe without quencher for detection of Pb2+ ions based on aggregation-caused quenching phenomenon

Lead is a highly toxic heavy metal, and various functional nucleic acid (FNA)-based biosensors have been developed for the detection of Pb²⁺ in environmental monitoring. However, most fluorescence biosensors that have been reported were designed on the basis of a double-labeled (fluorophore and quencher group) DNA sequence, which not only involved an inconvenient organic synthesis but also restricted their wider use in practical applications. Here, we utilized a G-rich DNA sequence as a recognition probe and conjugated fluorene (CF) to develop a fluorescence sensor without a quencher based on the aggregation-caused quenching (ACQ) effect. In the presence of Pb²⁺, the degree of aggregation of CF was reduced because Pb²⁺ induced the formation of a G-quadruplex structure of the CF-DNA probe, and the fluorescence signal increased with the concentration of Pb²⁺ (0–1 μM), with a limit of detection of 0.36 nM. This fluorescent probe without a quencher enables the sensitive and selective detection of Pb²⁺. On the basis of these advantages, the CF-DNA probe represents a promising analytical method for detecting Pb²⁺.

Fluorescent probe with only a fluorophore but no quencher for detecting Pb²⁺ on the basis of the aggregation-caused quenching (ACQ) phenomenon.

Visualization of mitochondrial DNA in living cells with super-resolution microscopy using thiophene-based terpyridine Zn(ii) complexes

The thiophene-based terpyridine Zn(ii) complex LC targeted mitochondria by intercalative binding with mtDNA. STED super-resolution micrographs visualized mitochondrial cristae/inner matrix mtDNA.

Quantitative Determination of Telomerase Activity by Combining Fluorescence Correlation Spectroscopy with Telomerase Repeat Amplification Protocol

Telomerase is a key enzyme for maintaining the telomere length and is regarded as a versatile cancer biomarker and a potential drug target due to its important role in cancer and aging. It is necessary to develop a sensitive and reliable method for detection of telomerase activity due to its very low level in cells. In this Article, we propose an ultrasensitive and robust method for quantitative determination of telomerase activity by combining single molecule fluorescence correlation spectroscopy (FCS) with telomerase repeat amplification protocol (TRAP). The principle of this new method (FCS-TRAP) is based on measurement of the change in characteristic diffusion time and molecule number of TRAP products by FCS. The characteristic diffusion time is related to the length of TRAP products, and the molecule number represents the concentration of TRAP products. We optimized the conditions of TRAP procedure and FCS measurements. We observed that the telomerase activities are positively correlated to characteristic diffusion time and molecule number of TRAP products at optimal conditions. This method was successfully used for determination of telomerase activity of different cells, and detection of a single cell was realized. Meanwhile, this method was used to evaluate the inhibition efficiency of inhibitors, and the IC₅₀ values obtained were in good agreement with the references. Compared to current TRAP methods, this method shows reliable quantification, ultrahigh sensitivity, and short detection time and is without separation. We believe that the FCS-TRAP method has a potential application in clinical diagnosis and screening of telomerase inhibitors.

An AIEgens and exonuclease III aided quadratic amplification assay for detecting and cellular imaging of telomerase activity

Monitoring telomerase activity with high sensitive and reliable is of great importance to cancer analysis. In this paper, we report a sensitive and facile method to detect telomerase activity using AIEgens modified probe (TPE-Py-DNA) as a fluorescence reporter and exonuclease III (Exo III) as a signal amplifier. With the aid of telomerase, repeat units (TTAGGG)n are extended from the end of template substrate oligonucleotides (TS primer) that form duplex DNAs with TPE-Py-DNA. Then, Exo III catalyzes the digestion of duplex DNAs, liberating elongation product and releasing hydrophobic TPE-Py. The released hydrophobic TPE-Py aggregate together and produce a telomerase-activity-related fluorescence signal. The liberated product hybridizes with another TPE-Py-DNA probe, starting the second cycle. Finally, we obtain the target-to-signal amplification ratio of 1:N². This strategy exhibits good performance for detecting clinical urine samples (distinguishing 15 cancer patients' samples from 8 healthy ones) and checking intracellular telomerase activity (differentiating cell lines including HeLa, MDA-MB-231, MCF-7, A375, HLF and MRC-5 from the cells pretreated with telomerase-related drug), which shows its potential in clinical diagnosis as well as therapeutic monitoring of cancer.

Advances in the detection of telomerase activity using isothermal amplification

Telomerase plays a significantly important role in keeping the telomere length of a chromosome. Telomerase overexpresses in nearly all tumor cells, suggesting that telomerase could be not only a promising biomarker but also a potential therapeutic target for cancers. Therefore, numerous efforts focusing on the detection of telomerase activity have been reported from polymerase chain reaction (PCR)-based telomeric repeat amplification protocol (TRAP) assays to PCR-free assays such as isothermal amplification in recent decade. In this review, we highlight the strategies for the detection of telomerase activity using isothermal amplification and discuss some of the challenges in designing future telomerase assays as well.