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Liu H, Zhang X, Li X, Wu H, Shi Y, Lu W. A G-quadruplex/thioflavin T-based label-free biosensor to detect ClO - in stress-induced hypertension. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 314:124231. [PMID: 38574610 DOI: 10.1016/j.saa.2024.124231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/25/2024] [Accepted: 03/30/2024] [Indexed: 04/06/2024]
Abstract
Hypochlorous acid (HClO), as an essential reactive oxygen species (ROS) in biological systems, plays a pivotal role in processes of physiology and pathology. Abnormal fluctuations in HClO concentration can lead to various diseases, such as inflammation, cardiovascular diseases, and neurodegeneration. Therefore, developing an approach to rapidly and sensitively quantify ClO- content is vital to biomedicine development and bioassays. Herein, we fabricated a novel "turn-on" label-free fluorescence DNA probe to specifically detect hypochlorite ion (ClO-) based on G-quadruplex formation. To this end, we designed a G-rich signal DNA sequence (S-DNA) and a block DNA sequence (B-DNA), followed by the introduction of ClO--responsive phosphorothioate (PS) into B-DNA. In the absence of ClO-, B-DNA hybridized with S-DNA, preventing G-quadruplex formation from S-DNA; this resulted in the relatively low fluorescence intensity of ThT. Once ClO- was added, the hydrolysis between PS and ClO- split the B-DNA into two fragments, resulting in B-DNA breaking away from S-DNA, allowing G-quadruplex formation from S-DNA and increasing the fluorescence intensity of ThT. Using this method, we can detect ClO- without the interference of additional reactive oxygen species. The detection limit of ClO- was as low as 10 nM. Furthermore, this method facilitates the detection of ClO- within the tissues of rats with stress-induced hypertension.
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Affiliation(s)
- Haisheng Liu
- College of Agriculture and Bioengineering, Heze University, Shandong, Heze 274000, China
| | - Xin Zhang
- College of Agriculture and Bioengineering, Heze University, Shandong, Heze 274000, China
| | - Xiangrong Li
- Shandong Provincial Hospital Group Heze Hospital, Shandong, Heze 274000, China
| | - Hongsong Wu
- College of Agriculture and Bioengineering, Heze University, Shandong, Heze 274000, China
| | - Yiwei Shi
- College of Agriculture and Bioengineering, Heze University, Shandong, Heze 274000, China
| | - Wen Lu
- College of Agriculture and Bioengineering, Heze University, Shandong, Heze 274000, China.
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Xu J, Zhou T, Xue D, Sui Z, Yang H, Yuan X, Wang Q. Integrating recombinase polymerase amplification with CRISPR/Cas9-initiated nicking-rolling circle amplification in Staphylococcus aureus assay. Chem Commun (Camb) 2024; 60:5314-5317. [PMID: 38666524 DOI: 10.1039/d4cc00238e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2024]
Abstract
We integrate recombinase polymerase amplification (RPA) with CRISPR/Cas9-initiated nicking rolling circle amplification (CRISPR/Cas9-nRCA) for detecting Staphylococcus aureus. This approach utilizes a unique dimeric G-triplex structure, demonstrating firstly enhanced ThT fluorescence for target detection. The proof-of-concept study introduces a new avenue for integrating isothermal amplifications with CRISPR/Cas9 in the fields of pathogen detection and disease diagnosis.
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Affiliation(s)
- Jianguo Xu
- Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Zhejiang, Jiaxing, 314001, P. R. China.
| | - Tong Zhou
- School of Biological and Food Engineering, Fuyang Normal University, Anhui, Fuyang, 236037, P. R. China.
| | - Danni Xue
- School of Biological and Food Engineering, Fuyang Normal University, Anhui, Fuyang, 236037, P. R. China.
| | - Zhuqi Sui
- Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Zhejiang, Jiaxing, 314001, P. R. China.
| | - Haidong Yang
- Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Zhejiang, Jiaxing, 314001, P. R. China.
| | - Xinyue Yuan
- Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Zhejiang, Jiaxing, 314001, P. R. China.
| | - Qi Wang
- School of Biological and Food Engineering, Fuyang Normal University, Anhui, Fuyang, 236037, P. R. China.
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Lai R, Zeng X, Xu Q, Xu Y, Li X, Ru Y, Wang Y, Wang D, Zhou X, Shao Y. Ratiometric G-quadruplex/hemin DNAzymes with low-dosage associative substrates. Anal Chim Acta 2024; 1295:342320. [PMID: 38355221 DOI: 10.1016/j.aca.2024.342320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 01/31/2024] [Indexed: 02/16/2024]
Abstract
BACKGROUND G-quadruplex (G4)/hemin DNAzymes with conversion of substrates into colorimetric readouts are well recognized as convenient biocatalysis tools in sensor development. However, the previously developed colorimetric G4/hemin DNAzymes are diffusive substrate-based DNAzymes (DSBDs). The current colorimetric DSBDs have several drawbacks including high dosage (∼mM) of diffusive substrates (DSs), colorimetric product toxicity, and single colorimetric readout without tolerance to fluctuation of experimental factors and background. In addition, the usage of high-dosage DSs can smear the G4 foldings and their discard is more harmful to environment. Therefore, exploring alternative DNAzymes with potential to overcome these drawbacks of DSBDs is urgently needed. RESULTS We herein developed associative substrate-based DNAzymes (ASBDs). Cyanine dyes were selected as associative substrates (ASs) due to their binding competency with G4/hemin DNAzymes. With respect to DSBDs, ASBDs needed only low dosage (∼10 μM) of ASs to be able to cause a rapid and visible substrate conversion. In addition, since cyanine dyes are NIR dyes with high extinction coefficients and their conversion products have absorption bands at shorter wavelength. Therefore, a colorimetric ratio response can be developed to follow activities of G4/hemin DNAzymes with competency to tolerate fluctuation of experimental factors and background. In particular, herein developed ASBDs can endure somewhat concentration fluctuation of H2O2. ASBDs are able to cowork with other enzymes (for example, glucose oxidase) to realize cascade sensing. SIGNIFICANCE The developed ASBDs can operate at low dosage of substrates with a colorimetric ratio response and can overcome the drawbacks met in DSBDs. We expect that, by designing ASs with fruitful color panel in the future, our work will inspire more interesting in developing environment-benign and low-carbon G4/hemin DNAzymes and desired colorful high-performance sensors.
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Affiliation(s)
- Rong Lai
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Xingli Zeng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Qiuda Xu
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Ying Xu
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Xueni Li
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Yulu Ru
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Yilin Wang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Dandan Wang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Xiaoshun Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Yong Shao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China.
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Ye T, Chen H, Bai L, Yuan M, Cao H, Hao L, Wu X, Yin F, Xu F. A colorimetric and fluorescent dual-mode sensor based on bifunctional G-quadruplex-hemin complex for the determination of Pb 2. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 309:123807. [PMID: 38154306 DOI: 10.1016/j.saa.2023.123807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 12/30/2023]
Abstract
Due to the threat of lead pollution to health, environmental and food safety, developing simple and fast detection methods is highly required. Whereas, traditional single-mode probe suffers from limited application scenario. In this study, a colorimetric and fluorometric dual-mode probe for Pb2+ determination was constructed by using bifunctional G-quadruplex-hemin complex. In this dual-mode probe, enzyme strand and substrate strand of 8-17 DNAzyme are labeled with G-quadruplex-hemin complex and fluorophore, respectively. In the absence of Pb2+, the self-assembly of enzyme strand and substrate strand inhibits intrinsic mimic peroxidase of G-quadruplex-hemin complex by base-pairing, which also quench the fluorescence via in proximity effect. When the DNAzyme is activated by Pb2+, the quenched fluorescence is restored as well as the inherent peroxidase mimetic activity, leading to dual signal output. Under optimal conditions, this dual-mode probe exhibit a good linear relationship between logarithm of Pb2+ concentration and signal difference within the range from 1.5 nM to 20 nM and 0.5 nM to 10 nM for colorimetric and fluorescence mode, respectively. The detection limits for the corresponding mode were estimated to be 1.29 nM and 0.16 nM, respectively. This dual-mode probe also successfully applied for the spiked river water assay with satisfactory recovery in the range of 93.2 %-115.3 %. This work paves a new way for DNAzyme based dual-mode probe construction.
