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Zhou W, Wan W, Miao W, Bao Y, Liu Y, Jia G, Li C. K +-Specification with Flavone P0 Probe in a G-Quadruplex DNA. Anal Chem 2024; 96:10835-10840. [PMID: 38889097 DOI: 10.1021/acs.analchem.4c02368] [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: 06/20/2024]
Abstract
G-quadruplex (G4) DNA is considered as a prospective therapeutic target due to its potential biological significance. To understand G4 biological roles and function, a G4-specific fluorescent probe is necessary. However, it is difficult for versatile G4 to precisely recognize without perturbing their folding dynamics. Herein, we reported that flavone P0 can be a fluorescent probe for G4 DNA-specific recognition and have developed a highly selective detection of K+ ion by dimeric G4/P0 system. When comparing various nucleic acid structures, including G4, i-motif, ss/ds-DNA, and triplex, an apparent fluorescence enhancement is observed in the presence of G4 DNA for 85-fold, but only 8-fold for non-G4 DNA. Furthermore, based on fluorescent probe of flavone P0 for G4 DNA screening, the noncovalent dimeric G4/P0 system is exploited as a K+ sensor, that selectively responds to K+ with a 513-fold fluorescence enhancement and a detection range for K+ ion concentration from 0 to 500 mM. This K+ sensor also has a remarkably anti-interference ability for other metal cations, especially for a high concentration of Na+. These results have demonstrated that flavone P0 is an efficient tool for monitoring G-quadruplex DNA and endows flavone P0 with bioanalytical and medicinal applications.
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Affiliation(s)
- Wenqin Zhou
- State Key Laboratory of Catalysis, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Wang Wan
- Key Laboratory of Separation Science for Analytical Chemistry, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Wenhui Miao
- State Key Laboratory of Catalysis, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Yu Bao
- State Key Laboratory of Catalysis, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Yu Liu
- Key Laboratory of Separation Science for Analytical Chemistry, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Guoqing Jia
- State Key Laboratory of Catalysis, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Can Li
- State Key Laboratory of Catalysis, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
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2
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Liu Q, Yang M, Zhang H, Ma W, Fu X, Li H, Gao S. A colorimetric tandem combination of CRISPR/Cas12a with dual functional hybridization chain reaction for ultra-sensitive detection of Mycobacterium bovis. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:3220-3230. [PMID: 38717230 DOI: 10.1039/d3ay02200e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2024]
Abstract
Tuberculosis caused by Mycobacterium bovis poses a global infectious threat to humans and animals. Therefore, there is an urgent need to develop a sensitive, precise, and easy-to-readout strategy. Here, a novel tandem combination of a CRISPR/Cas12a system with dual HCR (denoted as CRISPR/Cas12a-D-HCR) was constructed for detecting Mycobacterium bovis. Based on the efficient trans-cleavage activity of the active CRISPR/Cas12a system, tandem-dsDNA with PAM sites was established using two flexible hairpins, providing multiple binding sites with CRISPR/Cas12a for further amplification. Furthermore, the activation of Cas12a initiated the second hybridization chain reaction (HCR), which integrated complete G-quadruplex sequences to assemble the hemin/G-quadruplex DNAzyme. With the addition of H2O2 and ABTS, a colorimetric signal readout strategy was achieved. Consequently, CRISPR/Cas12a-D-HCR achieved a satisfactory detection linear range from 20 aM to 50 fM, and the limit of detection was as low as 2.75 aM with single mismatched recognition capability, demonstrating good discrimination of different bacterial species. Notably, the practical application performance was verified via the standard addition method, with the recovery ranging from 96.0% to 105.2% and the relative standard deviations (RSD) ranging from 0.95% to 6.45%. The proposed CRISPR/Cas12a-D-HCR sensing system served as a promising application for accurate detection in food safety and agricultural fields.
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Affiliation(s)
- Qiong Liu
- Hunan Provincial Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan 411104, China.
| | - Mei Yang
- Hunan Provincial Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan 411104, China.
| | - He Zhang
- Hunan Provincial Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan 411104, China.
| | - Wenjie Ma
- Hunan Provincial Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan 411104, China.
| | - Xin Fu
- Hunan Provincial Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan 411104, China.
| | - Huiqing Li
- Hunan Provincial Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan 411104, China.
| | - Sainan Gao
- Hunan Provincial Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan 411104, China.
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3
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Wei Y, Yang L, Ye Y, Liao L, Dai H, Wei Z, Lin Y, Zheng C. A simple aptamer-dye fluorescence sensor for detecting Δ9-tetrahydrocannabinol and its metabolite in urban sewage. Chem Commun (Camb) 2024; 60:5205-5208. [PMID: 38652014 DOI: 10.1039/d4cc00824c] [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: 04/25/2024]
Abstract
This work developed an aptamer-dye complex as a label-free ratiometric fluorescence sensor for rapid analysis of THC and its metabolite in sewage samples. Integrated with a portable fluorescence capture device, this sensor exhibited excellent sensitivity with visualization of as low as 0.6 μM THC via naked-eye observation, and THC analysis can be accomplished within 4 min, which would be a complementary tool for quantifying THC in sewage samples to estimate cannabis consumption.
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Affiliation(s)
- Yingnan Wei
- Key Laboratory of Green Chemistry & Technology of MOE, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China.
| | - Lin Yang
- West China School of Basic Medical Science & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China.
| | - Yi Ye
- West China School of Basic Medical Science & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China.
| | - Linchuan Liao
- West China School of Basic Medical Science & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China.
| | - Hao Dai
- West China School of Basic Medical Science & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China.
| | - Zeliang Wei
- Core Facilities of West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yao Lin
- West China School of Basic Medical Science & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China.
| | - Chengbin Zheng
- Key Laboratory of Green Chemistry & Technology of MOE, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China.
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4
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Lv M, Ren J, Wang E. Topological effect of an intramolecular split G-quadruplex on thioflavin T binding and fluorescence light-up. Chem Sci 2024; 15:4519-4528. [PMID: 38516084 PMCID: PMC10952102 DOI: 10.1039/d3sc06862e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 02/04/2024] [Indexed: 03/23/2024] Open
Abstract
In this work, the topological effect on binding interaction between a G-quadruplex and thioflavin T (ThT) ligand was systematically investigated on a platform of an intramolecular split G-quadruplex (Intra-SG). Distinct fluorescence changes from ThT were presented in the presence of distinct split modes of Intra-SG structures and an intriguing phenomenon of target-induced fluorescence light-up occurred for split modes 2 : 10, 5 : 7 and 8 : 4. It was validated that hybridization between the Intra-SG spacer and target did not unfold the G-quadruplex, but facilitated the ThT binding. Moreover, the 3' guanine-rich fragment of Intra-SG was very susceptible to topology variation produced by the bound target strand. Additionally, a bioanalytical method was developed for ultrasensitive gene detection, confirming the utility of the ThT/Intra-SG complex as a universal signal transducer. It is believed that the results and disclosed rules will inspire researchers to develop many new DNA-based signal transducers in the future.
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Affiliation(s)
- Mengmeng Lv
- College of Chemistry, Jilin University Changchun Jilin 130012 China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 China
| | - Jiangtao Ren
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 China
| | - Erkang Wang
- College of Chemistry, Jilin University Changchun Jilin 130012 China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 China
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5
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Metangle S, Ranjan N. Preferential Binding of a Red Emissive Julolidine Derivative to a Promoter G-Quadruplex. Chembiochem 2024; 25:e202300527. [PMID: 37926689 DOI: 10.1002/cbic.202300527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 10/23/2023] [Accepted: 11/02/2023] [Indexed: 11/07/2023]
Abstract
The therapeutic potential of G-quadruplexes has increased significantly with the growing understanding of their functional roles in pathogens apart from human diseases such as cancer. Here, we report the synthesis of three julolidine-based molecules and their binding to nucleic acids. Among the synthesized molecules, compound 1 exhibited red emissive fluorescence with a distinct preference for Pu22 G-quadruplex. The binding of compound 1 to Pu22 G-quadruplex, initially identified through a fluorescence-based screening, was further confirmed by UV-vis, fluorescence spectroscopy, and circular dichroism-based experiments. Thermal denaturation of compound 1 in the presence of Pu22 G-quadruplex revealed a concentration-dependent stabilization (~10.0 °C at 1 : 3 stoichiometry). Fluorescence-based experiments revealed 1 : 1 stoichiometry of the interaction and an association constant (Ka ) of 5.67×106 M-1 . CD experiments displayed that the parallel conformation of the G-quadruplex was retained on compound 1's binding and signs of higher order binding/complex formation were observed at high compound 1 to DNA ratio. Molecular docking studies revealed the dominance of stacking and van der Waals interactions in the molecular recognition which was aided by some close-distance interactions involving the quinolinium nitrogen atom.
