Specific and Sensitive Fluorescence Anisotropy Sensing of Guanine-Quadruplex Structures via a Photoinduced Electron Transfer Mechanism

Zhang, David; Shen, Hujun; Li, Guohui; Zhao, Bailin; A, Yu; Zhao, Qiang; Wang, Hailin

doi:10.1021/ac302320x

Cited by 33 publications

(34 citation statements)

References 56 publications

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“…S1). The increase in fluorescence lifetime and the enhancement of fluorescence intensity are consistent with PET mechanism reported by others and our previous studies [63,66,70,71,75]. These results suggest that the intramolecular interaction between the labeled TMR and adjacent guanine bases in the aptamer probe gives rise to PET, which is eliminated upon binding to Pb 2+ , resulting in the formation of a G-quadruplex.…”

Section: Principle Of Sensing Pb 2+ By Fasupporting

confidence: 91%

“…Based on our recent finding that the FA of a G-rich oligonucleotide probe dramatically decreased upon formation of a G-quadruplex [66], we hypothesize that if the reduction in FA is dependent on Pb 2+ , a novel FA method for Pb 2+ detection might be possible. Here TBA, a G-quadruplex oligonucleotide, was chosen as the recognition element for sensing aqueous Pb 2+ by measuring the reduction in FA.…”

Section: Principle Of Sensing Pb 2+ By Famentioning

confidence: 99%

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A sensitive fluorescence anisotropy method for detection of lead (II) ion by a G-quadruplex-inducible DNA aptamer

Zhang

Meng

et al. 2014

Analytica Chimica Acta

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h i g h l i g h t s• A fluorescence anisotropy approach for detection of Pb 2+ was developed.• The strategy was based on bindinginduced allosteric conformational change of aptamer probe.• The sensing mechanism was established by testing the photoinduced electron transfer interaction. in homogeneous solution by a G-rich thrombin binding aptamer (TBA). The TBA labeled with 6-carboxytetramethylrhodamine (TMR) at the seventh thymine nucleotide was used as a fluorescent probe for signaling Pb 2+ . It was found that the aptamer probe had a high FA in the absence of Pb 2+ . This is because the rotation of TMR is restricted by intramolecular interaction with the adjacent guanine bases, which results in photoinduced electron transfer (PET). When the aptamer probe binds to Pb 2+ to form G-quadruplex, the intramolecular interaction should be eliminated, resulting in faster rotation of the fluorophore TMR in solution. Therefore, FA of aptamer probe is expected to decrease significantly upon binding to Pb 2+ . Indeed, we observed a decrease in FA of aptamer probe upon Pb 2+ binding. Circular dichroism, fluorescence spectra, and fluorescence lifetime measurement were used to verify the reliability and reasonability of the sensing mechanism. By monitoring the FA change of the aptamer probe, we were able to real-time detect binding between the TBA probe and Pb 2+ . Moreover, the aptamer probe was exploited as a recognition element for quantification of Pb 2+ in homogeneous solution. The change in FA showed a linear response to Pb 2+ from 10 nM to 2.0 M, with 1.0 nM limit of detection. In addition, this sensing system exhibited good selectivity for Pb 2+ over other metal ions. The method is simple, quick and inherits the advantages of aptamer and FA.

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Section: Principle Of Sensing Pb 2+ By Fasupporting

confidence: 91%

Section: Principle Of Sensing Pb 2+ By Famentioning

confidence: 99%

A sensitive fluorescence anisotropy method for detection of lead (II) ion by a G-quadruplex-inducible DNA aptamer

Zhang

Meng

et al. 2014

Analytica Chimica Acta

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“…Then, the target binding may induce a change of the TMR-involved intramolecular interaction followed by the alteration of the rotational diffusion and fluorescence lifetime of TMR, and thus a remarkable FA change can be triggered upon target binding. 2,5,43 Taking these unique properties of TMR and aptamer, a simple direct FA strategy for small-molecule detection can be established. We chose ochratoxin A (OTA) as a model of a small molecule to propose this simple FA strategy for small-molecule analysis by using a TMR-labeled aptamer.…”

Section: ■ Results and Discussionmentioning

confidence: 99%

“…35−41 This intramolecular interaction restricts the local rotation of TMR on ssDNA and decreases the fluorescence lifetime of TMR, which affect the FA signal. 20,22,38,42,43 It is also known that the binding of target usually induces an adaptive conformation change of the aptamer. 13−17 This conformational change can bring a subsequent alteration of the interaction between labeled TMR and the bases of the aptamer, and the FA of the labeled TMR on the aptamer can be significantly changed upon target binding.…”

mentioning

confidence: 99%

“…The unique intramolecular interaction between TMR and guanine bases and the allosteric property of the aptamer provide another opportunity to develop a simple FA strategy for target analysis with TMR-labeled aptamer, differing from the mass change dependent FA strategy. 5,19,20,22,42,43 Considering that the binding of a small target cannot cause a large change of the molecular mass of the dye-labeled aptamer, this intramolecular interaction dependent FA strategy is more adaptable to small-molecule detection with a dye-labeled aptamer.…”

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Identification of Allosteric Nucleotide Sites of Tetramethylrhodamine-Labeled Aptamer for Noncompetitive Aptamer-Based Fluorescence Anisotropy Detection of a Small Molecule, Ochratoxin A

Zhao

Wang

2013

Anal. Chem.