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Affiliation(s)
- Tai Ye
- Shanghai Engineering Research Center for Food Rapid Detection, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Haohao Chen
- Shanghai Engineering Research Center for Food Rapid Detection, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Long Bai
- Shanghai Engineering Research Center for Food Rapid Detection, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Min Yuan
- Shanghai Engineering Research Center for Food Rapid Detection, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Hui Cao
- Shanghai Engineering Research Center for Food Rapid Detection, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Liling Hao
- Shanghai Engineering Research Center for Food Rapid Detection, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Xiuxiu Wu
- Shanghai Engineering Research Center for Food Rapid Detection, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Fengqin Yin
- Shanghai Engineering Research Center for Food Rapid Detection, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Fei Xu
- Shanghai Engineering Research Center for Food Rapid Detection, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China.
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Markovitsi D. Processes triggered in guanine quadruplexes by direct absorption of UV radiation: From fundamental studies toward optoelectronic biosensors. Photochem Photobiol 2024; 100:262-274. [PMID: 37365765 DOI: 10.1111/php.13826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/29/2023] [Accepted: 05/30/2023] [Indexed: 06/28/2023]
Abstract
Guanine quadruplexes (GQs) are four-stranded DNA/RNA structures exhibiting an important polymorphism. During the past two decades, their study by time-resolved spectroscopy, from femtoseconds to milliseconds, associated to computational methods, shed light on the primary processes occurring when they absorb UV radiation. Quite recently, their utilization in label-free and dye-free biosensors was explored by a few groups. In view of such developments, this review discusses the outcomes of the fundamental studies that could contribute to the design of future optoelectronic biosensors using fluorescence or charge carriers stemming directly from GQs, without mediation of other molecules, as it is the currently the case. It explains how the excited state relaxation influences both the fluorescence intensity and the efficiency of low-energy photoionization, occurring via a complex mechanism. The corresponding quantum yields, determined with excitation at 266/267 nm, fall in the range of (3.0-9.5) × 10-4 and (3.2-9.2) × 10-3 , respectively. These values, significantly higher than the corresponding values found for duplexes, depend strongly on certain structural factors (molecularity, metal cations, peripheral bases, number of tetrads …) which intervene in the relaxation process. Accordingly, these features can be tuned to optimize the desired signal.
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Affiliation(s)
- Dimitra Markovitsi
- CNRS, Institut de Chimie Physique, UMR8000, Université Paris-Saclay, Orsay, France
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6
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Fang Y, Wang C, Wang Y, Hu J, Lai M, Liu P, Zhang H. Naked-eye detection of plant viral disease using polymerase chain reaction amplification and DNAzyme. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:1003-1011. [PMID: 38269430 DOI: 10.1039/d3ay01367g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
Plant viral diseases can seriously affect the yield and quality of crops. In this work, a convenient and highly sensitive biosensor for the visual detection of plant viral disease is proposed by the PCR-induced generation of DNAzyme. In the absence of nucleic acid for a target plant virus, the primers prohibited the production of G-quadruplex by forming a hairpin structure. However, PCR amplification occurred and generated a number of specific PCR products with free G-quadruplex sequences at both ends in the presence of the target cDNA. A catalytically active G-quadruplex DNAzyme was formed with the help of K+ and hemin, resulting in the formation of colored products visible to the naked eye and a strong absorbance by the addition of ABTS2- and H2O2. The absorbance and the logarithm of target cDNA concentrations showed a good linear relationship in the range of 10 fM-1.0 nM, with a linear regression equation of A = 0.1402 lg c + 0.3761 (c: fM) and a detection limit of 0.19 fM. This method was successfully applied to the analysis of emerging tobacco mosaic virus (TMV) infections in tobacco leaf samples collected in the field due to its flexibility and convenience, indicating a potential application for the early detection of plant viral disease.
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Affiliation(s)
- Yongwei Fang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, Henan 450002, China.
| | - Chuang Wang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, Henan 450002, China.
| | - Yuli Wang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, Henan 450002, China.
| | - Jiandong Hu
- College of Mechanical and Electrical Engineering, Henan Agricultural University, Zhengzhou, Henan 450002, China
- Henan International Joint Laboratory of Laser Technology in Agriculture Sciences, Zhengzhou, Henan 450002, China
| | - Miao Lai
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, Henan 450002, China.
| | - Pengfei Liu
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, Henan 450002, China.
| | - Hong Zhang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, Henan 450002, China.
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7
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Xu Y, Komiyama M. G-Quadruplexes in Human Telomere: Structures, Properties, and Applications. Molecules 2023; 29:174. [PMID: 38202757 PMCID: PMC10780218 DOI: 10.3390/molecules29010174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/20/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
G-quadruplexes, intricate four-stranded structures composed of G-tetrads formed by four guanine bases, are prevalent in both DNA and RNA. Notably, these structures play pivotal roles in human telomeres, contributing to essential cellular functions. Additionally, the existence of DNA:RNA hybrid G-quadruplexes adds a layer of complexity to their structural diversity. This review provides a comprehensive overview of recent advancements in unraveling the intricacies of DNA and RNA G-quadruplexes within human telomeres. Detailed insights into their structural features are presented, encompassing the latest developments in chemical approaches designed to probe these G-quadruplex structures. Furthermore, this review explores the applications of G-quadruplex structures in targeting human telomeres. Finally, the manuscript outlines the imminent challenges in this evolving field, setting the stage for future investigations.
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Affiliation(s)
- Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Makoto Komiyama
- Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
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Zhou J, Wang TY, Lan Z, Yang HJ, Ye XJ, Min R, Wang ZH, Huang Q, Cao J, Gao YE, Wang WL, Sun XL, Zhang Y. Strategy of functional nucleic acids-mediated isothermal amplification for detection of foodborne microbial contaminants: A review. Food Res Int 2023; 173:113286. [PMID: 37803599 DOI: 10.1016/j.foodres.2023.113286] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 10/08/2023]
Abstract
Foodborne microbial contamination (FMC) is the leading cause of food poisoning and foodborne illness. The foodborne microbial detection methods based on isothermal amplification have high sensitivity and short detection time, and functional nucleic acids (FNAs) could extend the detectable object of isothermal amplification to mycotoxins. Therefore, the strategy of FNAs-mediated isothermal amplification has been emergingly applied in biosensors for foodborne microbial contaminants detection, making biosensors more sensitive with lower cost and less dependent on nanomaterials for signal output. Here, the mechanism of six isothermal amplification technologies and their application in detecting FMC is firstly introduced. Then the strategy of FNAs-mediated isothermal amplification is systematically discussed from perspectives of FNAs' versatility including recognition elements (Aptamer, DNAzyme), programming tools (DNA tweezer, DNA walker and CRISPR-Cas) and signal units (G-quadruplex, FNAs-based nanomaterials). Finally, challenges and prospects are presented in terms of addressing the issue of nonspecific amplification reaction, developing better FNAs-based sensing elements and eliminating food matrix effects.
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Affiliation(s)
- Jie Zhou
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Teng-Yu Wang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Zhi Lan
- Wuxi Medical School, Jiangnan University, Wuxi 214122, China
| | - Han-Jie Yang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xing-Jian Ye
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Rui Min
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Zhao-Hui Wang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Qing Huang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jing Cao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yu-E Gao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Wen-Long Wang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xiu-Lan Sun
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yi Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
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Li X, Wu Y, Zhang X, Liu J, Zhang Y, Yuan L, Liu M. Thermodynamic and cellular studies of doxorubicin/daunorubicin loaded by a DNA tetrahedron for diagnostic imaging, chemotherapy, and gene therapy. Int J Biol Macromol 2023; 251:126245. [PMID: 37562474 DOI: 10.1016/j.ijbiomac.2023.126245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/06/2023] [Accepted: 08/07/2023] [Indexed: 08/12/2023]
Abstract
The combined diagnostic imaging, chemotherapy, and gene therapy based on DNA nanocarriers can reduce the toxic side effects and overcome multidrug resistance (MDR). In this study, we designed an antisense oligonucleotides (ASOs)-linked DNA tetrahedron (ASOs-TD). The detection limit of ASOs-TD for MDR1 mRNA was 0.05 μM. By using fluorescence spectroscopy and isothermal titration calorimetry (ITC), the interactions between doxorubicin (DOX) /daunorubicin (DAU) and ASOs-TD were investigated. The number of binding sites (n), binding constant (Ka), entropy change (ΔSo), enthalpy change (ΔHo) and Gibbs free energy change (ΔGo) were obtained. The intercalation of DOX/DAU with ASOs-TD was demonstrated by differential scanning calorimetry (DSC) and quenching researches of potassium ferricyanide K4[Fe(CN)6]. The in vitro release rate of DOX/DAU loaded in ASOs-TD was accelerated by deoxyribonuclease I (DNase I). In vitro cytotoxicity proved the good gene therapy effect of ASOs-TD and the increased cytotoxicity of DOX/DAU to MCF-7/ADR cells. The results of confocal laser scanning microscope (CLSM) suggested that ASOs-TD could effectively identify drug-resistant cells due to its good imaging ability for MDR1 mRNA. This work offers theoretical significance for overcoming MDR using DNA nanostructures which combine diagnostic imaging, chemotherapy, and gene therapy.