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Affiliation(s)
- Sachin Metangle
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow, Uttar Pradesh, 226002, India
| | - Nihar Ranjan
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow, Uttar Pradesh, 226002, India
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6
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Mizunuma M, Suzuki M, Kobayashi T, Hara Y, Kaneko A, Furukawa K, Chuman Y. Development of Mn 2+-Specific Biosensor Using G-Quadruplex-Based DNA. Int J Mol Sci 2023; 24:11556. [PMID: 37511324 PMCID: PMC10380348 DOI: 10.3390/ijms241411556] [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: 06/23/2023] [Revised: 07/14/2023] [Accepted: 07/15/2023] [Indexed: 07/30/2023] Open
Abstract
Metal ions are used in various situations in living organisms and as a part of functional materials. Since the excessive intake of metal ions can cause health hazards and environmental pollution, the development of new molecules that can monitor metal ion concentrations with high sensitivity and selectivity is strongly desired. DNA can form various structures, and these structures and their properties have been used in a wide range of fields, including materials, sensors, and drugs. Guanine-rich sequences respond to metal ions and form G-quadruplex structures and G-wires, which are the self-assembling macromolecules of G-quadruplex structures. Therefore, guanine-rich DNA can be applied to a metal ion-detection sensor and functional materials. In this study, the IRDAptamer library originally designed based on G-quadruplex structures was used to screen for Mn2+, which is known to induce neurodegenerative diseases. Circular dichroism and fluorescence analysis using Thioflavin T showed that the identified IRDAptamer sequence designated MnG4C1 forms a non-canonical G-quadruplex structure in response to low concentrations of Mn2+. A serum resistance and thermostability analysis revealed that MnG4C1 acquired stability in a Mn2+-dependent manner. A Förster resonance energy transfer (FRET) system using fluorescent molecules attached to the termini of MnG4C1 showed that FRET was effectively induced based on Mn2+-dependent conformational changes, and the limit of detection (LOD) was 0.76 µM for Mn2+. These results suggested that MnG4C1 can be used as a novel DNA-based Mn2+-detecting molecule.
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Affiliation(s)
- Masataka Mizunuma
- Department of Chemistry, Faculty of Science, Niigata University, Niigata 950-2181, Japan
| | - Mirai Suzuki
- Department of Chemistry, Faculty of Science, Niigata University, Niigata 950-2181, Japan
| | - Tamaki Kobayashi
- Department of Chemistry, Faculty of Science, Niigata University, Niigata 950-2181, Japan
| | - Yuki Hara
- Department of Chemistry, Faculty of Science, Niigata University, Niigata 950-2181, Japan
| | - Atsushi Kaneko
- Department of Chemistry, Faculty of Science, Niigata University, Niigata 950-2181, Japan
| | - Kazuhiro Furukawa
- Department of Chemistry, Faculty of Science, Niigata University, Niigata 950-2181, Japan
| | - Yoshiro Chuman
- Department of Chemistry, Faculty of Science, Niigata University, Niigata 950-2181, Japan
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Yang M, Lai R, Peng S, Chang Y, Zeng X, Wang D, Zhou X, Shao Y. Selectively recognizing heptad-interfaced G-quadruplexes by a molecular rotor with an ESIPT emission. Chem Commun (Camb) 2023; 59:1189-1192. [PMID: 36629144 DOI: 10.1039/d2cc06156b] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Heptad-interfaced G-quadruplexes (G4s), formed with GGA repeats located in the nuclear proto-oncogene c-myb promoter, can be selectively targeted by a prenylated flavonol of sophoflavescenol (Sop) with restriction of molecular rotation to trigger strong excited state intramolecular proton transfer (ESIPT) emission.
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Affiliation(s)
- Mujing Yang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China.
| | - Rong Lai
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China.
| | - Shuzhen Peng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China.
| | - Yun Chang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China.
| | - Xingli Zeng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China.
| | - Dandan Wang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China.
| | - Xiaoshun Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China.
| | - Yong Shao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China.
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8
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Chen Z, Wang Y. A label- and enzyme-free fluorescence assay based on thioflavin T–induced G-quadruplexes for the detection of telomerase activity. JOURNAL OF CHEMICAL RESEARCH 2023. [DOI: 10.1177/17475198221139085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A label- and enzyme-free fluorescence assay based on thioflavin T–induced G-quadruplexes is developed to sensitively and specifically detect telomerase activity. Thioflavin T has a dual role as an efficient inducer and fluorescent probe, and the incorporation of thioflavin T into the thioflavin T–induced G-quadruplexes results in an intense fluorescence enhancement. In the presence of thioflavin T and K+, G-quadruplexes are formed by elongation of the telomerase substrate primer that is catalyzed by telomerase extracted from cancer cells. Thus, the telomerase activity in cancer cell extracts can be evaluated by measuring the thioflavin T fluorescence. More importantly, thioflavin T can specifically recognize and bind to G-quadruplexes, whereas it cannot recognize single- and double-stranded DNAs, which leads to the thioflavin T–based fluorescence assay exhibiting a reduced background and improved signal-to-noise ratio. As a result, the proposed assay has the linear range from 5 to 200 HeLa cells and the detection limit is 34 HeLa cells, which holds great potential for use in the detection of telomerase activity and the diagnosis of cancer.
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Affiliation(s)
- Zhe Chen
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, P.R. China
- Key Laboratory of Forensic Toxicology of Ministry of Public Security, Jinzhong, P.R. China
| | - Yunxia Wang
- Department of Laboratory Science, Shanxi Medical University, Taiyuan, P.R. China
- The Sixth Hospital of Shanxi Medical University (General Hospital of Tisco), Taiyuan, P.R. China
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9
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Yang T, Li J, Zhang D, Cheng X, Li J, Huang X, Ding S, Tang BZ, Cheng W. Pre-Folded G-Quadruplex as a Tunable Reporter to Facilitate CRISPR/Cas12a-Based Visual Nucleic Acid Diagnosis. ACS Sens 2022; 7:3710-3719. [PMID: 36399094 DOI: 10.1021/acssensors.2c01391] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a-based detection strategies with a fluorophore quencher-labeled ssDNA reporter or gold nanoparticle ssDNA reporter have been widely used in point-of-care (POC) molecular diagnostics. However, the potential of these CRISPR/Cas12a strategies for POC molecular diagnostics is often compromised due to the complex labeling, high cost, and low signal-to-noise ratio. Herein, we show a pre-folded G-quadruplex (G4) structure with tunable tolerance to CRISPR/Cas12a trans-cleavage and explore its mechanism. Two G4 structures (i.e., Tel22-10 and G16C) sensitive or tolerant to CRISPR/Cas12a trans-cleavage are designed and used as signal elements to fabricate a label-free visible fluorescent strategy or "signal-on" colorimetric strategy, respectively. These two strategies facilitate an ultrasensitive visual nucleic acid determination of Group B Streptococci with a naked-eye limit of detection of 1 aM. The feasibility of the developed G4-assisted CRISPR/Cas12a strategies for real-world applications is demonstrated in clinical vaginal/anal specimens and further verified by a commercial qPCR assay. This work suggests that the proposed G4 structures with tunable tolerance can act as promising signal reporters in the CRISPR/Cas12a system to enable ultrasensitive visible nucleic acid detection.
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Affiliation(s)
- Tiantian Yang
- The Centre for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing400016, China
| | - Juan Li
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Nanchang University, Nanchang330047, China
| | - Decai Zhang
- The Centre for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing400016, China
| | - Xiaoxue Cheng
- The Centre for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing400016, China
| | - Jia Li
- The Centre for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing400016, China
| | - Xiaolin Huang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Nanchang University, Nanchang330047, China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing400016, China
| | - Ben Zhong Tang
- School of Science and Engineering, Shenzhen Institute of Aggregate Science and Technology, The Chinese University of Hong Kong, Shenzhen, Guangdong518172, China
| | - Wei Cheng
- The Centre for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing400016, China
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Xu Q, Yang M, Chang Y, Peng S, Wang D, Zhou X, Shao Y. Switching G-quadruplex to parallel duplex by molecular rotor clustering. Nucleic Acids Res 2022; 50:10249-10263. [PMID: 36130267 PMCID: PMC9561263 DOI: 10.1093/nar/gkac811] [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] [Received: 05/05/2022] [Revised: 08/31/2022] [Accepted: 09/10/2022] [Indexed: 11/12/2022] Open
Abstract
Switching of G-quadruplex (G4) structures between variant types of folding has been proved to be a versatile tool for regulation of genomic expression and development of nucleic acid-based constructs. Various specific ligands have been developed to target G4s in K+ solution with therapeutic prospects. Although G4 structures have been reported to be converted by sequence modification or a unimolecular ligand binding event in K+-deficient conditions, switching G4s towards non-G4 folding continues to be a great challenge due to the stability of G4 in physiological K+ conditions. Herein, we first observed the G4 switching towards parallel-stranded duplex (psDNA) by multimolecular ligand binding (namely ligand clustering) to overcome the switching barrier in K+. Purine-rich sequences (e.g. those from the KRAS promoter region) can be converted from G4 structures to dimeric psDNAs using molecular rotors (e.g. thioflavin T and thiazole orange) as initiators. The formed psDNAs provided multiple binding sites for molecular rotor clustering to favor subsequent structures with stability higher than the corresponding G4 folding. Our finding provides a clue to designing ligands with the competency of molecular rotor clustering to implement an efficient G4 switching.
