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Zainudin AA, Fen YW, Yusof NA, Al-Rekabi SH, Mahdi MA, Omar NAS. Incorporation of surface plasmon resonance with novel valinomycin doped chitosan-graphene oxide thin film for sensing potassium ion. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 191:111-115. [PMID: 29024848 DOI: 10.1016/j.saa.2017.10.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 09/22/2017] [Accepted: 10/03/2017] [Indexed: 06/07/2023]
Abstract
In this study, the combination of novel valinomycin doped chitosan-graphene oxide (C-GO-V) thin film and surface plasmon resonance (SPR) system for potassium ion (K+) detection has been developed. The novel C-GO-V thin film was deposited on the gold surface using spin coating technique. The system was used to monitor SPR signal for K+ in solution with and without C-GO-V thin film. The K+ can be detected by measuring the SPR signal when C-GO-V thin film is exposed to K+ in solution. The sensor produces a linear response for K+ ion up to 100ppm with sensitivity and detection limit of 0.00948°ppm-1 and 0.001ppm, respectively. These results indicate that the C-GO-V film is high potential as a sensor element for K+ that has been proved by the SPR measurement.
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Affiliation(s)
- Afiq Azri Zainudin
- Department of Physics, Faculty of Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Yap Wing Fen
- Department of Physics, Faculty of Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Functional Devices Laboratory, Institute of Advanced Technology, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Nor Azah Yusof
- Functional Devices Laboratory, Institute of Advanced Technology, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Sura Hmoud Al-Rekabi
- Department of Computer and Communication Systems Engineering, Faculty of Engineering, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Mohd Adzir Mahdi
- Department of Computer and Communication Systems Engineering, Faculty of Engineering, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Nur Alia Sheh Omar
- Functional Devices Laboratory, Institute of Advanced Technology, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
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52
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Zhou H, Wu ZF, Han QJ, Zhong HM, Peng JB, Li X, Fan XL. Stable and Label-Free Fluorescent Probe Based on G-triplex DNA and Thioflavin T. Anal Chem 2018; 90:3220-3226. [PMID: 29378390 DOI: 10.1021/acs.analchem.7b04666] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
G-triplexes have recently been identified as a new kind of DNA structures. They perhaps possess specific biological and chemical functions similar as identified G-quadruplex but can be formed by shorter G-rich sequences with only three G-tracts. However, until now, limited G-triplexes sequences have been reported, which might be due to the fact that their stability is one of the biggest concerns during their functional studies and application research. Herein, we found a G-rich sequence (5'-TGGGTAGGGCGGG-3') which can form a stable G-triplex (Tm ∼ 60 °C) at room temperature. The stable G-triplex can combine with thioflavin T and function as an efficient fluorescence light-up probe. Comparing with the traditional G-quadruplex based probe, this triplex based probe was easy to be controlled and excited. Finally, the probe was successfully applied into constructing a label-free molecular beacon for miRNA detection. Taking advantage of these abilities of the G-triplex based fluorescent probe, the challenges faced during designing G-rich sequences based fluorescent biosensors can be efficiently solved. These findings provide important information for the future application of G-triplex.
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Affiliation(s)
- Hui Zhou
- College of Chemistry and Chemical Engineering , Gannan Normal University , Ganzhou , 341000 , China
| | - Zhi-Fang Wu
- College of Chemistry and Chemical Engineering , Gannan Normal University , Ganzhou , 341000 , China
| | - Qian-Jin Han
- College of Chemistry and Chemical Engineering , Gannan Normal University , Ganzhou , 341000 , China
| | - Hong-Mei Zhong
- College of Chemistry and Chemical Engineering , Gannan Normal University , Ganzhou , 341000 , China
| | - Jun-Bin Peng
- College of Chemistry and Chemical Engineering , Gannan Normal University , Ganzhou , 341000 , China
| | - Xun Li
- College of Chemistry and Chemical Engineering , Gannan Normal University , Ganzhou , 341000 , China
| | - Xiao-Lin Fan
- College of Chemistry and Chemical Engineering , Gannan Normal University , Ganzhou , 341000 , China
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53
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Zhang J, Li X, Sun X, Song A, Tan Y, Hao J. GMP-quadruplex-based hydrogels stabilized by lanthanide ions. Sci China Chem 2018. [DOI: 10.1007/s11426-017-9187-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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54
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Ethyl-substitutive Thioflavin T as a highly-specific fluorescence probe for detecting G-quadruplex structure. Sci Rep 2018; 8:2666. [PMID: 29422637 PMCID: PMC5805748 DOI: 10.1038/s41598-018-20960-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 01/26/2018] [Indexed: 12/31/2022] Open
Abstract
G-quadruplex has attracted considerable attention due to their prevalent distribution in functional genomic regions and transcripts, which can importantly influence biological processes such as regulation of telomere maintenance, gene transcription and gene translation. Artificial receptor study has been developed for accurate identification of G-quadruplex from DNA species, since it is important for the G-quadruplex related basic research, clinical diagnosis, and therapy. Herein, fluorescent dye ThT-E, a derivative of the known fluorescence probe Thioflavin T (ThT), was designed and synthesized to effectively differentiate various G-quadruplex structures from other nucleic acid forms. Compared with methyl groups in ThT, three ethyl groups were introduced to ThT-E, which leads to strengthened affinity, selectivity and little inducing effect on the G-quadruplex formation. More importantly, ThT-E could be served as a visual tool to directly differentiate G-quadruplex solution even with naked eyes under illumination of ultraviolet light. Thus, this probe reported herein may hold great promise for high-throughput assay to screen G-quadruplex, which may widely apply to G-quadruplex-based potential diagnosis and therapy.
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55
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Direct visualization of nucleolar G-quadruplexes in live cells by using a fluorescent light-up probe. Biochim Biophys Acta Gen Subj 2018; 1862:1101-1106. [PMID: 29410183 DOI: 10.1016/j.bbagen.2018.01.022] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 01/23/2018] [Accepted: 01/31/2018] [Indexed: 11/24/2022]
Abstract
BACKGROUND Direct detection of G-quadruplexes in human cells has become an important issue due to the vital role of G-quadruplex related to biological functions. Despite several probes have been developed for detection of the G-quadruplexes in cytoplasm or whole cells, the probe being used to monitor the nucleolar G-quadruplexes is still lacking. METHODS Formation of the nucleolar G-quadruplex structures was confirmed by using circular dichroism (CD) spectroscopy. The binding affinity and selectivity of Thioflavin T (ThT) towards various DNA/RNA motifs in solution and gel system were measured by using fluorescence spectroscopy and polyacrylamide gel electrophoresis (PAGE), respectively. G-quadruplex imaging in live cells was directly captured by using confocal laser scanning microscopy (CLSM). RESULTS Formation of the rDNA and rRNA G-quadruplex structures is demonstrated in vitro. ThT is found to show much higher affinity and selectivity towards these G-quadruplex structures versus other nucleic acid motifs either in solution or in gel system. The nucleolar G-quadruplexes in living cells are visualized by using ThT as a fluorescent probe. G-quadruplex-ligand treatments in live cells lead to sharp decrease of ThT signal. CONCLUSIONS The natural existence of the G-quadruplexes structure in the nucleoli of living cells is directly visualized by using ThT as an indicator. GENERAL SIGNIFICANCE The research provides substantive evidence for formation of the rRNA G-quadruplex structures, and also offers an effective probe for direct visualization of the nucleolar G-quadruplexes in living cells.
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56
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Suseela YV, Narayanaswamy N, Pratihar S, Govindaraju T. Far-red fluorescent probes for canonical and non-canonical nucleic acid structures: current progress and future implications. Chem Soc Rev 2018; 47:1098-1131. [DOI: 10.1039/c7cs00774d] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Our review presents the recent progress on far-red fluorescent probes of canonical and non-canonical nucleic acid (NA) structures, critically discusses the design principles, applications, limitations and outline the future prospects of developing newer probes with target-specificity for different NA structures.