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Affiliation(s)
- Xinyu Li
- School of Chemistry and Chemical Engineering, Liaocheng University, Hunan Road, Liaocheng 252059, China
| | - Yushu Wu
- Institute of Biopharmaceutical Research, Liaocheng University, Hunan Road, Liaocheng 252059, China
| | - Xinpeng Zhang
- Institute of Biopharmaceutical Research, Liaocheng University, Hunan Road, Liaocheng 252059, China
| | - Jie Liu
- Institute of Biopharmaceutical Research, Liaocheng University, Hunan Road, Liaocheng 252059, China
| | - Yanqing Zhang
- School of Chemistry and Chemical Engineering, Liaocheng University, Hunan Road, Liaocheng 252059, China
| | - Lixia Yuan
- Institute of Biopharmaceutical Research, Liaocheng University, Hunan Road, Liaocheng 252059, China
| | - Min Liu
- School of Chemistry and Chemical Engineering, Liaocheng University, Hunan Road, Liaocheng 252059, China; Institute of Biopharmaceutical Research, Liaocheng University, Hunan Road, Liaocheng 252059, China.
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10
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Chen Y, Han JJ, Li BW, Nie LB, Tang Y, Wang T. A Ratiometric Fluorescence Biosensor for Detection of Alkaline Phosphatase Via an Advanced Chemometric Model. J Fluoresc 2023:10.1007/s10895-023-03445-3. [PMID: 37870733 DOI: 10.1007/s10895-023-03445-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 09/18/2023] [Indexed: 10/24/2023]
Abstract
In this paper, a ratiometric fluorescence biosensor was introduced for alkaline phosphatase (ALP) detection based on 2-aminopurine (2-Amp) and thioflavin T (ThT)-G-quadruplex system. We designed a special DNA (5'-AGGGTTAGGGTTAGGGTTAGGGAAA/i2-Amp/AAAA-PO4-3', AP) modified with a phosphate moiety at the 3'-end, G-quadruplex at the 5'-end, and a fluorophore (2-Amp) in the middle. In the absence of ALP, the G-rich AP strand could be prone to fold into G-quadruplex structures in the presence of K+. Then, ThT combined with G-quandruplex, resulting in the enhancement of fluorescence emission peak at 485 nm. However, ALP-mediated hydrolysis of the 3'-phosphoryl end promoted the cleavage of AP by the exonuclease I (Exo I), releasing 2-Amp which displayed a strong fluorescence emission peak at 365 nm. Moreover, the quantitative fluorescence model (QFM) was derived for the analysis of the fluorescence measurements obtained by the proposed ratiometric fluorescent biosensor. With the aid of the advanced model, the proposed ratiometric fluorescent biosensor possessed satisfactory results for the detection of ALP in the human serum samples, with accuracy comparable to that of the reference method-the commercial ALP assay kit. Under the optimized experimental conditions, this method exhibited good selectivity and higher sensitivity, and the detection limit was found to be as low as 0.017 U/L. Therefore, it is reasonable to expect that the method had a great potential to detect ALP quantitatively in clinical diagnosis.
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Affiliation(s)
- Yao Chen
- Hunan Key Lab of Biomedical Materials and Devices, College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, 412007, PR China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Jing-Jing Han
- Hunan Key Lab of Biomedical Materials and Devices, College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, 412007, PR China
| | - Bo-Wen Li
- Hunan Key Lab of Biomedical Materials and Devices, College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, 412007, PR China
| | - Li-Bo Nie
- Hunan Key Lab of Biomedical Materials and Devices, College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, 412007, PR China
| | - Ying Tang
- Hunan Key Lab of Biomedical Materials and Devices, College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, 412007, PR China.
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China.
| | - Tong Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China.
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11
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Libera V, Ripanti F, Petrillo C, Sacchetti F, Ramos-Soriano J, Galan MC, Schirò G, Paciaroni A, Comez L. Stability of Human Telomeric G-Quadruplexes Complexed with Photosensitive Ligands and Irradiated with Visible Light. Int J Mol Sci 2023; 24:ijms24109090. [PMID: 37240437 DOI: 10.3390/ijms24109090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/16/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023] Open
Abstract
Guanine-rich DNA sequences can fold into non-canonical nucleic acid structures called G-quadruplexes (G4s). These nanostructures have strong implications in many fields, from medical science to bottom-up nanotechnologies. As a result, ligands interacting with G4s have attracted great attention as candidates in medical therapies, molecular probe applications, and biosensing. In recent years, the use of G4-ligand complexes as photopharmacological targets has shown significant promise for developing novel therapeutic strategies and nanodevices. Here, we studied the possibility of manipulating the secondary structure of a human telomeric G4 sequence through the interaction with two photosensitive ligands, DTE and TMPyP4, whose response to visible light is different. The effect of these two ligands on G4 thermal unfolding was also considered, revealing the occurrence of peculiar multi-step melting pathways and the different attitudes of the two molecules on the quadruplex stabilization.
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Affiliation(s)
- Valeria Libera
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
- Istituto Officina dei Materiali-IOM, National Research Council-CNR, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Francesca Ripanti
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Caterina Petrillo
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Francesco Sacchetti
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Javier Ramos-Soriano
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Maria Carmen Galan
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Giorgio Schirò
- CNRS, CEA, IBS, c/o University Grenoble Alpes, 38400 Grenoble, France
| | - Alessandro Paciaroni
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Lucia Comez
- Istituto Officina dei Materiali-IOM, National Research Council-CNR, Via Alessandro Pascoli, 06123 Perugia, Italy
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12
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Dong J, Qiu X, Huang M, Chen X, Li Y. G-quadruplex-hemin DNAzyme functionalized nanopipettes: Fabrication and sensing application. Talanta 2023; 257:124384. [PMID: 36812658 DOI: 10.1016/j.talanta.2023.124384] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 02/21/2023]
Abstract
Solid-nanopores/nanopipettes have the exquisite ability to reveal the changes in molecular volume due to the advantages of adjustable size, good rigidity and low noise. Herein, a new platform for sensing application was established based on G-quadruplex-hemin DNAzyme (GQH) functionalized gold-coated nanopipettes. In this method, GQH was immobilized on gold-coated nanopipette, which could be used as a catalyst for the reaction of H2O2 with 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS) to promote the conversion of ABTS to ABTS+ ions inside gold-coated nanopipette, and the change of transmembrane ion current could be monitored in real time. At the optimal conditions, there was a correlation between the ion current and the concentration of H2O2 in a certain range, which could be used for the hydrogen peroxide sensing. The GQH immobilized nanopipette provides a useful platform to investigate enzymatic catalysis in confined environment, which can be used in electrocatalysis, sensing and fundamental electrochemistry.
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Affiliation(s)
- Jingyi Dong
- Key Laboratory of Functional Molecular Solids (Ministry of Education), Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241000, PR China
| | - Xia Qiu
- Key Laboratory of Functional Molecular Solids (Ministry of Education), Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241000, PR China
| | - Mimi Huang
- Key Laboratory of Functional Molecular Solids (Ministry of Education), Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241000, PR China
| | - Xiaohu Chen
- Key Laboratory of Functional Molecular Solids (Ministry of Education), Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241000, PR China
| | - Yongxin Li
- Key Laboratory of Functional Molecular Solids (Ministry of Education), Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241000, PR China.