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Affiliation(s)
- Qiuda Xu
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, China
| | - Mujing Yang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, China
| | - Yun Chang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, China
| | - Shuzhen Peng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, China
| | - Dandan Wang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, China
| | - Xiaoshun Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, China
| | - Yong Shao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, China
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11
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Chitbankluai K, Thavarungkul P, Kanatharana P, Kaewpet M, Buranachai C. Newly found K +-Thioflavin T competitive binding to DNA G-quadruplexes and the development of a label-free fluorescent biosensor with extra low detection limit for K + determination in urine samples. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 276:121244. [PMID: 35429866 DOI: 10.1016/j.saa.2022.121244] [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: 10/29/2021] [Revised: 04/03/2022] [Accepted: 04/04/2022] [Indexed: 06/14/2023]
Abstract
The determination of potassium ion K+ in body fluids is important in health monitoring and diagnoses. One of the interesting and simple methods for K+ detection is the use of label-free biosensors based on DNA G-quadruplexes (GQs) coupled with a specific fluorescent probe, such as Thioflavin T (ThT), which lights up when bound with K+-stabilized GQs. However, these biosensors are not generally sensitive. In this work, we found a solution: at a low concentration, K+ competes with ThT in binding to a bimolecular GQ or a tetramolecular GQ, resulting in a decrease in ThT fluorescence emission with increasing K+. Therefore, we developed a label-free turn-off fluorescent K+ sensor. The sensor provides a very low detection limit of 21.87 ± 0.59 nM. Other possible interfering components in urine did not exert any effect even at quantities that were 10-fold greater than their upper limit of normal concentrations found in urine samples. With its only requirement of diluting samples, the developed low-cost label-free probe and simple sensor was successfully applied to the direct detection of K+ in normal urine samples with high accuracy (recoveries ranged from 90% to 100%).
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Affiliation(s)
- Khwanrudee Chitbankluai
- Division of Physical Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand; Center of Excellence for Trace Analysis and Biosensor, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand; Thailand Center of Excellence in Physics, Commission on Higher Education, 328 Si Ayutthaya Road, Bangkok, 10400, Thailand
| | - Panote Thavarungkul
- Division of Physical Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand; Center of Excellence for Trace Analysis and Biosensor, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand; Thailand Center of Excellence in Physics, Commission on Higher Education, 328 Si Ayutthaya Road, Bangkok, 10400, Thailand; Center of Excellence for Innovation in Chemistry, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Proespichaya Kanatharana
- Division of Physical Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand; Center of Excellence for Trace Analysis and Biosensor, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand; Center of Excellence for Innovation in Chemistry, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Morakot Kaewpet
- Division of Physical Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand; Center of Excellence for Trace Analysis and Biosensor, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Chittanon Buranachai
- Division of Physical Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand; Center of Excellence for Trace Analysis and Biosensor, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand; Thailand Center of Excellence in Physics, Commission on Higher Education, 328 Si Ayutthaya Road, Bangkok, 10400, Thailand.
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12
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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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13
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Gao C, Zhang Z, Zhang X, Chen J, Chen Y, Zhao C, Zhao L, Feng L. A molecular crowding thermo-switchable chiral G-quartet hydrogel with circularly polarized luminescence property. SOFT MATTER 2022; 18:3125-3129. [PMID: 35411907 DOI: 10.1039/d2sm00148a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A novel helix hydrogel with a G-quartet structure was synthesized from guanosine (Gua) and its derivative 5'-guanosine monophosphate (5'-GMP) under a molecular crowding environment. The chirality of the hydrogel is adjusted by controlling the gelling speed. The chiral hydrogel can induce an achiral dye Thioflavin T (ThT) to realize circularly polarized fluorescence (CPL). The CPL dissymmetry factor |glum| of the dye-hydrogels can reach 3 × 10-2 and can be switched easily.
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Affiliation(s)
- Chenqi Gao
- Materials Genome Institute, and Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, China.
| | - Zhiwei Zhang
- Materials Genome Institute, and Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, China.
| | - Xinying Zhang
- Materials Genome Institute, and Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, China.
| | - Jingqi Chen
- Materials Genome Institute, and Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, China.
- Institute of Molecular Medicine (IMM), Shanghai Jiao Tong University School of Medicine Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yingying Chen
- Materials Genome Institute, and Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, China.
| | - Chuanqi Zhao
- Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Jilin 130022, China.
| | - Lijuan Zhao
- Materials Genome Institute, and Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, China.
| | - Lingyan Feng
- Materials Genome Institute, and Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, China.
- Shanghai Engineering Research Center of Organ Repair, 200444, Shanghai, China
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14
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Label-free and highly sensitive APE1 detection based on rolling circle amplification combined with G-quadruplex. Talanta 2022; 244:123404. [PMID: 35349840 DOI: 10.1016/j.talanta.2022.123404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/12/2022] [Accepted: 03/22/2022] [Indexed: 12/13/2022]
Abstract
The highly sensitive detection of low-abundant apurinic/apyrimidinic endonuclease 1 (APE1) activity is of great significance for early diagnosis of disease and pathological research. Many methods for detecting APE1 based on isothermal nucleic acids amplification have been developed for improving its sensitivity. However, some of these methods have certain limitations, such as multiple reaction steps, narrow linear range, and complicated processes for fluorescent labeling. Herein, we develop a highly sensitive and label-free APE1 fluorescence detection method based on rolling circle amplification combined with G-quadruplex (RCA-G4). A hairpin probe (HP) labeled with the AP site can be recognized and cleaved by APE1, leading to the release of the primer sequence, which triggered RCA to produce long chain amplification products with a great amount of repeated sequences. The formed amplicon contains a series G-quadruplex structure, which can be combined with Thioflavin T (ThT) to produce fluorescence and achieve high sensitivity label-free detection of APE1. Benefit from the high amplification efficiency of RCA and the high fluorescence quantum yield of G-quadruplex/ThT, a detection limit as low as 1.52 × 10-6 U/mL and the linear range from 2 × 10-6 to 10 U/mL were obtained. The developed RCA-G4 method can be successfully used to detect APE1 in serum samples with a recovery from 96.3% to 105.7%. We believe that this approach is expected to play an important role in APE1-related disease research and drug development.
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15
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Yu Z, Huang W, Shi L, Ke S, Xu S. Selective probes targeting c-MYC Pu22 G-quadruplex and their application in live mice imaging. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.09.087] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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16
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Ma X, Lv M, Du F, Wu C, Lou B, Zeid AM, Xu G. Dimeric G-Quadruplex: An Efficient Probe for Ultrasensitive Fluorescence Detection of Mustard Compounds. Anal Chem 2022; 94:4112-4118. [PMID: 35196002 DOI: 10.1021/acs.analchem.2c00124] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Some mustard compounds (mustards) are highly toxic chemical warfare agents. Some are explored as new anticancer drugs. Therefore, the fast, selective, and sensitive detection of mustards is extremely important for public security and cancer therapy. Mustards mostly target the N7 position on the guanine bases of DNA. The guanine-rich G-quadruplex DNA (G4) has been widely studied in the sensing area, and it was found that dimeric G4 (D-G4) could dramatically light up the fluorescence intensity of thioflavin T (ThT). Based on this, we used for the first time the D-G4 DNA as a selective probe for ultrasensitive fluorescence detection of nitrogen mustard (NM). When NM occupies the N7 on guanine, it can block the formation of the D-G4 structure due to the steric hindrance, and hence, it inhibits the combination of D-G4 with ThT, leading to a sharp decrease of fluorescence intensity. The proposed reaction mechanism is proved using ultraviolet-visible (UV-Vis) spectra, circular dichroism (CD) spectra, and polyacrylamide gel electrophoresis. Herein, the concentration of D-G4/ThT used is as low as 50 nM due to its highly fluorescent performance, enabling both high sensitivity and low cost. NM can be detected with a wide linear range from 10 to 2000 nM. The detection limit of NM reaches a surprisingly low concentration of 6 nM, which is 2 or 3 orders of magnitude lower than that of previously developed fluorescence methods for mustards and simulants.