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Affiliation(s)
- Y. V. Suseela
- Bioorganic Chemistry Laboratory
- New Chemistry Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bengaluru 560064
- India
| | - Nagarjun Narayanaswamy
- Bioorganic Chemistry Laboratory
- New Chemistry Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bengaluru 560064
- India
| | - Sumon Pratihar
- Bioorganic Chemistry Laboratory
- New Chemistry Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bengaluru 560064
- India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory
- New Chemistry Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bengaluru 560064
- India
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57
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Liu S, Peng P, Wang H, Shi L, Li T. Thioflavin T binds dimeric parallel-stranded GA-containing non-G-quadruplex DNAs: a general approach to lighting up double-stranded scaffolds. Nucleic Acids Res 2017; 45:12080-12089. [PMID: 29059300 PMCID: PMC5716147 DOI: 10.1093/nar/gkx942] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 10/03/2017] [Indexed: 12/27/2022] Open
Abstract
A molecular rotor thioflavin T (ThT) is usually used as a fluorescent ligand specific for G-quadruplexes. Here, we demonstrate that ThT can tightly bind non-G-quadruplex DNAs with several GA motifs and dimerize them in a parallel double-stranded mode, accompanied by over 100-fold enhancement in the fluorescence emission of ThT. The introduction of reverse Watson–Crick T-A base pairs into these dimeric parallel-stranded DNA systems remarkably favors the binding of ThT into the pocket between G•G and A•A base pairs, where ThT is encapsulated thereby restricting its two rotary aromatic rings in the excited state. A similar mechanism is also demonstrated in antiparallel DNA duplexes where several motifs of two consecutive G•G wobble base pairs are incorporated and serve as the active pockets for ThT binding. The insight into the interactions of ThT with non-G-quadruplex DNAs allows us to introduce a new concept for constructing DNA-based sensors and devices. As proof-of-concept experiments, we design a DNA triplex containing GA motifs in its Hoogsteen hydrogen-bonded two parallel strands as a pH-driven nanoswitch and two GA-containing parallel duplexes as novel metal sensing platforms where C–C and T–T mismatches are included. This work may find further applications in biological systems (e.g. disease gene detection) where parallel duplex or triplex stretches are involved.
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Affiliation(s)
- Shuangna Liu
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Pai Peng
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Huihui Wang
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Lili Shi
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Tao Li
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
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58
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Patra SK, Sheet SK, Sen B, Aguan K, Roy DR, Khatua S. Highly Sensitive Bifunctional Probe for Colorimetric Cyanide and Fluorometric H2S Detection and Bioimaging: Spontaneous Resolution, Aggregation, and Multicolor Fluorescence of Bisulfide Adduct. J Org Chem 2017; 82:10234-10246. [DOI: 10.1021/acs.joc.7b01743] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Sumit Kumar Patra
- Centre
for Advanced Studies, Department of Chemistry, North Eastern Hill University, Shillong, Meghalaya 793022, India
| | - Sanjoy Kumar Sheet
- Centre
for Advanced Studies, Department of Chemistry, North Eastern Hill University, Shillong, Meghalaya 793022, India
| | - Bhaskar Sen
- Centre
for Advanced Studies, Department of Chemistry, North Eastern Hill University, Shillong, Meghalaya 793022, India
| | - Kripamoy Aguan
- Department
of Biotechnology and Bioinformatics, North Eastern Hill University, Shillong, Meghalaya 793022, India
| | - Debesh Ranjan Roy
- Applied
Physics Department, S.V. National Institute of Technology, Surat 395 007, India
| | - Snehadrinarayan Khatua
- Centre
for Advanced Studies, Department of Chemistry, North Eastern Hill University, Shillong, Meghalaya 793022, India
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59
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Affiliation(s)
- Wenhu Zhou
- Xiangya
School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Runjhun Saran
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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60
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Label-free fluorescent assay of T4 polynucleotide kinase phosphatase activity based on G-quadruplexe−thioflavin T complex. Talanta 2017; 165:653-658. [DOI: 10.1016/j.talanta.2017.01.027] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 12/27/2016] [Accepted: 01/06/2017] [Indexed: 02/06/2023]
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61
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Wu T, Ye M, Mao T, Lin F, Hu Y, Gan N, Shao Y. Human telomeric hybrid-2-over-hybrid-1 G-quadruplex targeting and a selective hypersaline-tolerant sensor using abasic site-engineered monomorphism. Anal Chim Acta 2017; 964:161-169. [DOI: 10.1016/j.aca.2017.01.041] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 01/13/2017] [Accepted: 01/21/2017] [Indexed: 02/02/2023]
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62
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Lu D, He L, Wang Y, Xiong M, Hu M, Liang H, Huan S, Zhang XB, Tan W. Tetraphenylethene derivative modified DNA oligonucleotide for in situ potassium ion detection and imaging in living cells. Talanta 2017; 167:550-556. [PMID: 28340760 DOI: 10.1016/j.talanta.2017.02.064] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 02/18/2017] [Accepted: 02/26/2017] [Indexed: 12/19/2022]
Abstract
The monitoring of K+ is very important and emergency because of their unique relationship in various disease diagnosis and treatment. G-quadruplex analogue is a classical recognition unit for K+ detection and has been widely applied in K+ relevant research. Common fluorescent dyes were employed for design of G-quadruplex structure-based K+ probes which suffered from the aggregation-caused quenching effect, and possibly limited the biological applications in living systems. Herein, we report an aggregation-induced emission (AIE) effect-based fluorescent probe for cellular K+ analysis and imaging. Benefitting from the K+ triggered AIE phenomenon, the designed TPE derivative modified guanine (G)-rich oligonucleotide fluorescent probe (TPE-oligonucleotide probe) exhibits high sensitivity (∼10-fold higher than most reported G-quadruplex-based probes) with extended photostability which facilitates the prolonged fluorescence observations of K+ in living cells. On the basis of these advantages, the TPE-oligonucleotide probe serves as a promising candidate for the functional study and analysis of K+.
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Affiliation(s)
- Danqing Lu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Lei He
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Yaya Wang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Mengyi Xiong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Miaomiao Hu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Hao Liang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Shuangyan Huan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Xiao-Bing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China.
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China.
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63
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Abstract
G-quadruplexes are noncanonical secondary structures formed in DNA sequences containing consecutive runs of guanines. It has been shown that the 3' G-rich single-stranded overhangs of human telomeres can form G-quadruplex structures, and the human telomeric DNA G-quadruplexes are considered attractive targets for anticancer drugs. G-quadruplex-interactive compounds have been shown to inhibit telomerase access as well as telomere capping. Nuclear magnetic resonance (NMR) spectroscopy is a powerful method in determining the G-quadruplex structures under physiologically relevant conditions. We present the NMR and biophysical methodology used in our research group for the study of G-quadruplex structures in physiologically relevant solution and their interactions with small-molecule compounds.
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Affiliation(s)
- Clement Lin
- Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Dr., West Lafayette, IN, 47907, USA
| | - Danzhou Yang
- Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Dr., West Lafayette, IN, 47907, USA.
- Purdue Center for Cancer Research, Purdue University, 201 S. University St., West Lafayette, IN, 47907, USA.
- Purdue Institute for Drug Discovery, Purdue University, 720 Clinic Dr., West Lafayette, IN, 47907, USA.
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64
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Sun X, Li Q, Xiang J, Wang L, Zhang X, Lan L, Xu S, Yang F, Tang Y. Novel fluorescent cationic benzothiazole dye that responds to G-quadruplex aptamer as a novel K+ sensor. Analyst 2017; 142:3352-3355. [DOI: 10.1039/c7an01062a] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A fluorescent cationic benzothiazole dye that selectively targets a G-quadruplex aptamer was designed and synthesized as a K+ sensor.