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13
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Yang X, Yuan L, Xu Y, He B. Target-catalyzed self-assembled spherical G-quadruplex/hemin DNAzymes for highly sensitive colorimetric detection of microRNA in serum. Anal Chim Acta 2023; 1247:340879. [PMID: 36781247 DOI: 10.1016/j.aca.2023.340879] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/16/2023] [Accepted: 01/20/2023] [Indexed: 01/22/2023]
Abstract
The accurate and visual detection of circulating microRNA (miRNA) has attracted increasing interest due to its pivotal role in clinical disease diagnosis. Taking advantages of nucleic acid isothermal amplification and enzyme-catalyzed chromogenic reaction, here, a colorimetric sensing strategy was proposed for sensitive miRNA analysis. When the target miRNA was present, local catalytic hairpin assembly (CHA) would be triggered and proceed continuously to form dozens of double-stranded oligonucleotides with G-rich sticky ends on the gold nanoparticle, which could self-assemble into a spherical G-quadruplex (GQ)/hemin DNAzyme by binding with hemin and potassium ions. As a horseradish peroxidase-mimic, GQ/hemin DNAzyme could catalyze the redox reaction and color change of the substrates. Taking miRNA-21 as an example, the developed method exhibited satisfactory specificity as well as high sensitivity with a detection limit of 90.3 fM. Furthermore, the sensing platform has been successfully employed to detect miRNA-21 in spiked serum, providing a promising tool for early diagnosis of cancers.
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Affiliation(s)
- Xuejiao Yang
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211816, China.
| | - Liquan Yuan
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Yue Xu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Bingfang He
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211816, China; College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China.
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14
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Shi S, Wang X, Li Z, Meng J, Chu X, Zhang P, Sun B, Zhang J, Gao Y, Xu W, Song Q, Xu X, Wu J, Zhou N. Multifunctional Integrated Superhydrophobic Coatings with Unique Fluorescence and Micro/Micro/Nano-Hierarchical Structures Enabled by In Situ Self-Assembly. ACS APPLIED MATERIALS & INTERFACES 2023; 15:7442-7453. [PMID: 36695810 DOI: 10.1021/acsami.2c21531] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Conferring versatility to superhydrophobic materials is extremely desirable to advance their utility. Herein, we have developed a superhydrophobic material with montmorillonite as microskeleton supports and in situ grown ZIF-8 nanoparticles and loaded them with newly developed fluorescent carbon dots. In situ growth of the ZIF-8 on OMMT constructs a dense nanoscale rough structure and meanwhile self-assembly generates abundant microporous, thus forming unique hierarchical microporous/microsheet/nanoparticle tri-tier micro and nano structures. Then the multifunctional superhydrophobic coating is fabricated by a facile spraying technique using polydimethylsiloxane (PDMS) as a multifunctional polymer binder. The PDMS/RB-CDs/ZIF-8@OMMT exhibits superhydrophobicity with a water contact angle of 164.7° and a water sliding angle of 1.4°, which also possesses good self-cleaning performance. Moreover, novel carbon dots are developed in this work which can confer unique fluorescent properties and photothermal properties to materials. Fluorescence characterization reveals the multiple emission peaks among 300-800 nm and excitation wavelength dependence and independence. Photothermal experiments unveil an efficient light-to-heat conversion caused by the light traps and absorption wavelengths associated with photothermal heating. Benefiting from the dense microporous/microsheet/nanoparticle structures, the superhydrophobicity is still maintained after 120 cycles of abrasion. Moreover, electrochemical impedance spectroscopy (EIS) reveals a significant increase in impedance, which is associated with excellent corrosion resistance. The superhydrophobic coating also exhibits superior UV resistance and good thermal stability. Multifunctional fluorescent superhydrophobic materials will enable the development of various and potential applications in different fields.
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Affiliation(s)
- Shaoze Shi
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of Bio-functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, Jiangsu210023, China
| | - Xiaotong Wang
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of Bio-functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, Jiangsu210023, China
| | - Zihan Li
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of Bio-functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, Jiangsu210023, China
| | - Jiawen Meng
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of Bio-functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, Jiangsu210023, China
| | - Xiaohong Chu
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of Bio-functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, Jiangsu210023, China
- Department of Pharmacy, Liaocheng University, Liaocheng, Shandong, 252000, China
| | - Pan Zhang
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of Bio-functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, Jiangsu210023, China
| | - Baohong Sun
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of Bio-functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, Jiangsu210023, China
| | - Juyang Zhang
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of Bio-functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, Jiangsu210023, China
| | - Yumeng Gao
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of Bio-functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, Jiangsu210023, China
| | - Wang Xu
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of Bio-functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, Jiangsu210023, China
| | - Qiuxian Song
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of Bio-functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, Jiangsu210023, China
| | - Xiaoyu Xu
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of Bio-functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, Jiangsu210023, China
| | - Jing Wu
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of Bio-functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, Jiangsu210023, China
| | - Ninglin Zhou
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of Bio-functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, Jiangsu210023, China
- Nanjing Zhou Ninglin Advanced Materials Technology Company Limited, Nanjing211505, China
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15
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Pandith A, Luo Y, Jang Y, Bae J, Kim Y. Self-Assembled Peptidyl Aggregates for the Fluorogenic Recognition of Mitochondrial DNA G-Quadruplexes. Angew Chem Int Ed Engl 2023; 62:e202215049. [PMID: 36396597 DOI: 10.1002/anie.202215049] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Indexed: 11/19/2022]
Abstract
The selective monitoring of G-quadruplex (G4) structures in living cells is important to elucidate their functions and reveal their value as diagnostic or therapeutic targets. Here we report a fluorogenic probe (CV2) able to selectively light-up parallel G4 DNA over antiparallel topologies. CV2 was constructed by conjugating the excimer-forming CV dye with a peptide sequence (l-Arg-l-Gly-glutaric acid) that specifically recognizes G4s. CV2 forms self-assembled, red excimer-emitting nanoaggregates in aqueous media, but specific binding to G4s triggers its disassembly into rigidified monomeric dyes, leading to a dramatic fluorescence enhancement. Moreover, selective permeation of CV2 stains G4s in mitochondria over the nucleus. CV2 was employed for tracking the folding and unfolding of G4s in living cells, and for monitoring mitochondrial DNA (mtDNA) damage. These properties make CV2 appealing to investigate the possible roles of mtDNA G4s in diseases that involve mitochondrial dysfunction.
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Affiliation(s)
- Anup Pandith
- Department of Chemistry and Research Institute of Basic Sciences, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Korea.,Current address, International Ph.D. Program in Biomedical Engineering (IPBME), College of Biomedical Engineering, Taipei Medical University, Taipei, 11031, Taiwan (R.O.C
| | - Yongyang Luo
- School of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Korea
| | - Yul Jang
- Department of Chemistry and Research Institute of Basic Sciences, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Korea
| | - Jeehyeon Bae
- School of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Korea
| | - Youngmi Kim
- Department of Chemistry and Research Institute of Basic Sciences, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Korea
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16
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Liu H, Chen Y, Ju H. Functional DNA structures for cytosensing. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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17
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Tong X, Ga L, Eerdun C, Zhao R, Ai J. Simple Monovalent Metal Ion Logical Order to Regulate the Secondary Conformation of G-Quadruplex. ACS OMEGA 2022; 7:39224-39233. [PMID: 36340069 PMCID: PMC9631730 DOI: 10.1021/acsomega.2c05243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/29/2022] [Indexed: 06/06/2023]
Abstract
Based on the reactions of different sequences with single ions K+, Na, NH4 +, double ions high + low, low + high, and triple ions with different addition orders, the best stable ion combinations of 12 quadruplexes with different DNA sequences were reported. From the fluorescence spectrum, except for HT-V15 and PW17 and AS1411 and HT-V18, the structural stability of G-quadrangle formed basically follows a certain rule. In terms of this experiment, according to circular dichroism, the antiparallel quadrupole structure has the largest proportion among quadrupole structures, and 12 optimal DNA addition schemes and sequences have been obtained through exploration. It is worth mentioning that, on the whole, the best addition scheme of AS1411 and HT-V18 is a three-ion scheme, which provides an effective reference for similar experiments in the future.