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Affiliation(s)
- Xiangui Ma
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China.,University of Science and Technology of China, Hefei 230026, Anhui, P. R. China
| | - Mengmeng Lv
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China
| | - Fangxin Du
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China.,University of Science and Technology of China, Hefei 230026, Anhui, P. R. China
| | - Cunqi Wu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China
| | - Baohua Lou
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China
| | - Abdallah M Zeid
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China.,Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Guobao Xu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China.,University of Science and Technology of China, Hefei 230026, Anhui, P. R. China
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17
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A fluorescent molecular rotor for the selective detection of the hybrid-conformation 22AG G-Quadruplex. Bioorg Med Chem Lett 2022; 55:128462. [PMID: 34813881 DOI: 10.1016/j.bmcl.2021.128462] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/09/2021] [Accepted: 11/12/2021] [Indexed: 01/07/2023]
Abstract
G-quadruplex (G4) DNA plays a vital role in myriad biological process and is linked to several human diseases, including Alzheimer's disease. Probing G4s with fluorescent probes can provide a better understanding their mechanisms of action and of their roles in Nature. In this study we developed a quinolinium-vinylaniline molecular rotor probe, featuring a diethylaminosalicylaldehyde unit that could discriminate the hybrid-22AG G4 sequence selectively amongst other G4 sequences. This probe underwent a significant red-shift upon binding to the target G4 (broad 575 nm → sharp 630 nm) with enhanced fluorescence (up to 14-fold). We suspect that the vinylaniline unit of the molecular rotor, when bound to the hybrid-22 A G4, experienced restricted rotation, thereby undergoing enhanced intramolecular charge transfer. The presence of the diethylaminosalicylaldehyde moiety appeared to play a major role in the enhanced selectivity toward the 22AG G4.
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18
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Zalmi GA, Jadhav RW, Mirgane HA, Bhosale SV. Recent Advances in Aggregation-Induced Emission Active Materials for Sensing of Biologically Important Molecules and Drug Delivery System. Molecules 2021; 27:150. [PMID: 35011382 PMCID: PMC8746362 DOI: 10.3390/molecules27010150] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/21/2021] [Accepted: 12/24/2021] [Indexed: 12/26/2022] Open
Abstract
The emergence and development of aggregation induced emission (AIE) have attracted worldwide attention due to its unique photophysical phenomenon and for removing the obstacle of aggregation-caused quenching (ACQ) which is the most detrimental process thereby making AIE an important and promising aspect in various fields of fluorescent material, sensing, bioimaging, optoelectronics, drug delivery system, and theranostics. In this review, we have discussed insights and explored recent advances that are being made in AIE active materials and their application in sensing, biological cell imaging, and drug delivery systems, and, furthermore, we explored AIE active fluorescent material as a building block in supramolecular chemistry. Herein, we focus on various AIE active molecules such as tetraphenylethylene, AIE-active polymer, quantum dots, AIE active metal-organic framework and triphenylamine, not only in terms of their synthetic routes but also we outline their applications. Finally, we summarize our view of the construction and application of AIE-active molecules, which thus inspiring young researchers to explore new ideas, innovations, and develop the field of supramolecular chemistry in years to come.
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Affiliation(s)
| | | | | | - Sheshanath V. Bhosale
- School of Chemical Sciences, Goa University, Taleigao Plateau 403206, India; (G.A.Z.); (R.W.J.); (H.A.M.)
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19
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Fu W, Jing H, Xu X, Xu S, Wang T, Hu W, Li H, Zhang N. Two coexisting pseudo-mirror heteromolecular telomeric G-quadruplexes in opposite loop progressions differentially recognized by a low equivalent of Thioflavin T. Nucleic Acids Res 2021; 49:10717-10734. [PMID: 34500466 PMCID: PMC8501994 DOI: 10.1093/nar/gkab755] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 07/24/2021] [Accepted: 08/31/2021] [Indexed: 11/13/2022] Open
Abstract
The final 3′-terminal residue of the telomeric DNA G-overhang is inherently less precise. Here, we describe how alteration of the last 3′-terminal base affects the mutual recognition between two different G-rich oligomers of human telomeric DNA in the formation of heteromolecular G-quadruplexes (hetero-GQs). Associations between three- and single-repeat fragments of human telomeric DNA, target d(GGGTTAGGGTTAGGG) and probe d(TAGGGT), in Na+ solution yield two coexisting forms of (3 + 1) hybrid hetero-GQs: the kinetically favourable LLP-form (left loop progression) and the thermodynamically controlled RLP-form (right loop progression). However, only the adoption of a single LLP-form has been previously reported between the same probe d(TAGGGT) and a target variant d(GGGTTAGGGTTAGGGT) having one extra 3′-end thymine. Moreover, the flanking base alterations of short G-rich probe variants also significantly affect the loop progressions of hetero-GQs. Although seemingly two pseudo-mirror counter partners, the RLP-form exhibits a preference over the LLP-form to be recognized by a low equivalent of fluorescence dye thioflavin T (ThT). To a greater extent, ThT preferentially binds to RLP hetero-GQ than with the corresponding telomeric DNA duplex context or several other representative unimolecular GQs.
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Affiliation(s)
- Wenqiang Fu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,University of Science and Technology of China, Hefei 230026, China
| | - Haitao Jing
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,University of Science and Technology of China, Hefei 230026, China
| | - Xiaojuan Xu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,University of Science and Technology of China, Hefei 230026, China
| | - Suping Xu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China
| | - Tao Wang
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China
| | - Wenxuan Hu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,University of Science and Technology of China, Hefei 230026, China
| | - Huihui Li
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,University of Science and Technology of China, Hefei 230026, China
| | - Na Zhang
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China.,Key Laboratory of Anhui Province for High Field Magnetic Resonance Imaging, Hefei 230031, China.,High Magnetic Field Laboratory of Anhui Province, Hefei 230031, China
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20
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Yan C, Chang Y, Gao H, Zhang Q, Peng S, Wang D, Zhou X, Shao Y. G-quadruplex apurinic site-programmed chiral cyanine assemblies for specifically recognizing guanosine and guanine. Analyst 2021; 146:5866-5872. [PMID: 34570847 DOI: 10.1039/d1an01110c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA-tuned dye assemblies have received considerable attention toward developing various devices. Owing to easy conformation implementation, G-quadruplexes (G4s) have been extensively used as initiators to grow dye assemblies with controllable chiralities. However, programmed chirality regulation of dye assemblies for a given G4 sequence has not been realized in a straightforward manner. In this work, we replaced a middle guanine in the G-tracts of a human telomeric G4 with an apurinic site (AP site) to meet the programmed dye assemblies. Although all of the AP site replacements altered the G4 conformation from the hybrid to the antiparallel folding, the handedness of pinacyanol (PIN) assemblies grown on the AP site-containing G4 was programmably regulated. The G4 with the AP site at the 5'-most G-tract grew right-handed assemblies, while that with the AP site at the 3'-most G-tract grew left-handed assemblies. The handedness of assemblies almost totally mirrored each other within 450-700 nm. Interestingly, we found that the AP site provided a specific binding site for guanosine and guanine, and this binding event sensitively broke the chiral assemblies. Thus, dye assembly-based sensors can be easily established based on the chiral responses with a high selectivity and sensitivity. Our work first demonstrates the AP site programmed chirality regulation of G4-grown dye assemblies and will find wide application in chiral devices.
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Affiliation(s)
- Chenxiao Yan
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China.
| | - Yun Chang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China.
| | - Heng Gao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China.
| | - Qingqing Zhang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China.
| | - Shuzhen Peng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China.
| | - Dandan Wang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China.
| | - Xiaoshun Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China.
| | - Yong Shao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China.
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21
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Verma S, Ravichandiran V, Ranjan N. Beyond amyloid proteins: Thioflavin T in nucleic acid recognition. Biochimie 2021; 190:111-123. [PMID: 34118329 DOI: 10.1016/j.biochi.2021.06.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 05/25/2021] [Accepted: 06/04/2021] [Indexed: 01/01/2023]
Abstract
Thioflavin T (ThT) is a commercially available fluorescent dye that is commonly used in biomedical research for over five decades. It was first reported as an extrinsic fluorescent probe for the detection of amyloid fibrils and related processes and it has also been used extensively for assessing protein binding in fluorescence-based assays. Although the nucleic acid binding of ThT was reported half of a century ago in the 1970s, it was not widely explored until the start of this decade. In recent years, Thioflavin T has become a major tool in the recognition of many types of non-canonical nucleic acid conformations including duplexes, triplexes, and G-quadruplexes. The propensity of ThT binding is more towards base aberrations, bulges, and mismatches highlighting its importance in serving as a diagnostic tool in a variety of ailments/disease conditions. In this review, we cover major advancements in nucleic acid detection/binding by ThT to a variety of nucleic acid structures.
