A pH-responsive colorimetric detection of human telomerase RNA based on a three-dimensional DNA amplifier

Construction of a 3D Quantum Dot Nanoassembly with Two-Step FRET for One-Step Sensing of Human Telomerase RNA in Breast Cancer Cells and Tissues

Telomerase is an important biomarker for early diagnosis of cancers, but current telomerase assays usually rely on measuring the extension products of telomerase substrates, which increases the assay complexity. More evidence indicates that human telomerase RNA (hTR), as a core component of telomerase, is positively correlated with the telomerase activity. Herein, we demonstrate the development of a duplex-specific nuclease (DSN)-propelled 3D quantum dot (QD) nanoassembly with two-step Föster resonance energy transfer (FRET) for the one-step sensing of hTR in breast cancer cells and tissues. This assay involves only one hairpin probe modified with a Cy5 at the sixth base from the 5'-biotin end and a BHQ2 at the 3'-terminus, which integrates three functions of target recognition, target recycling amplification, and signal readout. The anchoring of the hairpin probe on the 605QD surface results in the formation of a 3D 605QD-Cy5-probe-BHQ2 nanoassembly in which two-step FRET occurs among the 605QD, Cy5, and BHQ2 quencher. Notably, the formation of 605QD-Cy5-probe-BHQ2 nanoassembly facilitates the reduction of background signal and the increase of signal-to-background ratio due to its dense, highly oriented nucleic acid shell-induced steric hindrance effect. This assay can achieve one-step and rapid detection of hTR with a detection limit of 2.10 fM, which is the simplest and most rapid hTR assay reported so far. Moreover, this assay can efficiently distinguish single-base mismatched sequences, and it can discriminate the hTR level between breast cancer patients and healthy donors with a high accuracy of 100%, with great prospects for early diagnosis of cancers.

Aggregation-Induced Enhanced Electrochemiluminescence from Tris(bipyridine)ruthenium(II) Derivative Nanosheets for the Ultrasensitive Detection of Human Telomerase RNA

The traditional tris(bipyridine)ruthenium(II) complex suffers from the notorious aggregation-caused quenching effect, which greatly compromises its electrochemiluminescence (ECL) efficiency, thus hindering further applications in biosensing and clinical diagnosis. Here, the ultrathin tetraphenylethylene-active tris(bipyridine)ruthenium(II) derivative nanosheets (abbreviated as Ru-TPE NSs) are synthesized through a protein-assisted self-assembly strategy for ultrasensitive ECL detection of human telomerase RNA (hTR) for the first time. The synthesized Ru-TPE NSs exhibit the aggregation-induced enhanced ECL behavior and excellent water-dispersion. Surprisingly, up to a 106.5-fold increase in the ECL efficiency of Ru-TPE NSs is demonstrated compared with the dispersed molecules in an organic solution. The restriction of intramolecular motions is confirmed to be responsible for the significant ECL enhancement. Therefore, this proposed ECL biosensor shows high sensitivity and excellent selectivity for hTR based on Ru-TPE NSs as efficient ECL beacons and the catalytic hairpin assembly as signal amplification, whose detection limit is as low as 8.0 fm, which is far superior to the previously reported works. Here, a promising analytical method is provided for early clinical diagnosis and a new type of efficient ECL emitters with great application prospects is represented.

Spatiotemporal control of DNAzyme activity for fluorescent imaging of telomerase RNA in living cells

BACKGROUND

Human telomerase is a ribonucleoprotein complex that includes proteins and human telomerase RNA (hTR). Emerging evidence suggested that the expression level of hTR was high related with the development of tumor, so it is important to accurately detect the content of hTR. Optical control of DNAzyme activity shows a promising strategy for precise biosensing, biomedical imaging and modulation of biological processes. Although DNAzyme-based sensors can be controlled spatiotemporally by light, its application in the detection of hTR in living cells is still rare. Therefore, designing DNAzyme activity spatiotemporal controllable sensors for hTR detection is highly needed.

