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Binding and Structural Properties of DNA Aptamers with VEGF-A-Mimic Activity. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 19:1145-1152. [PMID: 32059340 PMCID: PMC7016029 DOI: 10.1016/j.omtn.2019.12.034] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 12/04/2019] [Accepted: 12/23/2019] [Indexed: 12/27/2022]
Abstract
Vascular endothelial growth factors (VEGFs) are hypoxia-inducible secreted proteins to promote angiogenesis, in which VEGF-A is an important molecule that binds and activates VEGF receptor-1 (VEGFR-1) and VEGFR-2. In this study, two DNA aptamers, Apt01 and Apt02, were successfully isolated by alternating consecutive systematic evolution of ligands by exponential enrichment (SELEX) against VEGFR-1 and -2 using deep sequencing analysis in an early selection round. Their binding affinities for VEGFR-2 were lower than that of VEGFR-1, which is similar to that of VEGF-A. Structural analyses with the measurements of circular dichroism spectra and ultraviolet melting curve showed that Apt01 possessed the stem-loop structure in the molecule, whereas Apt02 formed G-quadruplex structures. In addition, Apt02 accelerated a tube formation of human umbilical vein endothelial cells faster than Apt01, which was affected by difference of binding affinity and nuclease resistance due to G-quadruplex structures. These results demonstrated that Apt02 might have a potential to function as an alternative to VEGF-A.
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2
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Maruyama R, Makino K, Yoshitomi T, Yui H, Furusho H, Yoshimoto K. Estimation of G-quartet-forming guanines in parallel-type G-quadruplexes by optical spectroscopy measurements of their single-nucleobase substitution sequences. Analyst 2018; 143:4022-4026. [PMID: 30091430 DOI: 10.1039/c8an01131a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Since much attention has been paid to in vivo biological functions of G-quadruplexes, structural analyses of G-quadruplexes are essential for understanding their functional mechanisms. Here, we established a simple optical-spectroscopy-based method for the estimation of G-quartet-forming guanines in parallel-type G-quadruplexes using measurements of circular dichroism and the thermal melting temperature.
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Affiliation(s)
- Ryo Maruyama
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan.
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3
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Amirbekyan K, Mansot J, Ohara K, Markarian SA, Vasseur JJ, Smietana M. Template-directed excimer formation via specific non-covalent interactions between pyrene guanidinium derivatives and nucleic acids. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2017.12.046] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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4
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Sherlock ME, Rumble CA, Kwok CK, Breffke J, Maroncelli M, Bevilacqua PC. Steady-State and Time-Resolved Studies into the Origin of the Intrinsic Fluorescence of G-Quadruplexes. J Phys Chem B 2016; 120:5146-58. [PMID: 27267433 DOI: 10.1021/acs.jpcb.6b03790] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Stretches of guanines in DNA and RNA can fold into guanine quadruplex structures (GQSs). These structures protect telomeres in DNA and regulate gene expression in RNA. GQSs have an intrinsic fluorescence that is sensitive to different parameters, including loop sequence and length. However, the dependence of GQS fluorescence on solution and sequence parameters and the origin of this fluorescence are poorly understood. Herein we examine effects of dangling nucleotides and cosolute conditions on GQS fluorescence using both steady-state and time-resolved fluorescence spectroscopy. The quantum yield of dGGGTGGGTGGGTGGG, termed "dG3T", is found to be modest at ∼2 × 10(-3). Nevertheless, dG3T and its variants are significantly brighter than the common nucleic acid fluorophore 2-aminopurine (2AP) largely due to their sizable extinction coefficients. Dangling 5'-end nucleotides generally reduce emission and blue-shift the resultant spectrum, whereas dangling 3'-end nucleotides slightly enhance fluorescence, particularly on the red side of the emission band. Time-resolved fluorescence decays are broadly distributed in time and require three exponential components for accurate fits. Time-resolved emission spectra suggest the presence of two emitting populations centered at ∼330 and ∼390 nm, with the redder component being a well-defined long-lived (∼1 ns) entity. Insights into GQS fluorescence obtained here should be useful in designing brighter intrinsic RNA and DNA quadruplexes for use in label-free biotechnological applications.