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Affiliation(s)
- Smita Verma
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER)-Raebareli, New Transit Campus, Lucknow, Uttar Pradesh, 226002, India; Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER)-Kolkata, Maniktala Main Road, Kolkata, 700054, India
| | - Velayutham Ravichandiran
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER)-Kolkata, Maniktala Main Road, Kolkata, 700054, India
| | - Nihar Ranjan
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER)-Raebareli, New Transit Campus, Lucknow, Uttar Pradesh, 226002, India.
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22
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Fluorescent probes for the stabilization and detection of G-quadruplexes and their prospective applications. J INDIAN CHEM SOC 2021. [DOI: 10.1016/j.jics.2021.100078] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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23
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Cheng Y, Cheng M, Hao J, Miao W, Zhou W, Jia G, Li C. Highly Selective Detection of K + Based on a Dimerized G-Quadruplex DNAzyme. Anal Chem 2021; 93:6907-6912. [PMID: 33929188 DOI: 10.1021/acs.analchem.1c00872] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Potassium ion (K+) plays a crucial role in biological systems, such as maintaining cellular processes and causing diseases. However, specifically, the detection of K+ is extremely challenging because of the coexistence of the chemically similar ion of Na+ under physiological conditions. In this work, a K+ specific biosensor is constructed on the basis of a dimerized G-quadruplex (GQ) DNA, which is promoted by K+, and the enzymatic activity of the resulting DNAzyme depends on the concentration of the K+. The K+ in a 1-200 mM concentration range can be selectively detected by visual color, UV-Vis absorbance or fluorescence even if the concentration of the accompanying Na+ is up to 140 mM at an ambient condition up to 45 °C. In addition, this system can also be used to selectively detect NH4+ in a 5-200 mM concentration range. This dimerized DNAzyme offers a new type of biosensor with a potential application in the biological system.
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Affiliation(s)
- Yu Cheng
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Mingpan Cheng
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, China
| | - Jingya Hao
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Wenhui Miao
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Wenqin Zhou
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Guoqing Jia
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, China
| | - Can Li
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, China
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24
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Benzothiazole-based colorimetric chemosensors bearing naphthol aldehyde unit: Synthesis, characterization, selective detection of hypochlorite and its application as test strips. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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25
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Yan C, Zhang Q, Gao H, Zheng X, Yang T, Zheng G, Zhou X, Shao Y. Concurrent formation of H- and J-aggregates of dyes with chiralities individually determined by G-quadruplex handedness. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 248:119270. [PMID: 33310273 DOI: 10.1016/j.saa.2020.119270] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 11/06/2020] [Accepted: 11/19/2020] [Indexed: 06/12/2023]
Abstract
DNA templated dye assemblies pave an easy way to regulate the optical properties of molecular aggregates. G-quadruplexes (G4s) provide versatile DNA platforms for the dye assemblies since their foldings can be easily tuned by cation ions and sequences. In this work, we found that the G4 handedness can be used to control the aggregate chirality of a dye of 3,3'-diethylthiacarbocyanine (DiSC2(3)). The left-handed and right-handed G4s can template the concurrent formation of the J- and H-aggregates of DiSC2(3) with emergence of the featured absorption spectra. However, the chiral J-aggregate of DiSC2(3) can be formed only on the left-handed G4s, while the chiral H-aggregate is otherwise grown only on the right-handed G4s, as confirmed by the induced circular dichroism (ICD) spectra with the characteristic splitting bands. Additionally, these G4s even at tens of nM level are efficient to produce these chiral aggregates, demonstrating the high sensitivity of G4s in creating these optically active dye assemblies. The possible growth sites of the aggregates are proposed by the sequence length-dependent assemblies. Our work will provide a new way to control the chiral assemblies of dye aggregates via the G4 handedness.
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Affiliation(s)
- Chenxiao Yan
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Qingqing Zhang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Heng Gao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Xiong Zheng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Tong Yang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Guoxiang Zheng
- Undergraduate Teaching Department, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Xiaoshun Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Yong Shao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China.
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26
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Wang Q, Fang T, Zheng J, Shi L, Shi L, Li T. Proximity-Dependent Switchable ATP Aptasensors Utilizing a High-Performance FRET Reporter. ACS APPLIED MATERIALS & INTERFACES 2021; 13:9359-9368. [PMID: 33169604 DOI: 10.1021/acsami.0c15543] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Here, fluorescent molecular rotors are employed to develop a new type of high-performance FRET system with large Stokes shift, high photostability, and pH insensitivity, showing great promise for use in proximity-dependent DNA aptasensors. Two carboxylated benzothiazole-based molecular rotors are synthesized, displaying bright green and red fluorescence once labeled to DNA. In the proximity state, an efficient FRET occurs between the two dyes, comparable to that of the most commonly used Cy3/Cy5 pair. Similar phenomena are also observed if naphthothiazole-based analogues are adopted. Our developed FRET pair is then attached to the two parts of a split ATP aptamer in a dimeric DNA nanoscaffold controlled by a bimolecular i-motif. In this way, a pH-switched proximity-induced fluorescent ATP aptasensor is constructed, with good sensitivity, selectivity, and reconfiguration. Furthermore, by altering the linker length of the switching unit, the proximity effect is investigated systematically, providing new insight into DNA proximity reactions and their roles in some physiological processes.
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Affiliation(s)
- Qiwei Wang
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Tai Fang
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Jiao Zheng
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Lin Shi
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Lili Shi
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Tao Li
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
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Chen H, Sun H, Zhang W, Zhang Q, Ma J, Li Q, Guo X, Xu K, Tang Y. Chelerythrine as a fluorescent light-up ligand for an i-motif DNA structure. NEW J CHEM 2021. [DOI: 10.1039/d0nj04863a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A fluorescent light-up ligand for an i-motif structure has been reported in this study.
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Affiliation(s)
- Hongbo Chen
- Shenzhou Space Biology Science and Technology Coorporation, Ltd
- China Academy of Space Technology
- Beijing
- P. R. China
- Space Biology Research and Technology Center
| | - Hongxia Sun
- National Laboratory for Molecular Sciences
- Center for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
| | - Wende Zhang
- Shenzhou Space Biology Science and Technology Coorporation, Ltd
- China Academy of Space Technology
- Beijing
- P. R. China
- Space Biology Research and Technology Center
| | - Qin Zhang
- Shenzhou Space Biology Science and Technology Coorporation, Ltd
- China Academy of Space Technology
- Beijing
- P. R. China
- Space Biology Research and Technology Center
| | - Jun Ma
- Shenzhou Space Biology Science and Technology Coorporation, Ltd
- China Academy of Space Technology
- Beijing
- P. R. China
- Space Biology Research and Technology Center
| | - Qian Li
- National Laboratory for Molecular Sciences
- Center for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
| | - Xiaomeng Guo
- National Laboratory for Molecular Sciences
- Center for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
| | - Kanyan Xu
- Shenzhou Space Biology Science and Technology Coorporation, Ltd
- China Academy of Space Technology
- Beijing
- P. R. China
- Space Biology Research and Technology Center
| | - Yalin Tang
- National Laboratory for Molecular Sciences
- Center for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
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Jing S, Liu Q, Jin Y, Li B. Dimeric G-Quadruplex: An Effective Nucleic Acid Scaffold for Lighting Up Thioflavin T. Anal Chem 2020; 93:1333-1341. [PMID: 33347269 DOI: 10.1021/acs.analchem.0c02637] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
As a recently identified higher-order quadruplex (G4) structure, the G4 dimer possesses unique structure and biological functions. In this work, we found accidentally that two tandem PW17 (one known G4-forming DNA) sequences can fold into a stable G4 dimer, and the G4 dimer can enhance dramatically the fluorescence intensity of thioflavin T (ThT). The G4 dimer/ThT fluorescence intensity is about ninefold that of the corresponding G4 monomer/ThT. Meanwhile, compared with the common G4/ThT system, G4 dimer/ThT exhibited more stable fluorescence emission in the media with various concentrations of Na+ and K+. On the basis of these findings, G4 dimer/ThT was used as a fluorescence indicator to construct one arched DNA probe for label-free detection of DNA. By incorporating a G4 dimer sequence in amplified products, we further designed one rolling circle amplification-based biosensing strategy to show the utility of this G4 dimer/ThT fluorescence indicator. This study demonstrates that dimeric G4 is an effective nucleic acid scaffold for lighting up ThT, showing promising applications in a label-free bioassay.