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Affiliation(s)
- Xin 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
| | - 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
| | - Junfeng Xiang
- 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
| | - Lixia Wang
- 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
| | - Xiufeng Zhang
- 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
| | - Ling Lan
- 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
| | - Shujuan Xu
- 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
| | - Fengmin Yang
- 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
| | - 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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65
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Huang J, Li XY, Du YC, Zhang LN, Liu KK, Zhu LN, Kong DM. Sensitive fluorescent detection of DNA methyltransferase using nicking endonuclease-mediated multiple primers-like rolling circle amplification. Biosens Bioelectron 2016; 91:417-423. [PMID: 28063390 DOI: 10.1016/j.bios.2016.12.061] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/13/2016] [Accepted: 12/29/2016] [Indexed: 11/19/2022]
Abstract
Sensitive and reliable detection of DNA methyltransferase (MTase) is of great significance for both early tumor diagnosis and therapy. In this study, a simple, label-free and sensitive DNA MTase-sensing method was developed on the basis of a nicking endonuclease-mediated multiple primers-like rolling circle amplification (RCA) strategy. In this method, a dumbbell RCA template was prepared by blunt-end ligation of two molecules of hairpin DNA. In addition to the primer-binding sequence, the dumbbell template contained another three important parts: 5'-CCGG-3' sequences in double-stranded stems, nicking endonuclease recognition sites and C-rich sequences in single-stranded loops. The introduction of 5'-CCGG-3' sequences allows the dumbbell template to be destroyed by the restriction endonuclease, HpaII, but is not destroyed in the presence of the target MTase-M.SssI MTase. The introduction of nicking endonuclease recognition sites makes the M.SssI MTase-protected dumbbell template-mediated RCA proceed in a multiple primers-like exponential mode, thus providing the RCA with high amplification efficiency. The introduction of C-rich sequences may promote the folding of amplification products into a G-quadruplex structure, which is specifically recognized by the commercially available fluorescent probe thioflavin T. Improved RCA amplification efficiency and specific fluorescent recognition of RCA products provide the M.SssI MTase-sensing platform with high sensitivity. When a dumbbell template containing four nicking endonuclease sites is used, highly specific M.SssI MTase activity detection can be achieved in the range of 0.008-50U/mL with a detection limit as low as 0.0011U/mL. Simple experimental operation and mix-and-detection fluorescent sensing mode ensures that M.SssI MTase quantitation works well in a real-time RCA mode, thus further simplifying the sensing performance and making high throughput detection possible. The proposed MTase-sensing strategy was also demonstrated to be applicable for screening and evaluating the inhibitory activity of MTase inhibitors.
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Affiliation(s)
- Juan Huang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Nankai University, Tianjin 300071, PR China
| | - Xiao-Yu Li
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Nankai University, Tianjin 300071, PR China
| | - Yi-Chen Du
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Nankai University, Tianjin 300071, PR China
| | - Li-Na Zhang
- Department of Chemistry, Tianjin University, Tianjin 300072, PR China
| | - Ke-Ke Liu
- Department of Chemistry, Tianjin University, Tianjin 300072, PR China
| | - Li-Na Zhu
- Department of Chemistry, Tianjin University, Tianjin 300072, PR China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300071, PR China.
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Nankai University, Tianjin 300071, PR China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300071, PR China.
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66
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Wang J, Liu H, Ma C, Wang J, Zhong L, Wu K. Label-free monitoring of DNA polymerase activity based on a thrombin-binding aptamer G-quadruplex. Mol Cell Probes 2016; 32:13-17. [PMID: 27771441 DOI: 10.1016/j.mcp.2016.10.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/19/2016] [Accepted: 10/19/2016] [Indexed: 12/31/2022]
Abstract
We have developed a label-free assay for the detection of DNA polymerase activity based on a thrombin-binding aptamer (TBA) G-quadruplex. In the presence of DNA polymerase, the 3'-OH termini of the hairpin substrate are immediately elongated to replace the TBA, which can be recognized quickly by the ThT dye and results in an increase of fluorescence. This method is highly sensitive with a detection limit of 0.1 U/mL. It is simple and cost-effective without any requirement of labeling with a fluorophore-quencher pair. Furthermore, the proposed method can also be applied to analyze the inhibition of DNA polymerase, which clearly indicates that the proposed method can be applied for screening of potential DNA polymerase inhibitors.
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Affiliation(s)
- Jing Wang
- State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410013, China
| | - Haisheng Liu
- State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410013, China
| | - Changbei Ma
- State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410013, China.
| | - Jun Wang
- State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410013, China
| | - Linxiu Zhong
- State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410013, China
| | - Kefeng Wu
- State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410013, China
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Jin H, Liu Y, Xu T, Qu X, Bian F, Sun Q. Quantum Dots–Ligand Complex as Ratiometric Fluorescent Nanoprobe for Visual and Specific Detection of G-Quadruplex. Anal Chem 2016; 88:10411-10418. [DOI: 10.1021/acs.analchem.6b01967] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Haojun Jin
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Yuqian Liu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Tianshu Xu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Xiaojun Qu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Feika Bian
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Qingjiang Sun
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
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68
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Wang H, Peng P, Liu S, Li T. Thioflavin T behaves as an efficient fluorescent ligand for label-free ATP aptasensor. Anal Bioanal Chem 2016; 408:7927-7934. [PMID: 27682839 DOI: 10.1007/s00216-016-9926-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 08/29/2016] [Accepted: 09/01/2016] [Indexed: 12/22/2022]
Abstract
Here, we for the first time demonstrated thioflavin T (ThT) as an efficient fluorescent ligand for 27-mer ATP-binding aptamer (ABA27), providing a novel signal readout mode for label-free selective ATP detection. ABA27 can promote the fluorescence emission of ThT with an unprecedentedly high efficiency, attributed to the specific structure of ABA27 rather than the G-tracts. Polyacrylamide gel electrophoresis, fluorescence spectroscopy, and fluorometric titration reveal that ThT interacts with ABA27 with a lower binding affinity (Kd ~89 μM) than ATP, which allows ATP to easily compete with ThT for the DNA binder. In the presence of ThT, adding ATP induces ABA27 to undergo a structural change, thereby not favoring the binding to ThT, verified by circular dichroism and UV-Vis absorption spectroscopy. As a result, the fluorescence intensity of ThT decreases dramatically, enabling the sensitive detection of ATP with high selectivity over other analogs. Such a sensing strategy may make ThT able to serve as a facile signal reporter for DNA nanomechanical devices fueled with ATP. Graphical Abstract The principle of the displacement of ThT by ATP.
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Affiliation(s)
- Huihui Wang
- Department of Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Jinzhai Road 96, Hefei, Anhui, 230026, China
| | - Pai Peng
- Department of Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Jinzhai Road 96, Hefei, Anhui, 230026, China
| | - Shuangna Liu
- Department of Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Jinzhai Road 96, Hefei, Anhui, 230026, China
| | - Tao Li
- Department of Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Jinzhai Road 96, Hefei, Anhui, 230026, China.
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69
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Yang L, Qing Z, Liu C, Tang Q, Li J, Yang S, Zheng J, Yang R, Tan W. Direct Fluorescent Detection of Blood Potassium by Ion-Selective Formation of Intermolecular G-Quadruplex and Ligand Binding. Anal Chem 2016; 88:9285-92. [PMID: 27558922 DOI: 10.1021/acs.analchem.6b02667] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
G-quadruplex analogues have been widely used as molecular tools for detection of potassium ion (K(+)). However, interference from a higher concentration of sodium ion (Na(+)), enzymatic degradation of the oligonucleotide, and background absorption and fluorescence of blood samples have all limited the use of G-quadruplex for direct detection of K(+) in blood samples. Here, we reported, for the first time, an intermolecular G-quadruplex-based assay capable of direct fluorescent detection of blood K(+). Increased stringency of intermolecular G-quadruplex formation based on our screened G-rich oligonucleotide (5'-TGAGGGA GGGG-3') provided the necessary selectivity for K(+) against Na(+) at physiological ion level. To increase long-term stability of oligonucleotide in blood, the screened oligonucleotide was modified with an inverted thymine nucleotide whose 3'-terminus was connected to the 3'-terminus of the upstream nucleotide, acting as a blocking group to greatly improve antinuclease stability. Lastly, to avoid interference from background absorption and autofluorescence of blood, a G-quadruplex-binding, two-photon-excited ligand, EBMVC-B, was synthesized and chosen as the fluorescence reporter. Thus, based on selective K(+) ion-induced formation of intermolecular G-quadruplex and EBMVC-B binding, this approach could linearly respond to K(+) from 0.5 to 10 mM, which matches quite well with the physiologically relevant concentration of blood K(+). Moreover, the system was highly selective for K(+) against other metal ions, including Na(+), Ca(2+), Mg(2+), Zn(2+) common in blood. The practical application was demonstrated by direct detection of K(+) from real blood samples by two-photon fluorescence technology. To the best of our knowledge, this is the first attempt to exploit molecular G-quadruplex-based fluorescent sensing for direct assay of blood target. As such, we expect that it will promote the design and practical application of similar DNA-based sensors in complex real systems.