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Affiliation(s)
- Xin Tong
- College
of Chemistry and Enviromental Science, Inner Mongolia Key Laboratory
of Environmental Chemistry, Inner Mongolia
Normal University, 81 Zhaowudalu, Hohhot 010022, People’s Republic of China
| | - Lu Ga
- College
of Pharmacy, Inner Mongolia Medical University, Jinchuankaifaqu, Hohhot 010110, People’s Republic of China
| | - Chaolu Eerdun
- College
of Pharmacy, Inner Mongolia Medical University, Jinchuankaifaqu, Hohhot 010110, People’s Republic of China
| | - Ruiguo Zhao
- College
of Chemistry and Chemical Engineering, Inner
Mongolia University, Hohhot 010020, People’s Republic
of China
| | - Jun Ai
- College
of Chemistry and Enviromental Science, Inner Mongolia Key Laboratory
of Environmental Chemistry, Inner Mongolia
Normal University, 81 Zhaowudalu, Hohhot 010022, People’s Republic of China
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18
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Zhao L, Ahmed F, Zeng Y, Xu W, Xiong H. Recent Developments in G-Quadruplex Binding Ligands and Specific Beacons on Smart Fluorescent Sensor for Targeting Metal Ions and Biological Analytes. ACS Sens 2022; 7:2833-2856. [PMID: 36112358 DOI: 10.1021/acssensors.2c00992] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The G-quadruplex structure is crucial in several biological processes, including DNA replication, transcription, and genomic maintenance. G-quadruplex-based fluorescent probes have recently gained popularity because of their ease of use, low cost, excellent selectivity, and sensitivity. This review summarizes the latest applications of G-quadruplex structures as detectors of genome-wide, enantioselective catalysts, disease therapeutics, promising drug targets, and smart fluorescence probes. In every section, sensing of G-quadruplex and employing G4 for the detection of other analytes were introduced, respectively. Since the discovery of the G-quadruplex structure, several studies have been conducted to investigate its conformations, biological potential, stability, reactivity, selectivity for chemical modification, and optical properties. The formation mechanism and advancements for detecting different metal ions (Na+, K+, Ag+, Tl+, Cu+/Cu2+, Hg2+, and Pb2+) and biomolecules (AMP, ATP, DNA/RNA, microRNA, thrombin, T4 PNK, RNase H, ALP, CEA, lipocalin 1, and UDG) using fluorescent sensors based on G-quadruplex modification, such as dye labels, artificial nucleobase moieties, dye complexes, intercalating dyes, and bioconjugated nanomaterials (AgNCs, GO, QDs, CDs, and MOF) is described herein. To investigate these extremely efficient responsive agents for diagnostic and therapeutic applications in medicine, fluorescence sensors based on G-quadruplexes have also been employed as a quantitative visualization technique.
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Affiliation(s)
- Long Zhao
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, P. R. China.,College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, P. R. China
| | - Farid Ahmed
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, P. R. China
| | - Yating Zeng
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, P. R. China
| | - Weiqing Xu
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, P. R. China
| | - Hai Xiong
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, P. R. China
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19
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Fletcher M, Zhu J, Rubio-Sánchez R, Sandler SE, Nahas KA, Michele LD, Keyser UF, Tivony R. DNA-Based Optical Quantification of Ion Transport across Giant Vesicles. ACS NANO 2022; 16:17128-17138. [PMID: 36222833 PMCID: PMC9620405 DOI: 10.1021/acsnano.2c07496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
Accurate measurements of ion permeability through cellular membranes remains challenging due to the lack of suitable ion-selective probes. Here we use giant unilamellar vesicles (GUVs) as membrane models for the direct visualization of mass translocation at the single-vesicle level. Ion transport is indicated with a fluorescently adjustable DNA-based sensor that accurately detects sub-millimolar variations in K+ concentration. In combination with microfluidics, we employed our DNA-based K+ sensor for extraction of the permeation coefficient of potassium ions. We measured K+ permeability coefficients at least 1 order of magnitude larger than previously reported values from bulk experiments and show that permeation rates across the lipid bilayer increase in the presence of octanol. In addition, an analysis of the K+ flux in different concentration gradients allows us to estimate the complementary H+ flux that dissipates the charge imbalance across the GUV membrane. Subsequently, we show that our sensor can quantify the K+ transport across prototypical cation-selective ion channels, gramicidin A and OmpF, revealing their relative H+/K+ selectivity. Our results show that gramicidin A is much more selective to protons than OmpF with a H+/K+ permeability ratio of ∼104.
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Affiliation(s)
- Marcus Fletcher
- Cavendish
Laboratory, University of Cambridge, J.J. Thomson Avenue, CambridgeCB3 0HE, U.K.
| | - Jinbo Zhu
- Cavendish
Laboratory, University of Cambridge, J.J. Thomson Avenue, CambridgeCB3 0HE, U.K.
| | - Roger Rubio-Sánchez
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, LondonW12 0BZ, U.K.
- fabriCELL,
Molecular Sciences Research Hub, Imperial
College London, LondonW12 0BZ, U.K.
| | - Sarah E Sandler
- Cavendish
Laboratory, University of Cambridge, J.J. Thomson Avenue, CambridgeCB3 0HE, U.K.
| | - Kareem Al Nahas
- Cavendish
Laboratory, University of Cambridge, J.J. Thomson Avenue, CambridgeCB3 0HE, U.K.
| | - Lorenzo Di Michele
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, LondonW12 0BZ, U.K.
- fabriCELL,
Molecular Sciences Research Hub, Imperial
College London, LondonW12 0BZ, U.K.
| | - Ulrich F Keyser
- Cavendish
Laboratory, University of Cambridge, J.J. Thomson Avenue, CambridgeCB3 0HE, U.K.
| | - Ran Tivony
- Cavendish
Laboratory, University of Cambridge, J.J. Thomson Avenue, CambridgeCB3 0HE, U.K.
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20
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Kang Y, Wei C. A stilbene derivative as dual-channel fluorescent probe for mitochondrial G-quadruplex DNA in living cells. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 278:121316. [PMID: 35569198 DOI: 10.1016/j.saa.2022.121316] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/15/2022] [Accepted: 04/24/2022] [Indexed: 06/15/2023]
Abstract
G-quadruplex DNA has attracted the widespread attention as a novel target of anticancer strategy. Herein, two novel stilbene derivatives 2a and 2b were designed and synthesized under mild reaction conditions, and their interactions with G-quadruplex DNA, cytotoxicity, and distribution in living cells were investigated in detail. Both compounds display a low cytotoxicity and the higher affinity to G-quadruplex DNA than to the other secondary structures, including duplex, single-stranded and i-motif DNA, moreover, the affinity of 2b with m-allyl pyridine salt group to G-quadruplex DNA is about 10-fold stronger than that of 2a with p-allyl pyridine salt group. The interactions of the compounds with the promoter G-quadruplexes are enthalpy-driven by an ITC assay. 2a and 2b not only stabilize the G-quadruplex structure but also induce the G-rich sequences (bcl-2, HRCC and KSS) to fold into the mixed-type G-quadruplex in Na+/K+ free Tris-HCl buffer at pH 7.0, and 2b presents the higher stabilization to G-quadruplex than 2a by a FRET-melting assay. 2b presents a dual-emission at 508 and 600 nm and gives a turn-on and stronger and more sensitive fluorescence response over 2a to the promoter (bcl-2, c-kit 2 and c-myc) and mitochondrial (HRCC and KSS) G-quadruplex DNA at both emission wavelengths, moreover, the peak at 508 nm is blue-shifted to 466 nm after binding to DNA. The blue and red dual-channel CLSM images indicate that 2b is mainly distributed in the mitochondrion of living HepG2 cells. The results show that 2b is a potential dual-channel fluorescent probe for mitochondrial G-quadruplex DNA in living cells.
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Affiliation(s)
- Yongqiang Kang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Molecular Science, Shanxi University, Taiyuan 030006, PR China
| | - Chunying Wei
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Molecular Science, Shanxi University, Taiyuan 030006, PR China.
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21
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A highly sensitive method for the detection of alkaline phosphatase based on thioflavin T/G-quadruplex and strand displacement amplification. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Xiao X, Chen M, Zhang Y, Li L, Peng Y, Li J, Zhou W. Hemin-incorporating DNA nanozyme enabling catalytic oxygenation and GSH depletion for enhanced photodynamic therapy and synergistic tumor ferroptosis. J Nanobiotechnology 2022; 20:410. [PMID: 36109814 PMCID: PMC9479271 DOI: 10.1186/s12951-022-01617-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/31/2022] [Indexed: 11/18/2022] Open
Abstract
Photodynamic therapy (PDT) has emerged as a promising tumor treatment method via light-triggered generation of reactive oxygen species (ROS) to kill tumor cells. However, the efficacy of PDT is usually restricted by several biological limitations, including hypoxia, excess glutathione (GSH) neutralization, as well as tumor resistance. To tackle these issues, herein we developed a new kind of DNA nanozyme to realize enhanced PDT and synergistic tumor ferroptosis. The DNA nanozyme was constructed via rolling circle amplification, which contained repeat AS1411 G quadruplex (G4) units to form multiple G4/hemin DNAzymes with catalase-mimic activity. Both hemin, an iron-containing porphyrin cofactor, and chlorine e6 (Ce6), a photosensitizer, were facilely inserted into G4 structure with high efficiency, achieving in-situ catalytic oxygenation and photodynamic ROS production. Compared to other self-oxygen-supplying tools, such DNA nanozyme is advantageous for high biological stability and compatibility. Moreover, the nanostructure could achieve tumor cells targeting internalization and intranuclear transport of Ce6 by virtue of specific nucleolin binding of AS1411. The nanozyme could catalyze the decomposition of intracellular H2O2 into oxygen for hypoxia relief as evidenced by the suppression of hypoxia-inducible factor-1α (HIF-1α), and moreover, GSH depletion and cell ferroptosis were also achieved for synergistic tumor therapy. Upon intravenous injection, the nanostructure could effectively accumulate into tumor, and impose multi-modal tumor therapy with excellent biocompatibility. Therefore, by integrating the capabilities of O2 generation and GSH depletion, such DNA nanozyme is a promising nanoplatform for tumor PDT/ferroptosis combination therapy.