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Affiliation(s)
- Shaochun Jing
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Shaanxi Normal University, Xi'an 710062, China.,Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
| | - Qiang Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Shaanxi Normal University, Xi'an 710062, China.,Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
| | - Yan Jin
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Shaanxi Normal University, Xi'an 710062, China.,Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
| | - Baoxin Li
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Shaanxi Normal University, Xi'an 710062, China.,Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
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30
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Deore PS, Manderville RA. Ratiometric fluorescent sensing of the parallel G-quadruplex produced by PS2.M: implications for K + detection. Analyst 2020; 145:1288-1293. [PMID: 31895357 DOI: 10.1039/c9an02122a] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Fluorescent ligands that selectively bind to a specific G-quadruplex (GQ) topology (antiparallel, hybrid or parallel) are highly sought after for aptasensor development and nanodevice construction. The coumarin-benzothiazole hybrid (BnBtC) is an internal charge transfer (ICT) ratiometric fluorescent probe, which displays two well-resolved emission bands at ∼450 nm for the coumarin component and ∼650 nm for the ICT band. The red ICT emission of BnBtC displays turn-on responses to protic solvent polarity and upon binding GQ structures, especially those produced by the hemin binding aptamer (PS2.M). In the present work, BnBtC was found to exhibit enhanced ICT emission upon binding the parallel GQ topology of PS2.M that is selectively produced in the presence of K+. This ability to discriminate K+ from other cationic metal ions through a turn-on ratiometric fluorescent response demonstrates the potential utility of the BnBtC probe for biosensor applications.
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Affiliation(s)
- Prashant S Deore
- Departments of Chemistry & Toxicology, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
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Effects of Modifying Thioflavin T at the N3-Position on Its G4 Binding and Fluorescence Emission. Molecules 2020; 25:molecules25214936. [PMID: 33114506 PMCID: PMC7663003 DOI: 10.3390/molecules25214936] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 11/16/2022] Open
Abstract
We previously synthesized thioflavin T (ThT) with a hydroxyethyl group introduced at the N3-position (ThT-HE), which binds predominantly to the parallel G-quadruplex (G4) structure found in c-Myc and emits strong fluorescence. In this study, to investigate the effects of introduced substituents on G4 binding and fluorescence emission, a ThT derivative in which the hydroxyl group of ThT-HE was replaced with an amino group (ThT-AE) was synthesized for the first time. Furthermore, three other N3-modified ThT derivatives (ThT-OE2, ThT-SP, and ThT-OE11) having different substituent structures were synthesized by the N-acylation of the terminal amino group of ThT-AE, and their G4-binding and emission properties were investigated. The results showed that, although ThT-AE shows binding selectivity depending on the type of G4, its emission intensity is significantly decreased as compared to that of ThT-HE. However, ThT-OE11, which features an 11-unit oxyethylene chain attached to the terminal amino group of ThT-AE, regained about one-half of the emission intensity of ThT-HE while retaining selectivity for G4s. Accordingly, ThT-OE11 may be used as a key intermediate for synthesizing the conjugates of G4 binders and probes.
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Yu Y, Zhang Q, Gao H, Yan C, Zheng X, Yang T, Zhou X, Shao Y. Metalloenzyme-mimic innate G-quadruplex DNAzymes using directly coordinated metal ions as active centers. Dalton Trans 2020; 49:13160-13166. [PMID: 32936164 DOI: 10.1039/d0dt02871a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
G-quadruplex DNAs (G4s) have been reported to exhibit the DNAzyme activities by binding with some metal complexes and functional organic ligands. However, there is a challenge to develop metalloenzyme-mimic G4-based innate DNAzymes using the complexed metal ions directly serving as the active centers. This will diversify DNAzymes for developing novel devices since G4 structures are more polymorphic than the other DNA foldings. In this work, we found that the lanthanide trivalent cerium ion of Ce3+ can bind to the human telomere G4 (htG4) according to a 1 : 2 binding mode favorable for creating metalloenzymes-mimic G4 DNAzymes. This Ce3+-G4 entity exhibits a peroxidase activity towards the oxidation of the substrate of 3,3,5,5-tetramethylbenzidine (TMB) by hydrogen peroxide. The 5' G4 tetrads with the orderly arranged carbonyl oxygen atoms are believed to be the coordination sites for Ce3+ and favor the conversion between Ce3+ and Ce4+. Our work provides an alternative feasibility in developing the G4-based innate DNAzymes for variant applications.
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Affiliation(s)
- Yali Yu
- Zhejiang Key Laboratory for Reactive Chemistry on Solid Surfaces, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
| | - Qingqing Zhang
- Zhejiang Key Laboratory for Reactive Chemistry on Solid Surfaces, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
| | - Heng Gao
- Zhejiang Key Laboratory for Reactive Chemistry on Solid Surfaces, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
| | - Chenxiao Yan
- Zhejiang Key Laboratory for Reactive Chemistry on Solid Surfaces, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
| | - Xiong Zheng
- Zhejiang Key Laboratory for Reactive Chemistry on Solid Surfaces, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
| | - Tong Yang
- Zhejiang Key Laboratory for Reactive Chemistry on Solid Surfaces, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
| | - Xiaoshun Zhou
- Zhejiang Key Laboratory for Reactive Chemistry on Solid Surfaces, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
| | - Yong Shao
- Zhejiang Key Laboratory for Reactive Chemistry on Solid Surfaces, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
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34
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Dai Y, Zhang Y, Liao W, Wang W, Wu L. G-quadruplex specific thioflavin T-based label-free fluorescence aptasensor for rapid detection of tetracycline. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 238:118406. [PMID: 32387918 DOI: 10.1016/j.saa.2020.118406] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 04/12/2020] [Accepted: 04/21/2020] [Indexed: 06/11/2023]
Abstract
A label-free fluorescence aptasensor was developed for the rapid detection of tetracycline (TET) based on G-quadruplex structure of TET aptamers and G-quadruplex specific dye Thioflavin T (ThT). The fluorescence of free ThT is essentially weak in aqueous solution, whereas it selectively identifies the G-quadruplex of aptamers to form the G-quadruplex/ThT conjugates, resulting in an enormous increase of the fluorescence intensity. However, the fluorescence intensity of G-quadruplex/ThT conjugates was drastically suppressed due to the release of free ThT from G-quadruplex/ThT conjugates after the addition of TET via specific binding with TET aptamers. The key factors affecting sensitivity and selectivity including the reaction medium, binding time of ThT to TET aptamers, incubation time between TET aptamers and TET, concentration of ThT and TET aptamers were investigated in detail. The optimal conditions were as follows: ultrapure water as reaction medium, binding time of 5 min, incubation time of 1 min, 9.0 μmol/L ThT and 0.03 μmol/L aptamers. A good linear relationship (correlation coefficient of 0.9973) was obtained between the fluorescence quenching efficiency (F0 - F) / F0 and the logarithm of TET concentration in the range of 0.01-1.0 μmol/L. The limit of detection was 0.001 μmol/L (S/N = 3). The proposed assay was applied for the detection of TET in the spiked honey and milk samples with recoveries ranging from 93.5% to 106.9%. The developed label-free fluorescence aptasensor showed advantages of high specificity, low cost and short time-consuming, illustrating potential application for on-site detection of TET in foodstuffs.
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Affiliation(s)
- Yuanyuan Dai
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Ying Zhang
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Wanliang Liao
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Weiping Wang
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China.
| | - Liang Wu
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
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35
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Wu Z, Zhou H, Han Q, Lin X, Han D, Li X. A cost-effective fluorescence biosensor for cocaine based on a "mix-and-detect" strategy. Analyst 2020; 145:4664-4670. [PMID: 32458835 DOI: 10.1039/d0an00675k] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The efficient detection of illicit drugs such as cocaine continues to be important for the fight against drug trafficking. Herein, we report a one-step method for rapid and specific cocaine detection. The method is based on our finding that small-molecule Thioflavin T (ThT) can act as a fluorescence indicator, which can be bonded with the anti-cocaine aptamer (MNS-4.1) to generate an enhanced fluorescence signal. More interestingly, upon cocaine binding, the intercalated ThT can be replaced, causing a drastic fluorescence reduction. We further optimized the sequence of MNS-4.1 and a new anti-cocaine aptamer (coc.ap2-GC) was obtained. This aptamer showed a higher affinity to both ligands, which increased the ThT binding fluorescence intensity and showed the highest quenching efficiency. Based on the fluorescence change induced by competitive binding, cocaine detection could be accomplished by a "mix-and-detect" strategy within seconds. Such a label-free method exhibits high sensitivity to cocaine with a low detection limit of 250 nM. Moreover, the practical sample analysis (2.5% human urine and saliva) also exhibits good precision and high sensitivity.
