A versatile turn-on fluorometric biosensing profile based on split aptamers-involved assembly of nanocluster beacon sandwich

Suo, Tiying; Sohail, Muhammad; Ma, Yujie; Li, Bingzhi; Chen, Yue; Xing, Zhou; Zhou, Xuemin

doi:10.1016/j.snb.2020.128586

Cited by 27 publications

(5 citation statements)

References 47 publications

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“…Aside from these six DNA aptamer selections, there are also RNA aptamers for E2 . While these aptamers are quite different in length, sequence, and predicted secondary structure, they have been extensively used to detect E2 in various biosensors. − …”

Section: Introductionmentioning

confidence: 99%

Capture-SELEX of DNA Aptamers for Estradiol Specifically and Estrogenic Compounds Collectively

Niu

Zhang

Liu

2022

Environ. Sci. Technol.

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Estrogenic compounds such as estrone (E1), 17β-estradiol (E2), and 17α-ethynylestradiol (EE2) are serious environmental contaminants due to their potent biological activities. At least six selections were previously reported to obtain DNA aptamers for E2, highlighting its environmental importance. A careful analysis revealed that the previous aptamers either are too long or do not bind optimally. Herein, a series of new aptamers were obtained from the capture-SELEX method with dissociation constants down to 30 nM as determined by isothermal titration calorimetry (ITC). Two aptamers were converted to structure-switching fluorescent biosensors, which achieved a limit of detection down to 3.3 and 9.1 nM E2, respectively. One aptamer showed similar binding affinities to all the three estrogens, while the other aptamer is more selective for E2. Both aptamers required Mg2+ for binding. The proposed sensors were successfully applied in the determination of E2 in wastewater. Moreover, comparisons were made with previous aptamers based on primary sequence alignment and secondary structures. Among previously reported truncated aptamers, ITC showed binding only in one of them. The newly selected aptamers have the combined advantages of small size and high affinities.

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Section: Introductionmentioning

confidence: 99%

Capture-SELEX of DNA Aptamers for Estradiol Specifically and Estrogenic Compounds Collectively

Niu

Zhang

Liu

2022

Environ. Sci. Technol.

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“…We used the gel electrophoresis and fluorescence spectra to verify the design of the sensing scheme. In Figure a, six lanes can be seen in the gel image from native polyacrylamide gel electrophoresis (native-PAGE), which is the gold standard for analyzing the length, bending, and flexibility of nucleic acids. ,, Lane 1 contains a single bright band, which represents the FDP band that serves as a marker. The band uniformity observed in Lane 1 indicates that annealing of the ssDNA generated a uniform FDP.…”

Section: Resultsmentioning

confidence: 99%

Signal-Amplified Detection of the Tumor Biomarker FEN1 Based on Cleavage-Induced Ligation of a Dumbbell DNA Probe and Rolling Circle Amplification

Xia

Xie

et al. 2021

Anal. Chem.

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Flap endonuclease 1 (FEN1), an endogenous nuclease with the ability to cleave the 5′ overhang of branched dsDNA, is of significance in DNA replication and repair. The overexpression of FEN1 is common in cancer because of the ubiquitous upregulation of DNA replication; thus, FEN1 has been recognized as a potential biomarker in oncological investigations. However, few analytical methods targeting FEN1 with high sensitivity and simplicity have been developed. This work developed a signal-amplified detection of FEN1 based on the cleavage-induced ligation of a dumbbell DNA probe and rolling circle amplification (RCA). A flapped dumbbell DNA probe (FDP) was rationally designed with a FEN1 cleavable flap at the 5′ end. The cleavage generated a nick site with juxtaposed 5′ phosphate and 3′ hydroxyl ends, which were linkable by T4 DNA ligase to form a closed dumbbell DNA probe (CDP) with a circular conformation. The CDP functioned as a template for RCA, which produced abundant DNA that could be probed using SYBR Green I. The highly sensitive detection of FEN1 with a limit of detection of 15 fM was achieved, and this method showed high specificity, which enabled the quantification of FEN1 in real samples. The inhibitory effects of chemicals on FEN1 were also evaluated. This study represents the first attempt to develop an FEN1 assay that involves signal amplification, and the novel biosensor method enriches the tools for FEN1-based diagnostics.

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“…While the mechanism behind NCBs could be the aforementioned additive process (i.e., an originally small AgNC becomes larger), we were unable to characterize the stoichiometries of the AgNCs before and after hybridization (which leads to guanine proximity) due to the large size of NCBs (a duplex of a 42-nt-long and a 48-nt-long strand). Although NCBs have made a substantial impact in the molecular sensing field 34,35 , how exactly NCBs are transformed from a dark species into a bright species is still a mystery. In contrast, we have strong evidence that Subaks are converted from one species (e.g., green) into another (e.g., red) due to the subtractive process (e.g., Ag13-14 to Ag10).…”

Section: Discussionmentioning

confidence: 99%

A non-FRET DNA reporter that changes fluorescence colour upon nuclease digestion

Hong,

Walker,

Luong

et al. 2024

Nat. Nanotechnol.

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Fluorescence resonance energy transfer (FRET) reporters are commonly used in the final steps of nucleic acid amplification tests to indicate the presence of nucleic acid targets, where fluorescence is restored by nuclease activities cleaving the FRET reporters. However, the need for dual labeling and purification in manufacturing makes them expensive. Here we demonstrate a low-cost silver nanocluster reporter that does not rely on FRET as the on/off switching mechanism but can fluoresce differently upon nuclease digestion. A 90-nm red shift in emission is observed upon reporter cleavage, which a simple donor-quencher FRET reporter cannot achieve. Electrospray ionization mass spectrometry (ESI-MS) results suggest that the stoichiometric change of silver cluster from Ag13 (in the intact DNA host) to Ag10 (in the fragments) is likely responsible for the emission color change after reporter digestion. Our results demonstrate that DNA-templated silver nanocluster probes can be versatile reporters for detecting nuclease activities and provide insights into the interactions between nucleases and metallo-DNA nanomaterials.

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A versatile turn-on fluorometric biosensing profile based on split aptamers-involved assembly of nanocluster beacon sandwich

Cited by 27 publications

References 47 publications

Capture-SELEX of DNA Aptamers for Estradiol Specifically and Estrogenic Compounds Collectively

Capture-SELEX of DNA Aptamers for Estradiol Specifically and Estrogenic Compounds Collectively

Signal-Amplified Detection of the Tumor Biomarker FEN1 Based on Cleavage-Induced Ligation of a Dumbbell DNA Probe and Rolling Circle Amplification

A non-FRET DNA reporter that changes fluorescence colour upon nuclease digestion

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