RESULTS

We developed a UV light-activated DNAzyme-based nanoprobe for spatially accurate imaging of intracellular hTR. The proposed nanoprobe was named MDPH, which composed of an 8-17 DNAzyme (D) inactivated by a protector strand (P), a substrate strand (H), and MnO2 nanosheets. The MnO2 nanosheets can enhance the cellular uptake of DNA strands, so that MDPH probe can enter cells autonomously through endocytosis. Under the high concentration of GSH in cancer cells, MnO2 nanosheets can self-generate cofactors to maintain the catalytic activity of DNAzyme. When exposing UV light and in presence of target hTR, DNAzyme could cleave substrate H, resulting in the recovery of fluorescence of the system. The cells imaging results show that MDPH probe could be spatiotemporally controlled to image endogenous hTR in cancer cells.

SIGNIFICANCE

With this design, telomerase RNA-specific fluorescent imaging was achieved by MDPH probe in both cancer and normal cells. Our probe made a promising new platform for spatiotemporal controllable intracellular hTR monitoring. This current method can be applied to monitor a variety of other biomarkers in living cells and perform medical diagnosis, so it may has broad applications in the field of medicine.

Recent Advances in Design and Application of Nanomaterials-Based Colorimetric Biosensors for Agri-food Safety Analysis

A colorimetric sensor detects an analyte by utilizing the optical properties of the sensor unit, such as absorption or reflection, to generate a structural color that serves as the output signal to detect an analyte. Detecting the refractive index of an analyte by recording the color change of the sensor structure on its surface has several advantages, including simple operation, low cost, suitability for onsite analysis, and real-time detection. Colorimetric sensors have drawn much attention owing to their rapidity, simplicity, high sensitivity and selectivity. This Review discusses the use of colorimetric sensors in the food industry, including their applications for detecting food contaminants. The Review also provides insight into the scope of future research in this area.

Ratiometric fluorescence resonance energy transfer for reliable and sensitive detection of intracellular telomerase RNA via strand displacement reaction amplification

Human telomerase RNA (hTR) is one essential component of telomerase and is overexpressed in tumor cells. Therefore, the reliable and sensitive detection of hTR is essential for the early cancer diagnosis. Herein, to avoid the false positive signals caused by co-existing components in the cell, a ratiometric fluorescence resonance energy transfer (FRET) strategy was developed to achieve reliable detection of intracellular hTR. Manganese dioxide nanosheets (MnO₂NS) with good biocompatibility carry two fluorophore-labelled hairpin DNA probes into the cancer cell and then release the probes via decomposition of MnO₂NS by intracellular L-glutathione reduced (GSH). Then, hTR triggered the cyclic strand displacement reaction (SDR) between two hairpin DNA probes to continuously form DNA duplexes, which made two fluorophores close to each other and led to an effective FRET. Fluorescence imaging demonstrated a higher expression level of hTR in HeLa cells than that in normal HL-7702 cells. The high specificity of hairpin DNA probes and SDR make it easy to discriminate the single-base mutation. Therefore, it provides a highly sensitive, simple and reliable method for the extracellular and intracellular detection of hTR.

Translating cancer exosomes detection into the color change of phenol red based on target-responsive DNA microcapsules

Emerging evidence indicates that exosomes can be used as a potential biomarker for monitoring diseases, including cancer. However, enhancing the sensing performance in terms of convenience and sensitivity remains an urgent demand for exosomes detection. In this study, a pH-sensitive colorimetric biosensing strategy was developed for exosomes detection by integrating stimuli-responsive DNA microcapsules and acetylcholinesterase to produce acetic acid. The constructed DNA microcapsules consisted of DNA shells crosslinked by anti-CD63 aptamers and loaded with acetylcholinesterase. With exosomes addition, an energetically stabilized aptamer-CD63 compound was produced and microcapsules dissociated due to the reaction of surface protein CD63 of exosomes and aptamer of CD63, resulting in the release of encapsulated AChE. Through a simple centrifugation separation, unreacted DNA microcapsules were removed and the supernatant containing released acetylcholinesterase collected, which was then used for colorimetric exosomes detection through the ability of acetylcholinesterase to hydrolyze acetylcholine to release acetic acid. The resulting decreased solution pH was detected with phenol red indicator, with the sharp color transition conveniently by naked eye. Exosomes quantification was also achieved using the solution's absorption intensity ratio of 558 vs. 432 nm. The linear range was from 2.0 × 10³ to 5.0 × 10⁵ particles/μL, and the limit of detection and limit of quantification were 1.2 × 10³ particles/μL and 2.2 × 10³ particles/μL, respectively. In addition, this proposed strategy for exosomes detection showed a relative standard deviation of 3.1% and high recovery efficiency (>94%), exhibiting a bright application future in exsomes analysis.