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Affiliation(s)
- Le Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Molecular Science and Biomedicine Laboratory, Hunan University , Changsha 410082, P. R. China
| | - Zhihe Qing
- School of Chemistry and Biological Engineering, Changsha University of Science and Technology , Changsha 410004, P. R. China
| | - Changhui Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Molecular Science and Biomedicine Laboratory, Hunan University , Changsha 410082, P. R. China
| | - Qiao Tang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Molecular Science and Biomedicine Laboratory, Hunan University , Changsha 410082, P. R. China
| | - Jishan Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Molecular Science and Biomedicine Laboratory, Hunan University , Changsha 410082, P. R. China
| | - Sheng Yang
- School of Chemistry and Biological Engineering, Changsha University of Science and Technology , Changsha 410004, P. R. China
| | - Jing Zheng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Molecular Science and Biomedicine Laboratory, Hunan University , Changsha 410082, P. R. China
| | - Ronghua Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Molecular Science and Biomedicine Laboratory, Hunan University , Changsha 410082, P. R. China.,School of Chemistry and Biological Engineering, Changsha University of Science and Technology , Changsha 410004, P. R. China
| | - Weihong Tan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Molecular Science and Biomedicine Laboratory, Hunan University , Changsha 410082, P. R. China
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70
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Li Y, Xu S, Wu X, Xu Q, Zhao Y, Lou X, Yang X. Thioflavin T as a fluorescence light-up probe for both parallel and antiparallel G-quadruplexes of 29-mer thrombin binding aptamer. Anal Bioanal Chem 2016; 408:8025-8036. [PMID: 27590320 DOI: 10.1007/s00216-016-9901-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 08/08/2016] [Accepted: 08/23/2016] [Indexed: 12/31/2022]
Abstract
A wide range of pathologies have been targeted with bimodular aptamers that contain both G-quadruplex (G4) and duplex motifs, while the structures and functions are poorly understood. G4-selective fluorescent dyes have served as facile tools to probe G4s, but not for bimodular aptamers, yet. Here, taking the 29-mer thrombin binding aptamer (TBA29) as an example, we demonstrated that 3,6-dimethyl-2-(4-dimethylaminophenyl)-benzothiazolium (ThT) was the most effective dye compared to NMM and PPIX in recognizing TBA29. Binding studies indicate that ThT recognized TBA29 via distinct buffer-dependent mechanisms. Specifically, ThT induced the formation of a bimolecular parallel G4 in cation-deficient buffer, showing 341-fold fluorescent enhancement. The competitive binding of thrombin disrupted the complex, leading to the monotonic fluorescence decrease. A similar mechanism was previously reported for the interaction between ThT and the 15-mer thrombin binding aptamer (TBA15). However, TBA29 bound with ThT in a more favorable state than TBA15, showing hyperchromic effects and two times stronger fluorescence enhancement. Differently, ThT bound with antiparallel TBA29/TBA15 in an intercalating/groove binding mode in 100 mM KCl, generating 181/28-fold fluorescence enhancement, respectively. These results revealed that ThT recognized both parallel and antiparallel G4s of TBA29 more efficiently than it recognized TBA15. The duplex structure of TBA29 may play an important role in its interaction with ThT. Our study broadens the application of ThT in screening G4 to bimodular aptamers and provides some insights into the structures of TBA29, along with the interaction between ThT and TBA29. Our study also is useful for the development of structure-switching-based biosensors using bimodular aptamers. Graphical abstract The buffer-dependent binding mechanisms of ThT with TBA29, and the competitive (top)/noncompetitive (bottom) binding of thrombin with TBA29-ThT complex.
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Affiliation(s)
- Ye Li
- Department of Chemistry, Capital Normal University, Beijing, 100048, China
| | - Shi Xu
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Xiao Wu
- Department of Chemistry, Capital Normal University, Beijing, 100048, China
| | - Qing Xu
- Department of Chemistry, Capital Normal University, Beijing, 100048, China
| | - Yinhua Zhao
- Department of Chemistry, Capital Normal University, Beijing, 100048, China
| | - Xinhui Lou
- Department of Chemistry, Capital Normal University, Beijing, 100048, China.
| | - Xianbin Yang
- AM Biotechnologies, 12521 Gulf Freeway, Houston, TX, 77034, USA.
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71
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Zhang D, Han J, Li Y, Fan L, Li X. Aptamer-Based K(+) Sensor: Process of Aptamer Transforming into G-Quadruplex. J Phys Chem B 2016; 120:6606-11. [PMID: 27322753 DOI: 10.1021/acs.jpcb.6b05002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
G-rich aptamers have been widely applied to develop various sensors for detecting proteins, small molecules, and cations, which is based on the target-induced conformational transfer from single strand to G-quadruplex. However, the transforming process is unclear. Here, with PW17 as an aptamer example, the forming process of G-quadruplex induced by K(+) is investigated by circular dichroism spectroscopy, electrospray ionization mass spectroscopy, and native gel electrophoresis. The results demonstrate that PW17 undergoes a conformational transforming process from loose and unstable to compact and stable G-quadruplex, which is strictly K(+) concentration-dependent. The process contains three stages: (1) K(+) (<0.5 mM) could induce PW17 forming a loose and unstable G-quadruplex; (2) the compact and stable K(+)-stabilized G-quadruplex is almost formed when K(+) is equal to or larger than 7 mM; and (3) when K(+) ranges from 0.5 mM to 7 mM, the transformation of K(+)-stabilized PW17 from loose and unstable to compact and stable occurs. Interestingly, dimeric G-quadruplex through 5'-5' stacking is involved in the forming process until completely formed at 40 mM K(+). Moreover, the total process is thermodynamically controlled. With PW17 as a sensing probe and PPIX as a fluorescent probe for detection of K(+), three linear fluorescent ranges are observed, which corresponds to the three forming stages of G-quadruplex. Clarifying the forming process provides a representative example to deeply understand and further design aptamer-based biosensers and logic devices.
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Affiliation(s)
- Dongju Zhang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University , Beijing 100875, China
| | - Juan Han
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University , Beijing 100875, China
| | - Yunchao Li
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University , Beijing 100875, China
| | - Louzhen Fan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University , Beijing 100875, China
| | - Xiaohong Li
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University , Beijing 100875, China
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72
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Kocsis LS, Elbel KM, Hardigree BA, Brummond KM, Haidekker MA, Theodorakis EA. Cyclopenta[b]naphthalene cyanoacrylate dyes: synthesis and evaluation as fluorescent molecular rotors. Org Biomol Chem 2016; 13:2965-73. [PMID: 25614187 DOI: 10.1039/c4ob02563f] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe the design, synthesis and fluorescent profile of a family of environment-sensitive dyes in which a dimethylamino (donor) group is conjugated to a cyanoacrylate (acceptor) unit via a cyclopenta[b]naphthalene ring system. This assembly satisfies the typical D-π-A motif of a fluorescent molecular rotor and exhibits solvatochromic and viscosity-sensitive fluorescence emission. The central naphthalene ring system of these dyes was synthesized via a novel intramolecular dehydrogenative dehydro-Diels-Alder (IDDDA) reaction that permits incorporation of the donor and acceptor groups in variable positions around the aromatic core. A bathochromic shift of excitation and emission peaks was observed with increasing solvent polarity but the dyes exhibited a complex emission pattern with a second red emission band when dissolved in nonpolar solvents. Consistent with other known molecular rotors, the emission intensity increased with increasing viscosity. Interestingly, closer spatial proximity between the donor and the acceptor groups led to decreased viscosity sensitivity combined with an increased quantum yield. This observation indicates that structural hindrance of intramolecular rotation dominates when the donor and acceptor groups are in close proximity. The examined compounds give insight into how excited state intramolecular rotation can be influenced by both the solvent and the chemical structure.