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Affiliation(s)
- Madeline E Sherlock
- Department of Chemistry, ‡Center for RNA Molecular Biology, and §Department of Biochemistry and Molecular Biology, Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Christopher A Rumble
- Department of Chemistry, ‡Center for RNA Molecular Biology, and §Department of Biochemistry and Molecular Biology, Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Chun Kit Kwok
- Department of Chemistry, ‡Center for RNA Molecular Biology, and §Department of Biochemistry and Molecular Biology, Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Jens Breffke
- Department of Chemistry, ‡Center for RNA Molecular Biology, and §Department of Biochemistry and Molecular Biology, Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Mark Maroncelli
- Department of Chemistry, ‡Center for RNA Molecular Biology, and §Department of Biochemistry and Molecular Biology, Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Philip C Bevilacqua
- Department of Chemistry, ‡Center for RNA Molecular Biology, and §Department of Biochemistry and Molecular Biology, Pennsylvania State University , University Park, Pennsylvania 16802, United States
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Xu L, Sun N, Zhou L, Chen X, Wang J, Wang Q, Wang K, Zhang J, Pei R. A label-free fluorescence assay for potassium ions using riboflavin as a G-quadruplex ligand. Analyst 2015; 140:3352-5. [DOI: 10.1039/c5an00242g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A label-free fluorescence K+assay was developed using riboflavin, a new G-quadruplex ligand, and a G-quadruplex sequence (PW17).
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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
| | - Na Sun
- 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
| | - Lu Zhou
- 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
| | - Xing Chen
- 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
| | - Qinglin 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
| | - Kewei 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 450001
- 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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6
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Ren J, Wang T, Wang E, Wang J. Versatile G-quadruplex-mediated strategies in label-free biosensors and logic systems. Analyst 2015; 140:2556-72. [DOI: 10.1039/c4an02282c] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This review addresses how G-quadruplex (G4)-mediated biosensors convert the events of target recognition into a measurable physical signal. The application of label-free G4-strategies in the construction of logic systems is also discussed.
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Affiliation(s)
- Jiangtao Ren
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Tianshu Wang
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Jin Wang
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
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Wang Y, Chen J, Chen Y, Li W, Yu C. Polymer-Induced Perylene Probe Excimer Formation and Selective Sensing of DNA Methyltransferase Activity through the Monomer–Excimer Transition. Anal Chem 2014; 86:4371-8. [DOI: 10.1021/ac500195u] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Yan Wang
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People’s Republic of China
- University of the Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Jian Chen
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People’s Republic of China
| | - Yang Chen
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People’s Republic of China
| | - Wenying Li
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People’s Republic of China
- University of the Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Cong Yu
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People’s Republic of China
- University of the Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
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8
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Chen J, Liao D, Wang Y, Zhou H, Li W, Yu C. Real-time fluorometric assay for acetylcholinesterase activity and inhibitor screening through the pyrene probe monomer-excimer transition. Org Lett 2013; 15:2132-5. [PMID: 23590426 DOI: 10.1021/ol400619t] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A choline labeled pyrene probe (Py-Ch) was designed and synthesized. Poly(vinylsulfonate) (PVS) could induce Py-Ch aggregation. The aggregation and deaggregation process could be finely controlled by the acetylcholinesterase (AChE) enzymatic hydrolysis of Py-Ch. The resulting excimer-monomer transition provided a facile way for real-time AChE activity fluorometric assay and inhibitor screening.
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Affiliation(s)
- Jian Chen
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, PR China
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Sun H, Li X, Li Y, Fan L, Kraatz HB. A novel colorimetric potassium sensor based on the substitution of lead from G-quadruplex. Analyst 2013; 138:856-62. [DOI: 10.1039/c2an36564b] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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10
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Yang Y, Li W, Qi H, Zhang Q, Chen J, Wang Y, Wang B, Wang S, Yu C. Detection of silver(I) ions based on the controlled self-assembly of a perylene fluorescence probe. Anal Biochem 2012; 430:48-52. [PMID: 22864232 DOI: 10.1016/j.ab.2012.07.024] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2012] [Revised: 07/23/2012] [Accepted: 07/24/2012] [Indexed: 11/25/2022]
Abstract
In the current work, we report a label-free fluorescence turn-on approach for the sensitive and selective sensing of Ag(+). A cationic perylene derivative, compound A, was used as the fluorescence probe. Compound A monomer is strongly fluorescent, and the fluorescence can be efficiently quenched through self-aggregation (self-assembly). A cytosine (C)-rich oligonucleotide, oligo-C, was employed. In the absence of Ag(+), oligo-C induced strong compound A aggregation due to electrostatic interactions in aqueous media, and very weak fluorescence signal was detected. However, in the presence of Ag(+), the specific interactions between oligo-C and Ag(+) induced hairpin structure formation of oligo-C through C-Ag(+)-C bonding interactions. Oligo-C binding to compound A aggregates was weakened; therefore, compound A monomer could be released and detected. The intensity of the fluorescence signal was directly related to the amount of Ag(+) added to the assay solution. Our method is highly sensitive-a limit of detection of 5nM was obtained-and also very selective. Ag(+) detection in complex sample mixtures was also demonstrated.