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Affiliation(s)
- Xiaoxiong Xiao
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Xiangya Lung Cancer Center, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Min Chen
- Department of Thoracic Surgery, The Second People's Hospital of Huaihua City, Huaihua, China
| | - Yuchen Zhang
- Department of Pharmacy, Yichun People's Hospital, Yichun, Jiangxi, China
| | - Liang Li
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China
| | - Ying Peng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China
| | - Junyu Li
- Department of Radiation Oncology, Jiangxi Cancer Hospital, Nanchang, Jiangxi, China.
| | - Wenhu Zhou
- Xiangya Lung Cancer Center, Xiangya Hospital, Central South University, Changsha, Hunan, China. .,Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China.
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Ranjan A, Sharma D, Srivastava AK, Varma A, Magani SK, Joshi RK. Evaluation of anticancer activity of ferrocene based benzothiazole and β-ketooxothioacetal. J Organomet Chem 2022. [DOI: 10.1016/j.jorganchem.2022.122500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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24
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Hu C, Jin Y, Yang P, Zhou R, Xia L, Du L, Chen J, Cheng N, Hou X. Biomolecule-guided co-localization of intermolecular G-rich strands for the construction of a tetramolecular G-quadruplex sensing strategy. Chem Commun (Camb) 2022; 58:6914-6917. [PMID: 35621922 DOI: 10.1039/d2cc01587k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We herein introduce the principle of proximity assay into tetramolecular G-quadruplexes guided by various biomolecules for the construction of a sensing strategy. Our strategy is based on the co-localization of intermolecular G-rich strands guided by a recognition event of a specific biomolecule to its corresponding affinity ligand. In such case, the local concentration among intermolecular strands is significantly increased to trigger the following self-assembly that served as the peroxidase-mimicking activity. This strategy is versatile, homogenous and adaptable to different types of biomolecules.
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Affiliation(s)
- Changjia Hu
- Biliary Surgical Department, West China Hospital, Sichuan University, Chengdu, Sichuan, 610225, China. .,Analytical & Testing Center, Sichuan University, 29 Wangjiang Road, Chengdu 610064, China.
| | - Yanwen Jin
- Biliary Surgical Department, West China Hospital, Sichuan University, Chengdu, Sichuan, 610225, China.
| | - Peng Yang
- Analytical & Testing Center, Sichuan University, 29 Wangjiang Road, Chengdu 610064, China.
| | - Rongxing Zhou
- Biliary Surgical Department, West China Hospital, Sichuan University, Chengdu, Sichuan, 610225, China.
| | - Lingying Xia
- Biliary Surgical Department, West China Hospital, Sichuan University, Chengdu, Sichuan, 610225, China. .,Analytical & Testing Center, Sichuan University, 29 Wangjiang Road, Chengdu 610064, China.
| | - Lijie Du
- Analytical & Testing Center, Sichuan University, 29 Wangjiang Road, Chengdu 610064, China.
| | - Junbo Chen
- Analytical & Testing Center, Sichuan University, 29 Wangjiang Road, Chengdu 610064, China.
| | - Nansheng Cheng
- Biliary Surgical Department, West China Hospital, Sichuan University, Chengdu, Sichuan, 610225, China.
| | - Xiandeng Hou
- Analytical & Testing Center, Sichuan University, 29 Wangjiang Road, Chengdu 610064, China.
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25
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Cheng Z, Wei J, Gu L, Zou L, Wang T, Chen L, Li Y, Yang Y, Li P. DNAzyme-based biosensors for mercury (Ⅱ) detection: Rational construction, advances and perspectives. JOURNAL OF HAZARDOUS MATERIALS 2022; 431:128606. [PMID: 35278952 DOI: 10.1016/j.jhazmat.2022.128606] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/17/2022] [Accepted: 02/27/2022] [Indexed: 06/14/2023]
Abstract
Mercury contamination is one of the most severe issues in society due to its threats to public health and the ecological system. However, traditional methods for mercury ion detection are still limited by their time-consuming procedures, requirement of expensive instruments, and low selectivity. In recent decades, tremendous progress has been made in the development of functional nucleic acid-based, especially DNAzyme sensors for mercury (Ⅱ) (Hg2+) determination, including RNA-cleaving DNAzymes and G-quadruplex-based DNAzymes in particular. Researchers have heavily studied the construction of Hg2+ sensors, mainly originating from in vitro selection-derived DNAzymes, by incorporating T-Hg2+-T recognition moieties in existing DNAzyme scaffolds, and interfacing Hg2+-sensitive sequences with nanomaterials. In the last case, the employment of materials (as quenchers, signal transducers and DNA immobilizers) enriches the application scenarios of current Hg2+-DNAzymes, due to a combination of their functions. We summarize a broad range of sensing approaches, including optical, electrochemical, and other sensing methods, and compare their features. This review elaborates on the rational design strategies for engineering DNAzymes to selectively sense Hg2+, critically discusses their properties in different application scenarios, and summarizes recent advances in this field. Additionally, current progress, challenges and future perspectives are also discussed. This minireview provides deeper insights into the chemistry of these functional nucleic acids when working with Hg2+, explains the design ideas of DNAzyme-sensors in each platform, and reveals potential opportunities in developing more advanced DNAzyme sensors for the highly selective and sensitive recognition of Hg2+. ENVIRONMENTAL IMPLICATION: Mercury is one of the most toxic metallic contaminants due to its high toxicity, non-biodegradability, and serious human health risks when accumulated in the body. In the recent decade, intensive studies have focused on exploring mercury sensors by combining DNAzymes with various sensing methods, paving a promising avenue to gain ultra-high sensitivity and selectivity. However, so far, no review has introduced the recent advances on DNAzyme-based sensors for mercury detection in a critical way. In this review, we comprehensively summarized the studies on DNAzyme-based sensors for mercury detection using various sensing techniques including optical, electrochemical and other sensing methods.
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Affiliation(s)
- Zehua Cheng
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China
| | - Jinchao Wei
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China
| | - Liqiang Gu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China
| | - Liang Zou
- School of Medicine, Chengdu University, Chengdu 610106, China
| | - Ting Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China
| | - Ling Chen
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China
| | - Yuqing Li
- Institute of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, Jiangsu 215123, China; Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Yu Yang
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Peng Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China.
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26
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Bağda E, Kızılyar Y, İnci ÖG, Ghaffarlou M, Barsbay M. One-pot modification of oleate-capped UCNPs with AS1411 G-quadruplex DNA in a fully aqueous medium. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.128675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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27
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Li Q, Peng S, Chang Y, Yang M, Wang D, Zhou X, Shao Y. A G-triplex-Based Label-Free Fluorescence Switching Platform for the Specific Recognition of Chromium Species. J Photochem Photobiol A Chem 2022. [DOI: 10.1016/j.jphotochem.2022.114071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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28
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29
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Rational design of an allosteric G-quadruplex aptamer probe for ultra-sensitive detection of melamine in milk. Int J Biol Macromol 2022; 210:430-438. [PMID: 35500779 DOI: 10.1016/j.ijbiomac.2022.04.198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 11/22/2022]
Abstract
Efficient and accurate detection of melamine in dairy products remains a crucial yet challenging task. Herein, an allosterically modulated G-quadruplex-integrated aptamer is rationally designed with thymine-rich recognition termini for melamine binding. The detection process is facile by simply introducing the analyte into the mixture consisting of G-quadruplex aptamer probes, exonuclease III, and thioflavin T (ThT). The detection feasibility is confirmed by the polyacrylamide gel electrophoresis and fluorescence measurement results. This exonuclease III-assisted signal amplifiable approach works well in a linear range from 0.1 nM to 0.1 μM. Moreover, a detection limit as low as 83 pM is easily achieved, which is almost five orders of magnitude smaller than the maximum allowable melamine levels (about 8 μM) defined by many countries all over the world. The whole assay time for each test is no longer than 1 h. Additionally, the scheme is highly specific and satisfactory recovery rates (from 91% to 104%) are readily obtained when challenged with melamine-spiked milk samples. Therefore, the label-free, turn-on, low-cost, and time-efficient method can be used for reliable detection of melamine in an easily manipulated and ultra-sensitive manner, which may find its utilization in the field of food safety, biomedical engineering, and clinical diagnosis.
