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Li C, Chen J, Man T, Chen B, Li J, Li Q, Yang X, Wan Y, Fan C, Shen J. DNA Framework-Engineered Assembly of Cyanine Dyes for Structural Identification of Nucleic Acids. JACS AU 2024; 4:1125-1133. [PMID: 38559725 PMCID: PMC10976577 DOI: 10.1021/jacsau.3c00826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 02/02/2024] [Accepted: 02/07/2024] [Indexed: 04/04/2024]
Abstract
DNA nanostructures serve as precise templates for organizing organic dyes, enabling the creation of programmable artificial photonic systems with efficient light-harvesting and energy transfer capabilities. However, regulating the organization of organic dyes on DNA frameworks remains a great challenge. In this study, we investigated the factors influencing the self-assembly behavior of cyanine dye K21 on DNA frameworks. We observed that K21 exhibited diverse assembly modes, including monomers, H-aggregates, J-aggregates, and excimers, when combined with DNA frameworks. By manipulating conditions such as the ion concentration, dye concentration, and structure of DNA frameworks, we successfully achieved precise control over the assembly modes of K21. Leveraging K21's microenvironment-sensitive fluorescence properties on DNA nanostructures, we successfully discriminated between the chirality and topology structures of physiologically relevant G-quadruplexes. This study provides valuable insights into the factors influencing the dynamic assembly behavior of organic dyes on DNA framework nanostructures, offering new perspectives for constructing functional supramolecular aggregates and identifying DNA secondary structures.
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Affiliation(s)
- Cong Li
- School
of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory,
Frontiers Science Center for Transformative Molecules and National
Center for Translational Medicine, Shanghai
Jiao Tong University, Shanghai 200240, China
| | - Jielin Chen
- School
of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory,
Frontiers Science Center for Transformative Molecules and National
Center for Translational Medicine, Shanghai
Jiao Tong University, Shanghai 200240, China
| | - Tiantian Man
- School
of Mechanical Engineering, Nanjing University
of Science and Technology, Nanjing 210094, China
| | - Bin Chen
- School
of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Jiang Li
- Institute
of Materiobiology, Department of Chemistry, College of Science, Shanghai University, Shanghai 200444, China
| | - Qian Li
- School
of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory,
Frontiers Science Center for Transformative Molecules and National
Center for Translational Medicine, Shanghai
Jiao Tong University, Shanghai 200240, China
| | - Xiurong Yang
- School
of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory,
Frontiers Science Center for Transformative Molecules and National
Center for Translational Medicine, Shanghai
Jiao Tong University, Shanghai 200240, China
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Ying Wan
- School
of Mechanical Engineering, Nanjing University
of Science and Technology, Nanjing 210094, China
| | - Chunhai Fan
- School
of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory,
Frontiers Science Center for Transformative Molecules and National
Center for Translational Medicine, Shanghai
Jiao Tong University, Shanghai 200240, China
| | - Jianlei Shen
- School
of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory,
Frontiers Science Center for Transformative Molecules and National
Center for Translational Medicine, Shanghai
Jiao Tong University, Shanghai 200240, China
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Abstract
While the application of cryogenic electron microscopy (cryo-EM) to helical polymers in biology has a long history, due to the huge number of helical macromolecular assemblies in viruses, bacteria, archaea, and eukaryotes, the use of cryo-EM to study synthetic soft matter noncovalent polymers has been much more limited. This has mainly been due to the lack of familiarity with cryo-EM in the materials science and chemistry communities, in contrast to the fact that cryo-EM was developed as a biological technique. Nevertheless, the relatively few structures of self-assembled peptide nanotubes and ribbons solved at near-atomic resolution by cryo-EM have demonstrated that cryo-EM should be the method of choice for a structural analysis of synthetic helical filaments. In addition, cryo-EM has also demonstrated that the self-assembly of soft matter polymers has enormous potential for polymorphism, something that may be obscured by techniques such as scattering and spectroscopy. These cryo-EM structures have revealed how far we currently are from being able to predict the structure of these polymers due to their chaotic self-assembly behavior.