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Affiliation(s)
- Zhifang Wu
- College of Pharmacy, Guangdong Medical University, Dongguan 523000, P. R. China.
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36
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Chang W, Liu W, Shen H, Chen S, Liao P, Liu Y. Molecular AND logic gate for multiple single-nucleotide mutations detection based on CRISPR/Cas9n system-trigged signal amplification. Anal Chim Acta 2020; 1112:46-53. [DOI: 10.1016/j.aca.2020.03.058] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 03/27/2020] [Accepted: 03/28/2020] [Indexed: 12/26/2022]
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37
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Ma Y, Yin J, Li G, Gao W, Lin W. Simultaneous sensing of nucleic acid and associated cellular components with organic fluorescent chemsensors. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2019.213144] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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38
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In-Gel Probing Polymorphic Structures of G-Quadruplexes Derived from c-Myc Promoter. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1016/s1872-2040(20)60002-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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39
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Gao L, Tong X, Ye T, Gao H, Zhang Q, Yan C, Yu Y, Fei Y, Zhou X, Shao Y. G‐Quadruplex‐Based Photooxidase Driven by Visible Light. ChemCatChem 2019. [DOI: 10.1002/cctc.201901481] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Longlong Gao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials Institute of Physical Chemistry College of Chemistry and Life SciencesZhejiang Normal University Jinhua 321004 P.R. China
| | - Xingyu Tong
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials Institute of Physical Chemistry College of Chemistry and Life SciencesZhejiang Normal University Jinhua 321004 P.R. China
| | - Ting Ye
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials Institute of Physical Chemistry College of Chemistry and Life SciencesZhejiang Normal University Jinhua 321004 P.R. China
| | - Heng Gao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials Institute of Physical Chemistry College of Chemistry and Life SciencesZhejiang Normal University Jinhua 321004 P.R. China
| | - Qingqing Zhang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials Institute of Physical Chemistry College of Chemistry and Life SciencesZhejiang Normal University Jinhua 321004 P.R. China
| | - Chenxiao Yan
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials Institute of Physical Chemistry College of Chemistry and Life SciencesZhejiang Normal University Jinhua 321004 P.R. China
| | - Yali Yu
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials Institute of Physical Chemistry College of Chemistry and Life SciencesZhejiang Normal University Jinhua 321004 P.R. China
| | - Yifan Fei
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials Institute of Physical Chemistry College of Chemistry and Life SciencesZhejiang Normal University Jinhua 321004 P.R. China
| | - Xiaoshun Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials Institute of Physical Chemistry College of Chemistry and Life SciencesZhejiang Normal University Jinhua 321004 P.R. China
| | - Yong Shao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials Institute of Physical Chemistry College of Chemistry and Life SciencesZhejiang Normal University Jinhua 321004 P.R. China
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40
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Ye T, Gao H, Zhang Q, Yan C, Yu Y, Fei Y, Gao L, Zhou X, Shao Y. Polarity inversion sensitized G-quadruplex metal sensors with K + tolerance. Biosens Bioelectron 2019; 145:111703. [PMID: 31546203 DOI: 10.1016/j.bios.2019.111703] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 09/05/2019] [Accepted: 09/13/2019] [Indexed: 12/22/2022]
Abstract
Due to the high abundance of K+ in environments and K+-induced high stability of G-quadruplex (G4), developing a selective G4-based fluorescent sensor for other metal ions with K+ tolerance is a great challenge. Herein, we found that even in the presence of 15000-fold excess of K+, Ba2+ exhibits a highly specific binding with a human telomeric G4 (htG4) in comparison with other G4-binding metal ions such as Pb2+ and Sr2+. This specific binding event can be recognized by a natural fluorophore of hypericin with a lighting-up fluorescence response. Interestingly, inverting the polarity of the most 3' G in htG4 can sensitize the Ba2+ response with the retaining Ba2+ specificity and K+ tolerance. This polarity inversion of htG4 causes a G4 conformation change in K+ and the polarity-inverted htG4 tends to favorably dimerize in response to the Ba2+ specific binding. To our knowledge, this is the first report that polarity inversion of G4 can be applied to construct a selective metal sensor with K+ tolerance. Our findings will open a new way to conveniently regulate the G4 conformation and stability by polarity inversion towards developing high-performance sensors.
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Affiliation(s)
- Ting Ye
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, China
| | - Heng Gao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, China
| | - Qingqing Zhang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, China
| | - Chenxiao Yan
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, China
| | - Yali Yu
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, China
| | - Yifan Fei
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, China
| | - Longlong Gao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, China
| | - Xiaoshun Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, China
| | - Yong Shao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, China.
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Deore PS, Gray MD, Chung AJ, Manderville RA. Ligand-Induced G-Quadruplex Polymorphism: A DNA Nanodevice for Label-Free Aptasensor Platforms. J Am Chem Soc 2019; 141:14288-14297. [PMID: 31436972 DOI: 10.1021/jacs.9b06533] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
G-Quadruplexes (GQs) serve as popular recognition elements for DNA aptasensors and are incorporated into a DNA nanodevice capable of controlled conformational changes to activate a sensing mechanism. Herein we highlight the utility of a GQ-GQ nanodevice fueled by GQ-specific ligands as a label-free aptasensor detection strategy. The concept was first illustrated utilizing the prototypical polymorphic human telomeric repeat sequence (H-Telo22, d[AG3(T2AG3)3]) that can undergo ligand-induced topology changes between antiparallel, parallel, or hybrid GQ structures. The H-Telo22-ligand interactions served as a model of the GQ-GQ nanodevice. The utility of the device in a real aptasensor platform was then highlighted utilizing the ochratoxin A (OTA) binding aptamer (OTABA) that folds into an antiparallel GQ in the absence and presence of target OTA. Three cationic fluorogenic ligands served as GQ-specific light-up probes and as potential fuel for the GQ-GQ nanodevice by producing an inactive GQ topology (parallel or hybrid) of OTABA. Our findings demonstrate efficient OTA-mediated dye displacement with excellent emission sensitivity for OTA detection when the fluorogenic dyes induce a topology change in OTABA (parallel or hybrid). However, when the fluorogenic dye fails to induce a conformational change in the antiparallel fold of OTABA, subsequent additions of OTA to the aptamer-dye complex results in poor dye displacement with weak emission response for OTA detection. These results are the first to exemplify a ligand-induced GQ-GQ nanodevice as an aptasensor mechanism and demonstrate diagnostic applications for topology-specific GQ binders.
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Affiliation(s)
- Prashant S Deore
- Departments of Chemistry and Toxicology , University of Guelph , Guelph , Ontario N1G 2W1 , Canada
| | - Micaela D Gray
- Departments of Chemistry and Toxicology , University of Guelph , Guelph , Ontario N1G 2W1 , Canada
| | - Andrew J Chung
- Departments of Chemistry and Toxicology , University of Guelph , Guelph , Ontario N1G 2W1 , Canada
| | - Richard A Manderville
- Departments of Chemistry and Toxicology , University of Guelph , Guelph , Ontario N1G 2W1 , Canada
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42
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Zhou W, Yu Z, Ma G, Jin T, Li Y, Fan L, Li X. Thioflavin T specifically brightening “Guanine Island” in duplex-DNA: a novel fluorescent probe for single-nucleotide mutation. Analyst 2019; 144:2284-2290. [DOI: 10.1039/c8an02430h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Here, we found that Thioflavin T (ThT) could specifically bind with a G-GGG unit (named as “Guanine Island”) in double stranded DNA (ds-DNA).
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Affiliation(s)
- Wei Zhou
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
| | - Ze Yu
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
| | - Ge Ma
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
| | - Tian Jin
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
| | - Yunchao Li
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
| | - Louzhen Fan
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
| | - Xiaohong Li
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
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Zhang J, Li X, Sun X, Liu Y, Hao J, Tan Y, Song A. G-Quadruplex based hydrogels stabilized by a cationic polymer as an efficient adsorbent of picric acid. NEW J CHEM 2019. [DOI: 10.1039/c9nj03143j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Hydrogels based on G-quadruplexes (G-hydrogels) were prepared using guanosine 5′-monophosphate disodium salt, GMP, with a hyperbranched poly(ethylenimine), PEI, containing abundant –NH2 groups.