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Affiliation(s)
- Laura S Kocsis
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA 15260, USA.
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73
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Xu S, Li Q, Xiang J, Yang Q, Sun H, Guan A, Wang L, Liu Y, Yu L, Shi Y, Chen H, Tang Y. Thioflavin T as an efficient fluorescence sensor for selective recognition of RNA G-quadruplexes. Sci Rep 2016; 6:24793. [PMID: 27098781 PMCID: PMC4838840 DOI: 10.1038/srep24793] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 04/05/2016] [Indexed: 12/29/2022] Open
Abstract
RNA G-quadruplexes (G4s) play important roles in translational regulation, mRNA processing events and gene expression. Therefore, a fluorescent probe that is capable of efficiently recognizing RNA G-quadruplex structures among other RNA forms is highly desirable. In this study, a water-soluble fluorogenic dye (i.e., Thioflavin T (ThT)) was employed to recognize RNA G-quadruplex structures using UV-Vis absorption spectra, fluorescence spectra and emission lifetime experiments. By stacking on the G-tetrad, the ThT probe exhibited highly specific recognition of RNA G-quadruplex structures with striking fluorescence enhancement compared with other RNA forms. The specific binding demonstrates that ThT is an efficient fluorescence sensor that can distinguish G4 and non-G4 RNA structures.
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Affiliation(s)
- Shujuan Xu
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
- University of the Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Qian Li
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Junfeng Xiang
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Qianfan Yang
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Hongxia Sun
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Aijiao Guan
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Lixia Wang
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Yan Liu
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Lijia Yu
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Yunhua Shi
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
- University of the Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Hongbo Chen
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Yalin Tang
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
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74
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Label-free molecular beacon for real-time monitoring of DNA polymerase activity. Anal Bioanal Chem 2016; 408:3275-80. [DOI: 10.1007/s00216-016-9398-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 02/04/2016] [Accepted: 02/05/2016] [Indexed: 12/30/2022]
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75
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Yin J, Hu Y, Yoon J. Fluorescent probes and bioimaging: alkali metals, alkaline earth metals and pH. Chem Soc Rev 2016; 44:4619-44. [PMID: 25317749 DOI: 10.1039/c4cs00275j] [Citation(s) in RCA: 417] [Impact Index Per Article: 52.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
All living species and life forms have an absolute requirement for bio-functional metals and acid-base equilibrium chemistry owing to the critical roles they play in biological processes. Hence, a great need exists for efficient methods to detect and monitor biometals and acids. In the last few years, great attention has been paid to the development of organic molecule based fluorescent chemosensors. The availability of new synthetic fluorescent probes has made fluorescence microscopy an indispensable tool for tracing biologically important molecules and in the area of clinical diagnostics. This review highlights the recent advances that have been made in the design and bioimaging applications of fluorescent probes for alkali metals and alkaline earth metal cations, including lithium, sodium and potassium, magnesium and calcium, and for pH determination within biological systems.
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Affiliation(s)
- Jun Yin
- Department of Chemistry and Nano Science, Global Top 5 Research Program, Ewha Womans University, Seoul 120-750, Korea.
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76
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Wu T, Zhang C, Wang Z, Ren H, Kang Y, Du Y. Tuning the sensing range of potassium ions by changing the loop size of G-quadruplex sensors. NEW J CHEM 2016. [DOI: 10.1039/c6nj02136k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fluorescence spectroscopy and thermodynamics were combined for the study of the loop size effect of G-quadruplex sensors in the K+ sensing range.
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Affiliation(s)
- Ting Wu
- School of Chemistry and Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Chuanjing Zhang
- School of Chemistry and Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Zhenping Wang
- School of Chemistry and Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Hongxin Ren
- School of Chemistry and Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Yan Kang
- School of Chemistry and Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Yiping Du
- School of Chemistry and Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
- China
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77
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Lee SC, Heo J, Ryu JW, Lee CL, Kim S, Tae JS, Rhee BO, Kim SW, Kwon OP. Pyrrolic molecular rotors acting as viscosity sensors with high fluorescence contrast. Chem Commun (Camb) 2016; 52:13695-13698. [DOI: 10.1039/c6cc06521j] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Pyrrolic viscosity sensors exhibit one order of magnitude higher fluorescence contrast compared to that of the conventional phenolic analogues due to the viscosity-sensitive rotation of the rotational pyrrole group.
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Affiliation(s)
- Seung-Chul Lee
- Department of Molecular Science and Technology
- Ajou University
- Suwon 443-749
- Korea
| | - Jeongyun Heo
- Center for Theragnosis
- Korea Institute of Science and Technology (KIST)
- Seongbuk-gu
- Korea
| | - Jong-Wan Ryu
- Department of Molecular Science and Technology
- Ajou University
- Suwon 443-749
- Korea
| | - Chang-Lyoul Lee
- Advanced Photonics Research Institute (APRI)
- Gwangju Institute of Science and Technology (GIST)
- Buk-gu
- Korea
| | - Sehoon Kim
- Center for Theragnosis
- Korea Institute of Science and Technology (KIST)
- Seongbuk-gu
- Korea
| | - Joon-Sung Tae
- Department of Mechanical Engineering
- Ajou University
- Suwon
- Korea
| | - Byung-Ohk Rhee
- Department of Mechanical Engineering
- Ajou University
- Suwon
- Korea
| | - Sang-Wook Kim
- Department of Molecular Science and Technology
- Ajou University
- Suwon 443-749
- Korea
| | - O-Pil Kwon
- Department of Molecular Science and Technology
- Ajou University
- Suwon 443-749
- Korea
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78
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Raju M, Patel TJ, Nair RR, Chatterjee PB. Xanthurenic acid: a natural ionophore with high selectivity and sensitivity for potassium ions in an aqueous solution. NEW J CHEM 2016. [DOI: 10.1039/c5nj02540k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Synopsis: A well-known tryptophan metabolite, xanthurenic acid, a natural non-fluorescent intermediate siderophore, showed a very selective turn-on response to K+ over other competing metal ions and the detection limit of this natural ionophore was found to be 53 nM at physiological pH.