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30
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Chaperone Copolymer Assisted G-Quadruplex-Based Signal Amplification Assay for Highly Sensitive Detection of VEGF. BIOSENSORS 2022; 12:bios12050262. [PMID: 35624563 PMCID: PMC9138322 DOI: 10.3390/bios12050262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/10/2022] [Accepted: 04/19/2022] [Indexed: 11/17/2022]
Abstract
Vascular endothelial growth factor (VEGF) is a critical biomarker in the angiogenesis of several cancers. Nowadays, novel approaches to rapid, sensitive, and reliable VEGF detection are urgently required for early cancer diagnosis. Cationic comb-type copolymer, poly(L-lysine)-graft-dextran (PLL-g-Dex) accelerates DNA hybridization and chain exchange reaction while stabilizing the DNA assembly structure. In this work, we examined the chaperone activity of PLL-g-Dex to assist G-quadruplex-based fluorescent DNA biosensors for sensitive detection of VEGF. This convenient and effective strategy is based on chitosan hydrogel, c-myc, Thioflavin T (ThT), VEGF aptamer, and its partially complementary strand. The results show that chaperone copolymer PLL-g-Dex significantly promotes the accumulation of G-quadruplex and assembles into G-wires, allowing an effective signal amplification. Using this method, the detection limit of VEGF was as low as 23 pM, better than many previous works on aptamer-based VEGF detection. This chaperone copolymer-assisted signal amplification strategy has potential applications in the highly sensitive detection of target proteins, even including viruses.
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31
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Song X, Yang C, Yuan R, Xiang Y. Electrochemical label-free biomolecular logic gates regulated by distinct inputs. Biosens Bioelectron 2022; 202:114000. [DOI: 10.1016/j.bios.2022.114000] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/27/2021] [Accepted: 01/11/2022] [Indexed: 11/29/2022]
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32
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Jiao Y, Shang Y, Li N, Ding B. DNA-based enzymatic systems and their applications. iScience 2022; 25:104018. [PMID: 35313688 PMCID: PMC8933709 DOI: 10.1016/j.isci.2022.104018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA strands with unique secondary structures can catalyze various chemical reactions and mimic natural enzymes with the assistance of cofactors, which have attracted much research attention. At the same time, the emerging DNA nanotechnology provides an efficient platform to organize functional components of the enzymatic systems and regulate their catalytic performances. In this review, we summarize the recent progress of DNA-based enzymatic systems. First, DNAzymes (Dzs) are introduced, and their versatile utilities are summarized. Then, G-quadruplex/hemin (G4/hemin) Dzs with unique oxidase/peroxidase-mimicking activities and representative examples where these Dzs served as biosensors are explicitly elaborated. Next, the DNA-based enzymatic cascade systems fabricated by the structural DNA nanotechnology are depicted. In addition, the applications of catalytic DNA nanostructures in biosensing and biomedicine are included. At last, the challenges and the perspectives of the DNA-based enzymatic systems for practical applications are also discussed.
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33
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Vannutelli A, Perreault JP, Ouangraoua A. G-quadruplex occurrence and conservation: more than just a question of guanine–cytosine content. NAR Genom Bioinform 2022; 4:lqac010. [PMID: 35261973 PMCID: PMC8896161 DOI: 10.1093/nargab/lqac010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 12/06/2021] [Accepted: 02/25/2022] [Indexed: 12/14/2022] Open
Abstract
G-quadruplexes are motifs found in DNA and RNA that can fold into tertiary structures. Until now, they have been studied experimentally mainly in humans and a few other species. Recently, predictions have been made with bacterial and archaeal genomes. Nevertheless, a global comparison of predicted G4s (pG4s) across and within the three living kingdoms has not been addressed. In this study, we aimed to predict G4s in genes and transcripts of all kingdoms of living organisms and investigated the differences in their distributions. The relation of the predictions with GC content was studied. It appears that GC content is not the only parameter impacting G4 predictions and abundance. The distribution of pG4 densities varies depending on the class of transcripts and the group of species. Indeed, we have observed that, in coding transcripts, there are more predicted G4s than expected for eukaryotes but not for archaea and bacteria, while in noncoding transcripts, there are as many or fewer predicted G4s in all species groups. We even noticed that some species with the same GC content presented different pG4 profiles. For instance, Leishmania major and Chlamydomonas reinhardtii both have 60% of GC content, but the former has a pG4 density of 0.07 and the latter 1.16.
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Affiliation(s)
- Anaïs Vannutelli
- Department of Computer Science, Faculté des sciences, Université de Sherbrooke, QC, J1K 2R1, Canada
- Department of Biochemistry and Functional Genomics, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, QC J1E 4K8, Canada
| | - Jean-Pierre Perreault
- Department of Computer Science, Faculté des sciences, Université de Sherbrooke, QC, J1K 2R1, Canada
| | - Aïda Ouangraoua
- Department of Computer Science, Faculté des sciences, Université de Sherbrooke, QC, J1K 2R1, Canada
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34
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Tong X, Ga L, Ai J, Wang Y. Progress in cancer drug delivery based on AS1411 oriented nanomaterials. J Nanobiotechnology 2022; 20:57. [PMID: 35101048 PMCID: PMC8805415 DOI: 10.1186/s12951-022-01240-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/02/2022] [Indexed: 02/07/2023] Open
Abstract
Targeted cancer therapy has become one of the most important medical methods because of the spreading and metastatic nature of cancer. Based on the introduction of AS1411 and its four-chain structure, this paper reviews the research progress in cancer detection and drug delivery systems by modifying AS1411 aptamers based on graphene, mesoporous silica, silver and gold. The application of AS1411 in cancer treatment and drug delivery and the use of AS1411 as a targeting agent for the detection of cancer markers such as nucleoli were summarized from three aspects of active targeting, passive targeting and targeted nucleic acid apharmers. Although AS1411 has been withdrawn from clinical trials, the research surrounding its structural optimization is still very popular. Further progress has been made in the modification of nanoparticles loaded with TCM extracts by AS1411.
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Affiliation(s)
- Xin Tong
- College of Chemistry and Environmental Science, College of Geographical Science, Inner Mongolia Key Laboratory of Environmental Chemistry, Inner Mongolia Normal University, 81 Zhaowudalu, Hohhot, 010022, China
| | - Lu Ga
- College of Pharmacy, Inner Mongolia Medical University, Jinchuankaifaqu, Hohhot, 010110, China
| | - Jun Ai
- College of Chemistry and Environmental Science, College of Geographical Science, Inner Mongolia Key Laboratory of Environmental Chemistry, Inner Mongolia Normal University, 81 Zhaowudalu, Hohhot, 010022, China.
| | - Yong Wang
- College of Chemistry and Environmental Science, College of Geographical Science, Inner Mongolia Key Laboratory of Environmental Chemistry, Inner Mongolia Normal University, 81 Zhaowudalu, Hohhot, 010022, China.
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35
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Kang Y, Wei C. Crescent‐shaped carbazole derivatives as light‐up fluorescence probes for G‐quadruplex DNA and live cell imaging. Chem Biodivers 2022; 19:e202101030. [DOI: 10.1002/cbdv.202101030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 01/28/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Yongqiang Kang
- Shanxi University Institute of Molecular Science 92 Wucheng Road Taiyuan CHINA
| | - Chunying Wei
- Shanxi University Institute of Molecular Science No.92 Road Wucheng 030006 Taiyuan CHINA
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36
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Yin L, Zhang H, Wang Y, He L, Lu L. Exploring the fluorescence enhancement of the split G-quadruplex towards DNA-templated AgNCs and their application in omethoate detection. J Mater Chem B 2022; 10:8856-8861. [DOI: 10.1039/d2tb01755e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Based on the enhancement of split G-quadruplex on the fluorescence of DNA-templated AgNCs, a facile label-free and enzyme-free omethoate detection platform has been successfully constructed through the interaction between split G4 with DNA-AgNCs.