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Aptamer-based fluorescence anisotropy (FA) assay combines the advantages of affinity aptamers in good stability, easy generation, and facile labeling and the benefits of FA in homogeneous analysis, such as robustness, simplicity, and high reproducibility. By using a fluorophore-labeled aptamer, FA detection of a small molecule is not as easy as detection of protein because the binding of a small molecule cannot cause significant increase of molecular weight of the dye-labeled aptamer. The intramolecular interaction between labeled tetramethylrhodamine (TMR) and DNA aptamer bases dramatically affects the local rotation and FA of TMR. This intramolecular interaction can be altered by aptamer conformation change upon target binding, leading to a significant change of FA of TMR. Taking this unique feature of a TMR-labeled aptamer, we described a noncompetitive aptamer-based fluorescence anisotropy assay for detection of small molecules by using ochratoxin A (OTA) as a model. We successfully identified the specific TMR-labeling sites of aptamers with sensitive FA response to OTA from the 5′-end, 3′-end and the internal thymine (T) bases. The aptamer with a TMR labeled on the 10th T base exhibited a remarkable FA reduction response to OTA (Δr = 0.078), without requiring any proteins or nanomaterials as FA signal enhancers. This FA approach for OTA showed high sensitivity with a detection limit of 3 nM, a dynamic range from 3 nM to 3 μM, and good selectivity over the tested compounds with similar structures to OTA. The new strategy allowed the detection of OTA in diluted red wine and urine samples. F luorescence anisotropy (FA) is a powerful and unique analytical technique for molecular interactions study and assay developments, which relies on the rotational diffusion of fluorescent tracers or probes under polarized excitation light. 1−5Fluorescence anisotropy shows strength in real-time analysis, simplicity, robustness, and sensitivity. FA assays have been applied to the studies about protein−protein interaction and protein−DNA interaction and the immunoassays for drug discovery, diagnostics, environmental monitoring, and food analysis. 1−7The emergence of aptamers as affinity ligands makes the aptamer-based FA assay attractive due to their advantages over antibodies in ease of synthesis and labeling, great stability, good selectivity, and high binding affinity. 8−12 Target-dependent allosteric structural change is one unique feature of an aptamer, and it allows the construction of an aptamer switch for target analysis through the adaptive transition converting a binding event into a detectable signal. 8,13−17 The applications of fluorophore-labeled aptamers to direct FA analysis of proteins are relatively straightforward as aptamers are usually smaller than proteins in size. 5,8,11,12 The binding of the fluorophorelabeled aptamers to proteins can cause enhanced FA signals by restricting the rotational diffusion of the labeled fluorophore as a result of increased molecular size. 18−23 In contrast, the ...

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A New Architecture for DNA‐Templated Synthesis in Which Abasic Sites Protect Reactants from Degradation

Frommer,

Oppenheimer,

Allott

et al. 2024

Angewandte Chemie

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The synthesis of artificial sequence‐defined polymers that match and extend the functionality of proteins is an important goal in materials science. One way of achieving this is to program a sequence of chemical reactions between precursor building blocks by means of attached oligonucleotide adapters. However, hydrolysis of the reactive building blocks has so far limited the length and yield of product that can be obtained using DNA‐templated reactions. Here, we report an architecture for DNA‐templated synthesis in which reactants are tethered at internal abasic sites on opposite strands of a DNA duplex. We show that an abasic site within a DNA duplex can protect a nearby thioester from degradation, significantly increasing the yield of a DNA‐templated reaction. This protective effect has the potential to overcome the challenges associated with programmable sequence‐controlled synthesis of long non‐natural polymers by extending the lifetime of the reactive building blocks.

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Specific and Sensitive Fluorescence Anisotropy Sensing of Guanine-Quadruplex Structures via a Photoinduced Electron Transfer Mechanism

Cited by 33 publications

References 56 publications

A sensitive fluorescence anisotropy method for detection of lead (II) ion by a G-quadruplex-inducible DNA aptamer

A sensitive fluorescence anisotropy method for detection of lead (II) ion by a G-quadruplex-inducible DNA aptamer

Identification of Allosteric Nucleotide Sites of Tetramethylrhodamine-Labeled Aptamer for Noncompetitive Aptamer-Based Fluorescence Anisotropy Detection of a Small Molecule, Ochratoxin A

A New Architecture for DNA‐Templated Synthesis in Which Abasic Sites Protect Reactants from Degradation

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