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Affiliation(s)
- M. Raju
- Analytical Discipline and Centralized Instrument Facility
- CSIR-CSMCRI
- Bhavnagar
- India
| | - Tapasya J. Patel
- Analytical Discipline and Centralized Instrument Facility
- CSIR-CSMCRI
- Bhavnagar
- India
| | - Ratish R. Nair
- Analytical Discipline and Centralized Instrument Facility
- CSIR-CSMCRI
- Bhavnagar
- India
| | - Pabitra B. Chatterjee
- Analytical Discipline and Centralized Instrument Facility
- CSIR-CSMCRI
- Bhavnagar
- India
- Academy of Scientific and Innovative Research
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79
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Wang M, Wang W, Kang TS, Leung CH, Ma DL. Development of an Iridium(III) Complex as a G-Quadruplex Probe and Its Application for the G-Quadruplex-Based Luminescent Detection of Picomolar Insulin. Anal Chem 2015; 88:981-7. [DOI: 10.1021/acs.analchem.5b04064] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Modi Wang
- Department
of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Wanhe Wang
- Department
of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Tian-Shu Kang
- State
Key Laboratory of Quality Research in Chinese Medicine, Institute
of Chinese Medical Sciences, University of Macau, Macao, China
| | - Chung-Hang Leung
- State
Key Laboratory of Quality Research in Chinese Medicine, Institute
of Chinese Medical Sciences, University of Macau, Macao, China
| | - Dik-Lung Ma
- Department
of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
- Partner
State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China
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80
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Siraj N, El-Zahab B, Hamdan S, Karam TE, Haber LH, Li M, Fakayode SO, Das S, Valle B, Strongin RM, Patonay G, Sintim HO, Baker GA, Powe A, Lowry M, Karolin JO, Geddes CD, Warner IM. Fluorescence, Phosphorescence, and Chemiluminescence. Anal Chem 2015; 88:170-202. [PMID: 26575092 DOI: 10.1021/acs.analchem.5b04109] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Noureen Siraj
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Bilal El-Zahab
- Department of Mechanical and Materials Engineering, Florida International University , Miami, Florida 33174, United States
| | - Suzana Hamdan
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Tony E Karam
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Louis H Haber
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Min Li
- Process Development Center, Albemarle Corporation , Baton Rouge, Louisiana 70805, United States
| | - Sayo O Fakayode
- Department of Chemistry, Winston-Salem State University , Winston-Salem, North Carolina 27110, United States
| | - Susmita Das
- Department of Civil Engineering, Adamas Institute of Technology , Barasat, Kolkata 700126, West Bengal India
| | - Bertha Valle
- Department of Chemistry, Texas Southern University , Houston, Texas 77004, United States
| | - Robert M Strongin
- Department of Chemistry, Portland State University , Portland, Oregon 97207, United States
| | - Gabor Patonay
- Department of Chemistry, Georgia State University , Atlanta, Georgia 30302-4098, United States
| | - Herman O Sintim
- Department of Chemistry and Biochemistry, University of Maryland , College Park, Maryland 20742, United States
| | - Gary A Baker
- Department of Chemistry, University of Missouri Columbia , Columbia, Missouri 65211-7600, United States
| | - Aleeta Powe
- Department of Chemistry, University of Louisville , Louisville, Kentucky 40208, United States
| | - Mark Lowry
- Department of Chemistry, Portland State University , Portland, Oregon 97207, United States
| | - Jan O Karolin
- Institute of Fluorescence, University of Maryland Baltimore County , Baltimore, Maryland 21202, United States
| | - Chris D Geddes
- Institute of Fluorescence, University of Maryland Baltimore County , Baltimore, Maryland 21202, United States
| | - Isiah M Warner
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
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81
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Wang Y, Hu Y, Wu T, Zhou X, Shao Y. Triggered Excited-State Intramolecular Proton Transfer Fluorescence for Selective Triplex DNA Recognition. Anal Chem 2015; 87:11620-4. [DOI: 10.1021/acs.analchem.5b02851] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Ying Wang
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People’s Republic of China
| | - Yuehua Hu
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People’s Republic of China
| | - Tao Wu
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People’s Republic of China
| | - Xiaoshun Zhou
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People’s Republic of China
| | - Yong Shao
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People’s Republic of China
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82
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Zhang Y, Fan J, Nie J, Le S, Zhu W, Gao D, Yang J, Zhang S, Li J. Timing readout in paper device for quantitative point-of-use hemin/G-quadruplex DNAzyme-based bioassays. Biosens Bioelectron 2015; 73:13-18. [DOI: 10.1016/j.bios.2015.04.081] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 04/23/2015] [Accepted: 04/24/2015] [Indexed: 12/31/2022]
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83
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Lee IJ, Patil SP, Fhayli K, Alsaiari S, Khashab NM. Probing structural changes of self assembled i-motif DNA. Chem Commun (Camb) 2015; 51:3747-9. [PMID: 25350559 DOI: 10.1039/c4cc06824f] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We report an i-motif structural probing system based on Thioflavin T (ThT) as a fluorescent sensor. This probe can discriminate the structural changes of RET and Rb i-motif sequences according to pH change.
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Affiliation(s)
- Il Joon Lee
- Controlled Release and Delivery Lab (CRD), Advanced Membranes and Porous Materials Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Makkah 23955-6900, Kingdom of Saudi Arabia.
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84
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G-quadruplex − based homogenous fluorescence platform for ultrasensitive DNA detection through isothermal cycling and cascade signal amplification. Mikrochim Acta 2015. [DOI: 10.1007/s00604-015-1608-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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85
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Liu X, Hua X, Fan Q, Chao J, Su S, Huang YQ, Wang L, Huang W. Thioflavin T as an Efficient G-Quadruplex Inducer for the Highly Sensitive Detection of Thrombin Using a New Föster Resonance Energy Transfer System. ACS APPLIED MATERIALS & INTERFACES 2015; 7:16458-16465. [PMID: 26173915 DOI: 10.1021/acsami.5b03662] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We report a new Föster resonance energy transfer (FRET) system that uses a special dye, thioflavin T (ThT), as an energy acceptor and a water-soluble conjugated polymer (CP) with high fluorescence as an energy donor. A simple, label-free, and sensitive strategy for the detection of thrombin in buffer and in diluted serum was designed based on this new system using ThT as an efficient inducer of the G-quadruplex. The difference between the blank and the positive samples was amplified due to distinctive FRET signals because thrombin has little effect on the intercalation of ThT into the G-quadruplex. In the absence of the target, ThT induces the aptamer to form a G-quadruplex and intercalates into it with strong fluorescence. The electrostatic attractions between the negatively charged G-quadruplex and positively charged CP allow a short donor-acceptor distance, resulting in a high FRET signal. However, in the presence of the target, the aptamer forms a G-quadruplex-thrombin complex first, followed by the intercalation of ThT into the G-quadruplex. A long distance exists between the donor and acceptor due to the strong steric hindrance from the large-sized thrombin, which leads to a low FRET signal. Compared with previously reported strategies based on the FRET between the CP and dye, our strategy is label-free, and the sensitivity was improved by an order of magnitude. Our strategy also shows the advantages of being simple, rapid (about 50 min), sensitive, label-free, and low-cost in comparison to strategies based on the FRET between quantum dots and dyes.
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86
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Luo D, Mu Y. All-atomic simulations on human telomeric G-quadruplex DNA binding with thioflavin T. J Phys Chem B 2015; 119:4955-67. [PMID: 25806428 DOI: 10.1021/acs.jpcb.5b01107] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Ligand-stabilized human telomeric G-quadruplex DNA is believed to be an anticancer agent, as it can impede the continuous elongation of telomeres by telomerase in cancer cells. In this study, five well-established human telomeric G-quadruplex DNA models were probed on their binding behaviors with thioflavin T (ThT) via both conventional molecular dynamics (MD) and well-tempered metadynamics (WT-MetaD) simulations. Novel dynamics and characteristic binding patterns were disclosed by the MD simulations. It was observed that the K(+) promoted parallel and hybridized human telomeric G-quadruplex conformations pose higher binding affinities to ThT than the Na(+) and K(+) promoted basket conformations. It is the end, sandwich, and base stacking driven by π-π interactions that are identified as the major binding mechanisms. As the most energy favorable binding mode, the sandwich stacking observed in (3 + 1) hybridized form 1 G-quadruplex conformation is triggered by reversible conformational change of the G-quadruplex. To further examine the free energy landscapes, WT-MetaD simulations were utilized on G-quadruplex-ThT systems. It is found that all of the major binding modes predicted by the MD simulations are confirmed by the WT-MetaD simulations. The results in this work not only accord with existing experimental findings, but also reinforce our understanding on the dynamics of G-quadruplexes and aid future drug developments for G-quadruplex stabilization ligands.