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Affiliation(s)
- Jin Zhang
- Key Laboratory of Colloids and Interface Chemistry (Shandong University)
- Ministry of Education
- Jinan 250100
- China
| | - Xiaoyang Li
- Key Laboratory of Colloids and Interface Chemistry (Shandong University)
- Ministry of Education
- Jinan 250100
- China
| | - Xiuping Sun
- Key Laboratory of Colloids and Interface Chemistry (Shandong University)
- Ministry of Education
- Jinan 250100
- China
| | - Yihan Liu
- Key Laboratory of Colloids and Interface Chemistry (Shandong University)
- Ministry of Education
- Jinan 250100
- China
| | - Jingcheng Hao
- Key Laboratory of Colloids and Interface Chemistry (Shandong University)
- Ministry of Education
- Jinan 250100
- China
| | - Yebang Tan
- Key Laboratory of Colloids and Interface Chemistry (Shandong University)
- Ministry of Education
- Jinan 250100
- China
| | - Aixin Song
- Key Laboratory of Colloids and Interface Chemistry (Shandong University)
- Ministry of Education
- Jinan 250100
- China
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Kataoka Y, Fujita H, Afanaseva A, Nagao C, Mizuguchi K, Kasahara Y, Obika S, Kuwahara M. High-Contrast Facile Imaging with Target-Directing Fluorescent Molecular Rotors, the N3-Modified Thioflavin T Derivatives. Biochemistry 2018; 58:493-498. [DOI: 10.1021/acs.biochem.8b01181] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yuka Kataoka
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Hiroto Fujita
- Graduate School of Integrated Basic Sciences, Nihon University, 3-25-40 Sakurajosui, Setagaya-ku, Tokyo 156-8550, Japan
| | - Arina Afanaseva
- National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Chioko Nagao
- National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Kenji Mizuguchi
- National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Yuuya Kasahara
- National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Satoshi Obika
- National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masayasu Kuwahara
- Graduate School of Integrated Basic Sciences, Nihon University, 3-25-40 Sakurajosui, Setagaya-ku, Tokyo 156-8550, Japan
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45
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Yeasmin Khusbu F, Zhou X, Chen H, Ma C, Wang K. Thioflavin T as a fluorescence probe for biosensing applications. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2018.09.013] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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46
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Qin Y, Liao S, Huang Y, Zhao J, Zhao S. Ultrasensitive fluorescent detection of nucleic acids based on label-free enzymatic-assisted cascade signal amplification. Anal Chim Acta 2018; 1039:91-97. [DOI: 10.1016/j.aca.2018.07.038] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 07/01/2018] [Accepted: 07/17/2018] [Indexed: 01/21/2023]
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47
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Xie X, Reznichenko O, Chaput L, Martin P, Teulade-Fichou MP, Granzhan A. Topology-Selective, Fluorescent “Light-Up” Probes for G-Quadruplex DNA Based on Photoinduced Electron Transfer. Chemistry 2018; 24:12638-12651. [DOI: 10.1002/chem.201801701] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Xiao Xie
- CNRS UMR9187, INSERM U1196; Institut Curie; PSL Research University; 91405 Orsay France
- CNRS UMR9187, INSERM U1196; Université Paris Sud, Université Paris-Saclay; 91405 Orsay France
| | - Oksana Reznichenko
- CNRS UMR9187, INSERM U1196; Institut Curie; PSL Research University; 91405 Orsay France
- CNRS UMR9187, INSERM U1196; Université Paris Sud, Université Paris-Saclay; 91405 Orsay France
| | - Ludovic Chaput
- CNRS UMR9187, INSERM U1196; Institut Curie; PSL Research University; 91405 Orsay France
- CNRS UMR9187, INSERM U1196; Université Paris Sud, Université Paris-Saclay; 91405 Orsay France
- CNRS UPR2301; Institut de Chimie des Substances Naturelles (ICSN); 91198 Gif-sur-Yvette France
| | - Pascal Martin
- ITODYS, CNRS UMR7086; Université Paris Diderot; 75205 Paris France
| | - Marie-Paule Teulade-Fichou
- CNRS UMR9187, INSERM U1196; Institut Curie; PSL Research University; 91405 Orsay France
- CNRS UMR9187, INSERM U1196; Université Paris Sud, Université Paris-Saclay; 91405 Orsay France
| | - Anton Granzhan
- CNRS UMR9187, INSERM U1196; Institut Curie; PSL Research University; 91405 Orsay France
- CNRS UMR9187, INSERM U1196; Université Paris Sud, Université Paris-Saclay; 91405 Orsay France
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48
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Zhu J, Yan Z, Zhou W, Liu C, Wang J, Wang E. Lighting Up the Thioflavin T by Parallel-Stranded TG(GA) n DNA Homoduplexes. ACS Sens 2018; 3:1118-1125. [PMID: 29749724 DOI: 10.1021/acssensors.8b00141] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Thioflavin T (ThT) was once regarded to be a specific fluorescent probe for the human telomeric G-quadruplex, but more other kinds of DNA were found that can also bind to ThT in recent years. Herein, we focus on G-rich parallel-stranded DNA and utilize fluorescence, absorbance, circular dichroism, and surface plasmon resonance spectroscopy to investigate its interaction with ThT. Pyrene label and molecular modeling are applied to unveil the binding mechanism. We find a new class of non-G-quadruplex G-rich parallel-stranded ( ps) DNA with the sequence of TG(GA) n can bind to ThT and increase the fluorescence with an enhancement ability superior to G-quadruplex. The optimal binding specificity for ThT is conferred by two parts. The first part is composed of two bases TG at the 5' end, which is a critical domain and plays an important role in the formation of the binding site for ThT. The second part is the rest alternative d(GA) bases, which forms the ps homoduplex and cooperates with the TG bases at the 5' end to bind the ThT.
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Affiliation(s)
- Jinbo Zhu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Zhiqiang Yan
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
| | - Weijun Zhou
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Chuanbo Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jin Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
- College of Physics, Jilin University, Changchun 130022, P. R. China
- Department of Chemistry and of Physics, State University of New York at Stony Brook, Stony Brook, New York 11794-3400, United States
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
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49
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Li Q, Fei Y, Gao L, Yu Y, Zhou Y, Ye T, Zhou XS, Shao Y, Yin ZZ. G-Quadruplex DNA with an Apurinic Site as a Soft Molecularly Imprinted Sensing Platform. Anal Chem 2018; 90:5552-5556. [PMID: 29642702 DOI: 10.1021/acs.analchem.8b01097] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Molecularly imprinted polymers (MIPs) provide versatile sensor platforms to recognize targets by shape complementarity. However, the rigid structure of the classic MIPs compromises the signal transduction with necessary polymer and target modifications. Herein, we tried to use a flexible DNA that has a perfectly structured folding as the soft molecularly imprinted polymer (SMIP) for a straightforward sensor. As a proof of concept, the guanosine SMIP recognition was achieved by removal of a guanosine from a G-quadruplex-forming sequence (G4). The G4 folding structure with such an apurinic site (AP site) provides a well-defined MIP binding accommodation for guanosine according to the shape complementarity. The guanosine binding at the AP site subsequently leads to a conformation change suitable for remote readout using a G4-specific fluorescent ligand. The G4 sequence and AP site position were optimized for this SMIP behavior. Due to the G4 compact structure and the remaining hydrogen bonding pattern, nucleosides other than guanosine and negatively charged nucleotides exhibit no binding with the AP site, suggesting a high selectivity in the SMIP recognition. The proposed rationale was then convinced by the alkaline phosphatase-catalyzed GMP hydrolysis. Our work will inspire more interest in exploring nucleic acids as the SMIP frameworks due to their variant conformations and well-established molecular engineering.
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Affiliation(s)
- Qiusha Li
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences , Zhejiang Normal University , Jinhua 321004 , Zhejiang , China
| | - Yifan Fei
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences , Zhejiang Normal University , Jinhua 321004 , Zhejiang , China
| | - Longlong Gao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences , Zhejiang Normal University , Jinhua 321004 , Zhejiang , China
| | - Yali Yu
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences , Zhejiang Normal University , Jinhua 321004 , Zhejiang , China
| | - Yufeng Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences , Zhejiang Normal University , Jinhua 321004 , Zhejiang , China
| | - Ting Ye
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences , Zhejiang Normal University , Jinhua 321004 , Zhejiang , China
| | - Xiao-Shun Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences , Zhejiang Normal University , Jinhua 321004 , Zhejiang , China
| | - Yong Shao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences , Zhejiang Normal University , Jinhua 321004 , Zhejiang , China
| | - Zheng-Zhi Yin
- College of Biological, Chemical Sciences and Engineering , Jiaxing University , Jiaxing 314001 , Zhejiang , China
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50
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Cai H, Zhou C, Yang Q, Ai T, Huang Y, Lv Y, Geng J, Xiao D. Single-molecule investigation of human telomeric G-quadruplex interactions with Thioflavin T. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2017.09.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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