Improving the Sensitivity of the miRNA Assay Coupled with the Mismatched Catalytic Hairpin Assembly Reaction by Optimization of Hairpin Annealing Conditions

The mismatched catalytic hairpin assembly (mCHA), a programmable oligonucleotide circuit, is one of the promising isothermal amplification methods used in nucleic acid detection. Its limitations are related to a high background noise observed due to the target-independent hybridization of the reacting hairpins (HPs). In this work, it was shown that the introduction of salts such as NaCl and MgCl₂ to HP1/HP2 annealing solutions sharply reduces the background in mCHA and simultaneously increases the signal-to-background (S/B) ratio. A comparison of the salts demonstrated the higher activity of MgCl₂ as compared to NaCl. A similar effect of reducing the background was observed with a decrease in the concentration of H1/H2 probes in annealing solutions. Using the favorable annealing conditions allowed the development of an ultrasensitive chemiluminescence assay coupled with mCHA for miRNA quantitation. Except mCHA, the use of a streptavidin-polyHRP conjugate and an enhanced chemiluminescence reaction additionally increased the assay sensitivity. Notably, the optimization of the HP annealing diminished the detection limit of the assay by 2 orders of magnitude and increased the sensitivity and precision of miRNA-141 determination. The discovered fact of reducing the background by the variation of HP annealing conditions may be valuable not only for the mCHA performance but also likely for other HP-based biochemical methods.

Hairpin DNA-Mediated isothermal amplification (HDMIA) techniques for nucleic acid testing

Nucleic acid detection is of great importance in a variety of areas, from life science and clinical diagnosis to environmental monitoring and food safety. Unfortunately, nucleic acid targets are always found in trace amounts and their response signals are difficult to be detected. Amplification mechanisms are then practically needed to either duplicate nucleic acid targets or enhance the detection signals. Polymerase chain reaction (PCR) is one of the most popular and powerful techniques for nucleic acid analysis. But the requirement of costly devices for precise thermo-cycling procedures in PCR has severely hampered the wide applications of PCR. Fortunately, isothermal molecular reactions have emerged as promising alternatives. The past decade has witnessed significant progress in the research of isothermal molecular reactions utilizing hairpin DNA probes (HDPs). Based on the nucleic acid strand interaction mechanisms, the hairpin DNA-mediated isothermal amplification (HDMIA) techniques can be mainly divided into three categories: strand assembly reactions, strand decomposition reactions, and strand creation reactions. In this review, we introduce the basics of HDMIA methods, including the sensing principles, the basic and advanced designs, and their wide applications, especially those benefiting from the utilization of G-quadruplexes and nanomaterials during the past decade. We also discuss the current challenges encountered, highlight the potential solutions, and point out the possible future directions in this prosperous research area.

Highly sensitive fluorescence biosensing of BCR-ABL1 fusion gene based on exponential transcription-triggered hemin catalysis

Simple, sensitive and specific detection of the transcription level of BCR-ABL1 mRNA possesses vital clinical significance in diagnosis and treatment of chronic myeloid leukemia (CML). In this study, an innovative fluorescence biosensing methodology has been developed for sensitive and specific detection of BCR-ABL1 mRNA by integrating high-efficiency of exponential transcription and superior catalytic performance of DNA-grafted hemin. Exponential transcription was triggered by BCR-ABL1 mRNA to produce plenty of RNA products. They can specifically hybridize with circular dual-labeled hemin (DLH) probe to dissociate the intramolecular hemin dimmers into highly active hemin monomers for catalyzing fluorescence substrate tyramine. This exponential transcription-triggered hemin catalysis (ET-HC) strategy showed highly sensitive and specific for BCR-ABL1 detection with a limit of detection at 0.5 aM and a good linear range from 2 aM to 200 fM. This method was successfully applied to directly detect as low as 0.001% e13a2 transcript isoforms from complex genomic RNA extraction. Compared with clinical routine, the overall process is a thermostatic reaction and eliminates additional reverse transcription operation. Therefore, the developed ET-HC strategy might provide a promising alternative tool for precise diagnosis and personalized treatment of CML.