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Affiliation(s)
- Di Luo
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
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87
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Zhang L, Liu H, Shao Y, Lin C, Jia H, Chen G, Yang D, Wang Y. Selective lighting up of epiberberine alkaloid fluorescence by fluorophore-switching aptamer and stoichiometric targeting of human telomeric DNA G-quadruplex multimer. Anal Chem 2015; 87:730-7. [PMID: 25429435 PMCID: PMC5515279 DOI: 10.1021/ac503730j] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Aptamers, that exist naturally in living cells as functional elements and can switch nonfluorescent natural targets to fluorophores, are very useful in developing highly sensitive and selective biosensors and screening functional agents. This work demonstrates that human telomeric G-quadruplex (HTG) can serve as a potential fluorophore-switching aptamer (FSA) to target a natural isoquinoline alkaloid. We found that, among the G-quadruplexes studied here and the various structurally similar alkaloids including epiberberine (EPI), berberine (BER), palmatine (PAL), jatrorrhizine (JAT), coptisine (COP), worenine (WOR), sanguinarine (SAN), chelerythrine (CHE), and nitidine (NIT), only the HTG DNA, especially with a 5'-TA-3' residue at the 5' end of the G-quadruplex tetrad (5'-TAG3(TTAG3)3-3', TA[Q]) as the minimal sequence, is the most efficient FSA to selectively light up the EPI fluorescence. Compared to the 5' end flanking sequences, the 3' end flanking sequences of the tetrad contribute significantly less to the recognition of EPI. The binding affinity of EPI to TA[Q] (K(d) = 37 nM) is at least 20 times tighter than those of the other alkaloids. The steady-state absorption, steady-state/time-resolved fluorescence, and NMR studies demonstrate that EPI most likely interact with the 5' end flanking sequence substructure beyond the core [Q] and the G-quadruplex tetrad in a much more specific manner than the other alkaloids. The highly selective and tight binding of EPI with the FSA and significantly enhanced fluorescence suggest the potential development of a selective EPI sensor (detection limit of 10 nM). More importantly, EPI, as the brightest FSA emitter among the alkaloids, can also serve as an efficient conformation probe for HTG DNA and discriminate the DNA G-quadruplex from the RNA counterpart. Furthermore, EPI can bind stoichiometrically to each G-quadruplex unit of long HTG DNA multimer with the most significant fluorescence enhancement, which has not been achieved by the previously reported probes. Our work suggests the potential use of EPI as a bioimaging probe and a therapeutic DNA binder.
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Affiliation(s)
- Lihua Zhang
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, Zhejiang 321004, China
| | - Hua Liu
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, Zhejiang 321004, China
| | - Yong Shao
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, Zhejiang 321004, China
| | - Clement Lin
- College of Pharmacy, BIO5 Institute, Arizona Cancer Center, Department of Chemistry, University of Arizona, 1703 East Mabel Street, Tucson, Arizona 85721, United States
| | - Huan Jia
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Danzhou Yang
- College of Pharmacy, BIO5 Institute, Arizona Cancer Center, Department of Chemistry, University of Arizona, 1703 East Mabel Street, Tucson, Arizona 85721, United States
| | - Ying Wang
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, Zhejiang 321004, China
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88
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Wang Y, Hu Y, Wu T, Liu H, Zhang L, Zhou X, Shao Y. Specific G-quadruplex structure recognition of human telomeric RNA over DNA by a fluorescently activated hyperporphyrin. Analyst 2015; 140:5169-75. [DOI: 10.1039/c5an00937e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Selective recognition of the G-quadruplex structure of human telomeric RNA (TERRA) over DNA was achieved using an activated hyperporphyrin as a fluorescent probe.
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Affiliation(s)
- Ying Wang
- Institute of Physical Chemistry
- Zhejiang Normal University
- Jinhua 321004
- Zhejiang, People's Republic of China
| | - Yuehua Hu
- Institute of Physical Chemistry
- Zhejiang Normal University
- Jinhua 321004
- Zhejiang, People's Republic of China
| | - Tao Wu
- Institute of Physical Chemistry
- Zhejiang Normal University
- Jinhua 321004
- Zhejiang, People's Republic of China
| | - Hua Liu
- Institute of Physical Chemistry
- Zhejiang Normal University
- Jinhua 321004
- Zhejiang, People's Republic of China
| | - Lihua Zhang
- Institute of Physical Chemistry
- Zhejiang Normal University
- Jinhua 321004
- Zhejiang, People's Republic of China
| | - Xiaoshun Zhou
- Institute of Physical Chemistry
- Zhejiang Normal University
- Jinhua 321004
- Zhejiang, People's Republic of China
| | - Yong Shao
- Institute of Physical Chemistry
- Zhejiang Normal University
- Jinhua 321004
- Zhejiang, People's Republic of China
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89
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Xu H, Geng F, Wang Y, Xu M, Lai X, Qu P, Zhang Y, Liu B. A label-free fluorescent molecular switch for a DNA hybridization assay utilizing a G-quadruplex-selective auramine O. Chem Commun (Camb) 2015; 51:8622-5. [DOI: 10.1039/c5cc02624e] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A G-quadruplex molecular switch (G4-MS) assembled using auramine O and the G-rich single stranded DNA is developed for a DNA assay.
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Affiliation(s)
- Huiying Xu
- Department of Chemistry
- State Key Lab of Molecular Engineering of Polymers and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200433
- China
| | - Fenghua Geng
- Key Laboratory of Biomolecule Recognition and Sensing
- College of Chemistry and Chemical Engineering
- Shangqiu Normal University
- Shangqiu
- China
| | - Yongxiang Wang
- Key Laboratory of Biomolecule Recognition and Sensing
- College of Chemistry and Chemical Engineering
- Shangqiu Normal University
- Shangqiu
- China
| | - Maotian Xu
- Key Laboratory of Biomolecule Recognition and Sensing
- College of Chemistry and Chemical Engineering
- Shangqiu Normal University
- Shangqiu
- China
| | - Xinhe Lai
- Key Laboratory of Biomolecule Recognition and Sensing
- College of Chemistry and Chemical Engineering
- Shangqiu Normal University
- Shangqiu
- China
| | - Peng Qu
- Key Laboratory of Biomolecule Recognition and Sensing
- College of Chemistry and Chemical Engineering
- Shangqiu Normal University
- Shangqiu
- China
| | - Yintang Zhang
- Key Laboratory of Biomolecule Recognition and Sensing
- College of Chemistry and Chemical Engineering
- Shangqiu Normal University
- Shangqiu
- China
| | - Baohong Liu
- Department of Chemistry
- State Key Lab of Molecular Engineering of Polymers and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200433
- China
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90
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Xu L, Shen X, Hong S, Wang J, Zhang Y, Wang H, Zhang J, Pei R. Turn-on and label-free fluorescence detection of lead ions based on target-induced G-quadruplex formation. Chem Commun (Camb) 2015; 51:8165-8. [DOI: 10.1039/c5cc01590a] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Using a guanine-rich sequence (AGRO100) and N-methyl mesoporphyrin IX (NMM), a turn-on and label-free fluorescent Pb2+ sensor with high sensitivity and low background fluorescence was presented as a representative of five turn-on sensing systems.
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Affiliation(s)
- Lijun Xu
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Collaborative Innovation Center of Suzhou Nano Science and Technology
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
| | - Xiaoqiang Shen
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Collaborative Innovation Center of Suzhou Nano Science and Technology
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
| | - Shanni Hong
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Collaborative Innovation Center of Suzhou Nano Science and Technology
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
| | - Jine Wang
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Collaborative Innovation Center of Suzhou Nano Science and Technology
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
| | - Yuanyuan Zhang
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Collaborative Innovation Center of Suzhou Nano Science and Technology
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
| | - Hongyan Wang
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Collaborative Innovation Center of Suzhou Nano Science and Technology
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
| | - Jianye Zhang
- School of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- P. R. China
| | - Renjun Pei
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Collaborative Innovation Center of Suzhou Nano Science and Technology
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
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91
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Bhasikuttan AC, Mohanty J. Targeting G-quadruplex structures with extrinsic fluorogenic dyes: promising fluorescence sensors. Chem Commun (Camb) 2015; 51:7581-97. [DOI: 10.1039/c4cc10030a] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This article provides a brief account of the recent reports on the fluorescence properties of some of the fluorogenic dyes towards G-quadruplex DNAs, which have been turned into promising bio-analytical methods.