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Affiliation(s)
- Yue Yang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, People's Republic of China
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Kim B, Jung IH, Kang M, Shim HK, Woo HY. Cationic conjugated polyelectrolytes-triggered conformational change of molecular beacon aptamer for highly sensitive and selective potassium ion detection. J Am Chem Soc 2012; 134:3133-8. [PMID: 22280349 DOI: 10.1021/ja210360v] [Citation(s) in RCA: 151] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We demonstrate highly sensitive and selective potassium ion detection against excess sodium ions in water, by modulating the interaction between the G-quadruplex-forming molecular beacon aptamer (MBA) and cationic conjugated polyelectrolyte (CPE). The K(+)-specific aptamer sequence in MBA is used as the molecular recognition element, and the high binding specificity of MBA for potassium ions offers selectivity against a range of metal ions. The hairpin-type MBA labeled with a fluorophore and quencher at both termini undergoes a conformational change (by complexation with CPEs) to either an open-chain form or a G-quadruplex in the absence or presence of K(+) ions. Conformational changes of MBA as well as fluorescence (of the fluorophore in MBA) quenching or amplification via fluorescence resonance energy transfer from CPEs provide clear signal turn-off and -on in the presence or absence of K(+). The detection limit of the K(+) assays is determined to be ~1.5 nM in the presence of 100 mM Na(+) ions, which is ~3 orders of magnitude lower than those reported previously. The successful detection of 5'-adenosine triphosphate (ATP) with the MBA containing an ATP-specific aptamer sequence is also demonstrated using the same sensor scheme. The scheme reported herein is applicable to the detection of other kinds of G-rich aptamer-binding chemicals and biomolecules.
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Affiliation(s)
- Boram Kim
- Department of Nano Fusion Technology, Pusan National University, Miryang 627-706, Republic of Korea
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Ju E, Yang X, Lin Y, Pu F, Ren J, Qu X. Exonuclease-aided amplification for label-free and fluorescence turn-on DNA detection based on aggregation-induced quenching. Chem Commun (Camb) 2012; 48:11662-4. [DOI: 10.1039/c2cc37039e] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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13
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Wang B, Zhu Q, Liao D, Yu C. Perylene probe induced gold nanoparticle aggregation. ACTA ACUST UNITED AC 2011. [DOI: 10.1039/c0jm04527f] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Zhou Y, Deng M, Du Y, Yan S, Huang R, Weng X, Yang C, Zhang X, Zhou X. A novel cationic triazatetrabenzcorrole: selective detection of mercury(II) by nucleic acid-induced aggregation. Analyst 2010; 136:955-61. [PMID: 21157605 DOI: 10.1039/c0an00927j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the present work, a novel water-soluble cationic triazatetrabenzcorrole compound was synthesised. Its aggregation and fluorescence quenching properties are demonstrated by serval methods, such as UV-vis and fluorescence spectroscopic studies and naked-eye visualization. Unlike the traditional Hg(2+) sensor based on thymine-Hg(2+)-thymine, we use a novel approach, exploiting the high affinity of Hg(2+) for sulfur in phosphorothioate DNA. Based on the S-Hg(2+)-S pairs, we designed the phosphorothioate DNA T4G4-S3 as an Hg(2+) sensor, which can detect Hg(2+) sensitively and selectively in aqueous solution. And this sensing system is fairly fast and convenient.
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Affiliation(s)
- Yangyang Zhou
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei, Wuhan, 430072, P. R. of China
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