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Affiliation(s)
- Li Yin
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Hui Zhang
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Ying Wang
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Liang He
- Penglai Jiaxin Dye Chemical., LTD, Yantai 265600, China
| | - Lihua Lu
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, China
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37
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Xu J, Huang H, Zhou X. G-Quadruplexes in Neurobiology and Virology: Functional Roles and Potential Therapeutic Approaches. JACS AU 2021; 1:2146-2161. [PMID: 34977886 PMCID: PMC8715485 DOI: 10.1021/jacsau.1c00451] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Indexed: 05/11/2023]
Abstract
A G-quadruplex (G4) is a four-stranded nucleic acid secondary structure maintained by Hoogsteen hydrogen bonds established between four guanines. Experimental studies and bioinformatics predictions support the hypothesis that these structures are involved in different cellular functions associated with both DNA and RNA processes. An increasing number of diseases have been shown to be associated with abnormal G4 regulation. Here, we describe the existence of G4 and then discuss G4-related pathogenic mechanisms in neurodegenerative diseases and the viral life cycle. Furthermore, we focus on the role of G4s in the design of antiviral therapy and neuropharmacology, including G4 ligands, G4-based aptamers, G4-related proteins, and CRISPR-based sequence editing, along with a discussion of limitations and insights into the prospects of this unusual nucleic acid secondary structure in therapeutics. Finally, we highlight progress and challenges in this field and the potential G4-related research fields.
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Affiliation(s)
- Jinglei Xu
- The
Institute of Advanced Studies, Key Laboratory of Biomedical Polymers-Ministry
of Education, Wuhan University, Wuhan 430072, China
| | - Haiyan Huang
- Key
Laboratory of Biomedical Polymers-Ministry of Education, College of
Chemistry and Molecular Sciences, Wuhan
University, Wuhan 430072, China
| | - Xiang Zhou
- The
Institute of Advanced Studies, Key Laboratory of Biomedical Polymers-Ministry
of Education, Wuhan University, Wuhan 430072, China
- Key
Laboratory of Biomedical Polymers-Ministry of Education, College of
Chemistry and Molecular Sciences, Wuhan
University, Wuhan 430072, China
- Email to X.Z.:
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38
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Recent Development of Nanomaterials-Based Cytosensors for the Detection of Circulating Tumor Cells. BIOSENSORS-BASEL 2021; 11:bios11080281. [PMID: 34436082 PMCID: PMC8391755 DOI: 10.3390/bios11080281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/13/2021] [Accepted: 08/16/2021] [Indexed: 12/12/2022]
Abstract
The accurate analysis of circulating tumor cells (CTCs) holds great promise in early diagnosis and prognosis of cancers. However, the extremely low abundance of CTCs in peripheral blood samples limits the practical utility of the traditional methods for CTCs detection. Thus, novel and powerful strategies have been proposed for sensitive detection of CTCs. In particular, nanomaterials with exceptional physical and chemical properties have been used to fabricate cytosensors for amplifying the signal and enhancing the sensitivity. In this review, we summarize the recent development of nanomaterials-based optical and electrochemical analytical techniques for CTCs detection, including fluorescence, colorimetry, surface-enhanced Raman scattering, chemiluminescence, electrochemistry, electrochemiluminescence, photoelectrochemistry and so on.
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39
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Yan Y, Hu T, Xiang X, Li W, Ma C. Fluorometric Detection of Streptavidin with a Cationic Conjugated Polymer and Hairpin DNA Probe. ChemistrySelect 2021. [DOI: 10.1002/slct.202100800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Ying Yan
- School of Life Sciences Central South University Changsha 410013 China
| | - Tingting Hu
- School of Life Sciences Central South University Changsha 410013 China
| | - Xinying Xiang
- School of Life Sciences Central South University Changsha 410013 China
| | - Wenkai Li
- School of Life Sciences Central South University Changsha 410013 China
| | - Changbei Ma
- School of Life Sciences Central South University Changsha 410013 China
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40
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Ai X, Zhao H, Hu T, Yan Y, He H, Ma C. A signal-on fluorescence-based strategy for detection of microRNA-21 based on graphene oxide and λ exonuclease-based signal amplification. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:2107-2113. [PMID: 33870957 DOI: 10.1039/d1ay00309g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
MicroRNA (miRNA) expression is perturbed in various diseases. Herein, we have aimed to develop a novel and rapid fluorescence-based assay for detecting microRNA-21 (miR-21) activity based on FAM molecular signal amplification and graphene oxide (GO) quenching. In this system, a single stranded DNA (ssDNA) with a phosphate group at the 5'-end is labeled with a FAM molecular label at the 3'-end. In the presence of miR-21, this ssDNA forms a DNA/RNA duplex, which is cleaved by λ exonuclease (λ-exo), releasing FAM and resulting in fluorescence signal amplification at 530 nm. However, the DNA/RNA duplex is not generated in the absence of miR-21, which impedes λ-exo cleavage; subsequently, GO quenches the fluorescence intensity. The results show a detection limit of 0.02 nM and a wide linear range of 0.02-5 nM. The high sensitivity and easy operability of this assay can be applied for detecting miR-21 during clinical diagnosis of certain diseases and in biological research.
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Affiliation(s)
- Xiaojuan Ai
- School of Life Sciences, Central South University, Changsha 410013, China.
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41
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A Label-Free Fluorometric Glutathione Assay Based on a Conformational Switch of G-quadruplex. Molecules 2021; 26:molecules26092743. [PMID: 34066991 PMCID: PMC8124632 DOI: 10.3390/molecules26092743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/27/2021] [Accepted: 05/03/2021] [Indexed: 11/16/2022] Open
Abstract
In this paper, a label-free fluorescent method for glutathione (GSH) detection based on a thioflavin T/G-quadruplex conformational switch is developed. The sensing assay is fabricated depending on the virtue of mercury ions to form a thymine–thymine mismatch, which collapses the distance between two ssDNA and directs the guanine-rich part to form an intra-strand asymmetric split G-quadruplex. The newly formed G-quadruplex efficiently reacts with thioflavin T and enhances the fluorescent intensity. In the presence of GSH, Hg2+ is absorbed, destroying the G-quadruplex formation with a significant decrease in fluorescence emission. The proposed fluorescent assay exhibits a linear range between 0.03–5 μM of GSH with a detection limit of 9.8 nM. Furthermore, the efficacy of this method is examined using human serum samples to detect GSH. Besides GSH, other amino acids are also investigated in standard samples, which display satisfactory sensitivity and selectivity. Above all, we develop a method with features including potentiality, facility, sensitivity, and selectivity for analyzing GSH for clinical diagnostics.
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42
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Wang Y, Yan Y, Liu X, Ma C. An Exonuclease I-Aided Turn-Off Fluorescent Strategy for Alkaline Phosphatase Assay Based on Terminal Protection and Copper Nanoparticles. BIOSENSORS-BASEL 2021; 11:bios11050139. [PMID: 33946723 PMCID: PMC8145916 DOI: 10.3390/bios11050139] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 04/27/2021] [Accepted: 04/27/2021] [Indexed: 12/19/2022]
Abstract
As an important DNA 3'-phosphatase, alkaline phosphatase can repair damaged DNA caused by replication and recombination. It is essential to measure the level of alkaline phosphatase to indicate some potential diseases, such as cancer, related to alkaline phosphatase. Here, we designed a simple and fast method to detect alkaline phosphatase quantitively. When alkaline phosphatase is present, the resulting poly T-DNA with a 3'-hydroxyl end was cleaved by exonuclease I, prohibiting the formation of fluorescent copper nanoparticles. However, the fluorescent copper nanoparticles can be monitored with the absence of alkaline phosphatase. Hence, we can detect alkaline phosphatase with this turn-off strategy. The proposed method is able to quantify the concentration of alkaline phosphatase with the LOD of 0.0098 U/L. Furthermore, we utilized this method to measure the effects of inhibitor Na3VO4 on alkaline phosphatase. In addition, it was successfully applied to quantify the level of alkaline phosphatase in human serum. The proposed strategy is sensitive, selective, cost effective, and timesaving, having a great potential to detect alkaline phosphatase quantitatively in clinical diagnosis.
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Affiliation(s)
| | | | - Xinfa Liu
- Correspondence: (X.L.); (C.M.); Tel.: +86-731-8265-0230 (X.L. & C.M.)
| | - Changbei Ma
- Correspondence: (X.L.); (C.M.); Tel.: +86-731-8265-0230 (X.L. & C.M.)
| |
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