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Affiliation(s)
| | - Jyotirmayee Mohanty
- Radiation & Photochemistry Division
- Bhabha Atomic Research Centre
- Mumbai 400 085
- India
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92
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Dziuba D, Pohl R, Hocek M. Polymerase synthesis of DNA labelled with benzylidene cyanoacetamide-based fluorescent molecular rotors: fluorescent light-up probes for DNA-binding proteins. Chem Commun (Camb) 2015; 51:4880-2. [DOI: 10.1039/c5cc00530b] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Fluorescent molecular rotors are for the first time used as light-up probes for sensing of DNA–protein interaction.
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Affiliation(s)
- Dmytro Dziuba
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Gilead & IOCB Research Center
- CZ-16610 Prague 6
- Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Gilead & IOCB Research Center
- CZ-16610 Prague 6
- Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Gilead & IOCB Research Center
- CZ-16610 Prague 6
- Czech Republic
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93
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GUO Y, SUN Y, SHEN X, ZHANG K, HU J, PEI R. Label-free Detection of Zn 2+ Based on G-quadruplex. ANAL SCI 2015; 31:1041-5. [DOI: 10.2116/analsci.31.1041] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Yahui GUO
- Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences
| | - Yan SUN
- Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences
| | - Xiaoqiang SHEN
- Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences
| | - Kunchi ZHANG
- Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences
| | - Jiming HU
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry & Molecular Sciences, Wuhan University
| | - Renjun PEI
- Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences
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94
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Kataoka Y, Fujita H, Kasahara Y, Yoshihara T, Tobita S, Kuwahara M. Minimal Thioflavin T Modifications Improve Visual Discrimination of Guanine-Quadruplex Topologies and Alter Compound-Induced Topological Structures. Anal Chem 2014; 86:12078-84. [DOI: 10.1021/ac5028325] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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 Science and Technology, Gunma University, 1-5-1
Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Yuuya Kasahara
- Graduate School of Science and Technology, Gunma University, 1-5-1
Tenjin-cho, Kiryu, Gunma 376-8515, Japan
- National Institute of Biomedical Innovation (NIBIO), 7-6-8 Asagi, Saito, Ibaraki, Osaka 567-0085, Japan
| | - Toshitada Yoshihara
- Graduate School of Science and Technology, Gunma University, 1-5-1
Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Seiji Tobita
- Graduate School of Science and Technology, Gunma University, 1-5-1
Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Masayasu Kuwahara
- Graduate School of Science and Technology, Gunma University, 1-5-1
Tenjin-cho, Kiryu, Gunma 376-8515, Japan
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95
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Siters KE, Fountain MA, Morrow JR. Selective binding of Zn2+ complexes to human telomeric G-quadruplex DNA. Inorg Chem 2014; 53:11540-51. [PMID: 25310175 DOI: 10.1021/ic501484p] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The Zn(2+) complex of 5-(1,4,7,10-tetraazacyclododecan-1-ylsulfonyl)-N,N-dimethylnaphthalen-1-amine, Zn(DSC), binds selectively to the biologically relevant human telomeric (H-Telo) G-quadruplex. An increase in the Zn(DSC) dansyl group fluorescence with a simultaneous shift in emission is consistent with the complex binding to H-Telo. The H-Telo G-quadruplex has two binding sites for Zn(DSC) with binding constants in the low micromolar range (2.5 μM). Isothermal calorimetric titrations confirm low micromolar dissociation constants with a 2:1 stoichiometry. The interaction between H-Telo and Zn(DSC) is highly pH-dependent, consistent with binding to the unpaired thymines in the G-quadruplex loops. As a result, Zn(DSC) selectively binds to H-Telo over duplex DNA. In contrast to Zn(2+), Fe(2+) and Co(2+) do not complex to the DSC macrocycle appreciably under the conditions of the experiment. The Cu(2+) complex of DSC does not interact measurably with the H-Telo G-quadruplex. Interestingly, the H-Telo-Zn(DSC) adduct self-assembles from its individual components at physiological pH and 100 mM KCl. The self-assembly feature, which is specific for the Zn(2+) ion, suggests that this system may be viable as a Zn(2+) sensor. Pentanucleotides were studied in order to better describe the binding of Zn(DSC) to thymine sequences. NMR studies were consistent with the binding of Zn(DSC) to thymine-containing oligonucleotides including CCTCC, CTTCC, and CTCTC. Studies showed that the dansyl group of Zn(DSC) interacts with thymines in CTTCC. Fluorescence spectroscopy and ITC data indicate that Zn(DSC) forms 2:1 adducts with thymines that are spaced (CTCTC) but not tandem thymines (CTTCC). These data are consistent with one Zn(DSC) complex binding to two separate loops in the G-quadruplex. A second Zn(2+) complex containing an acridine pendent, Zn(ACR), binds tightly to pentanucleotides with both tandem and spaced thymines. Zn(ACR) indiscriminately binds to both H-Telo and duplex DNA.
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Affiliation(s)
- Kevin E Siters
- Department of Chemistry, University at Buffalo, State University of New York , Buffalo, New York 14260, United States
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96
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Zhang FT, Nie J, Zhang DW, Chen JT, Zhou YL, Zhang XX. Methylene blue as a G-quadruplex binding probe for label-free homogeneous electrochemical biosensing. Anal Chem 2014; 86:9489-95. [PMID: 25211349 DOI: 10.1021/ac502540m] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Herein, G-quadruplex sequence was found to significantly decrease the diffusion current of methylene blue (MB) in homogeneous solution for the first time. Electrochemical methods combined with circular dichroism spectroscopy and UV-vis spectroscopy were utilized to systematically explore the interaction between MB and an artificial G-quadruplex sequence, EAD2. The interaction of MB and EAD2 (the binding constant, K ≈ 1.3 × 10(6) M(-1)) was stronger than that of MB and double-stranded DNA (dsDNA) (K ≈ 2.2 × 10(5) M(-1)), and the binding stoichiometry (n) of EAD2/MB complex was calculated to be 1.0 according to the electrochemical titration curve combined with Scatchard analysis. MB was proved to stabilize the G-quadruplex structure of EAD2 and showed a competitive binding to G-quadruplex in the presence of hemin. EAD2 might mainly interact with MB, a positive ligand of G-quadruplex, through the end-stacking with π-system of the guanine quartet, which was quite different from the binding mechanism of dsDNA with MB by intercalation. A novel signal read-out mode based on the strong affinity between G-quadruplex and MB coupling with aptamer/G-quadruplex hairpin structure was successfully implemented in cocaine detection with high specificity. G-quadruplex/MB complex will function as a promising electrochemical indicator for constructing homogeneous label-free electrochemical biosensors, especially in the field of simple, rapid, and noninvasive biochemical assays.
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Affiliation(s)
- Fang-Ting Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry, Peking University , Beijing 100871, China
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97
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Verdian-Doghaei A, Housaindokht MR, Abnous K. A fluorescent aptasensor for potassium ion detection-based triple-helix molecular switch. Anal Biochem 2014; 466:72-5. [PMID: 25173515 DOI: 10.1016/j.ab.2014.08.014] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 08/12/2014] [Accepted: 08/15/2014] [Indexed: 12/21/2022]
Abstract
Here, a biosensor based on a quadruplex-forming aptamer for the determination of potassium ion (K(+)) is presented. The aptamer was used as a molecular recognition element; it was adjacent to two arm fragments and a dual-labeled oligonucleotide serving as a signal transduction probe (STP) that is complementary of the arm fragment sequence. In the presence of K(+), the aptamer was displaced from the STP, which was accompanied by decreased signal. The quenching percentage of fluorescence intensity was proportional to the concentration of K(+) in the range of 0.05 to 1.4mM. A detection limit of 0.014 mM was achieved. Furthermore, other metal ions, such as Na(+), Li(+), NH4(+), Mg(2+), and Ca(2+), caused no notable interference on the detection of K(+).
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Affiliation(s)
- A Verdian-Doghaei
- Biophysical Chemistry Laboratory, Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - M R Housaindokht
- Biophysical Chemistry Laboratory, Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Kh Abnous
- Pharmaceutical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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