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Affiliation(s)
- Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908, United States
| | - Ordy Gnewou
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Armin Solemanifar
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
- School of Chemical Engineering, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Vincent P Conticello
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908, United States
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Singh PK, Prabhune A, Ogale S. Pulsed Laser-Driven Molecular Self-assembly of Cephalexin: Aggregation-Induced Fluorescence and Its Utility as a Mercury Ion Sensor. Photochem Photobiol 2015; 91:1340-7. [DOI: 10.1111/php.12526] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 08/05/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Pradeep Kumar Singh
- Physical and Materials Chemistry Division; National Chemical Laboratory (NCL); Council of Scientific and Industrial Research (CSIR); Pashan Pune India
- Biochemical Sciences Division; National Chemical Laboratory (NCL); Council of Scientific and Industrial Research (CSIR); Pashan Pune India
| | - Asmita Prabhune
- Biochemical Sciences Division; National Chemical Laboratory (NCL); Council of Scientific and Industrial Research (CSIR); Pashan Pune India
| | - Satishchandra Ogale
- Physical and Materials Chemistry Division; National Chemical Laboratory (NCL); Council of Scientific and Industrial Research (CSIR); Pashan Pune India
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4
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Sun Z, Wang J, Wei H, Wang G, Jian Y, Luo S, Zhou Z. Spectroscopic Investigation of a Synthetic Cyanine Amine Derivative upon Various Scaffolds. ANAL LETT 2014. [DOI: 10.1080/00032719.2014.919505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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5
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Desai NK, Kolekar GB, Patil SR. Off–on fluorescent polyanthracene for recognition of ferric and fluoride ions in aqueous acidic media: application in pharmaceutical and environmental analysis. NEW J CHEM 2014. [DOI: 10.1039/c4nj00675e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The sensing mechanism of PAT as a fluorescent probe is illustrated using a band diagram and spectral results.
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Affiliation(s)
- Netaji K. Desai
- Fluorescence Spectroscopy Research Laboratory
- Department of Chemistry
- Shivaji University
- Kolhapur - 416 004, India
| | - Govind B. Kolekar
- Fluorescence Spectroscopy Research Laboratory
- Department of Chemistry
- Shivaji University
- Kolhapur - 416 004, India
| | - Shivajirao R. Patil
- Fluorescence Spectroscopy Research Laboratory
- Department of Chemistry
- Shivaji University
- Kolhapur - 416 004, India
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Zhang Y, Wang JH, Zheng W, Chen T, Tong QX, Li D. An ESIPT fluorescent dye based on HBI with high quantum yield and large Stokes shift for selective detection of Cys. J Mater Chem B 2014; 2:4159-4166. [DOI: 10.1039/c4tb00190g] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
DPIN shows prominent ESIPT emission even in protic/polar solvents, and is further employed as a sensor for selective detection of Cys.
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Affiliation(s)
- Ying Zhang
- Department of Chemistry
- School of Life Science and Technology
- Jinan University
- Guangzhou 510632, China
- Department of Chemistry and Research Institute for Biomedical and Advanced Materials
| | - Jun-Hao Wang
- Department of Chemistry and Research Institute for Biomedical and Advanced Materials
- Shantou University
- Guangdong 515063, China
| | - Wenjie Zheng
- Department of Chemistry
- School of Life Science and Technology
- Jinan University
- Guangzhou 510632, China
| | - Tianfeng Chen
- Department of Chemistry
- School of Life Science and Technology
- Jinan University
- Guangzhou 510632, China
| | - Qing-Xiao Tong
- Department of Chemistry and Research Institute for Biomedical and Advanced Materials
- Shantou University
- Guangdong 515063, China
| | - Dan Li
- Department of Chemistry and Research Institute for Biomedical and Advanced Materials
- Shantou University
- Guangdong 515063, China
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Zhu Q, Huang L, Chen Z, Zheng S, Lv L, Zhu Z, Cao D, Jiang H, Liu S. A New Series of C-6 Unsubstituted Tetrahydropyrimidines: Convenient One-Pot Chemoselective Synthesis, Aggregation-Induced and Size-Independent Emission Characteristics. Chemistry 2012. [DOI: 10.1002/chem.201203012] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Polymethine dyes as spectral-fluorescent probes for biomacromolecules. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2012. [DOI: 10.1016/j.jphotochemrev.2011.11.001] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Akimkin TM, Tatikolov AS, Panova IG, Yarmoluk SM. Spectral study of the noncovalent interaction of thiacarbocyanine dyes with hyaluronic acid. HIGH ENERGY CHEMISTRY 2011. [DOI: 10.1134/s0018143911060026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Li B, Qin C, Li T, Wang L, Dong S. Fluorescent switch constructed based on hemin-sensitive anionic conjugated polymer and its applications in DNA-related sensors. Anal Chem 2009; 81:3544-50. [PMID: 19344125 DOI: 10.1021/ac900110a] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Here, a fluorescent switch is constructed combining hemin, hemin aptamer, and a newly synthesized anionic conjugated polymer (ACP), poly(9,9-bis(6'-phosphatehexyl) fluorenealt-1,4-phenylene) sodium salt (PFHPNa/PFP). In the "off-state", the fluorescence of PFP is sensitively quenched by hemin, with a high K(sv) value of approximately 10(7). While in the "on-state", the formation of the aptamer/hemin complex recovers the fluorescence intensity. The fluorescent switch is sensitive and selective to hemin. To testify the universality and practicality of the fluorescent switch, a series of label-free DNA-related sensing platforms are developed, containing three DNA sensing strategies and one ATP recognition strategy. The fluorescent switch developed is simple, sensitive, and universal, which extends applications of the anionic conjugated polymers.
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Affiliation(s)
- Bingling Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Graduate School of Chinese Academy of Sciences, Changchun, 130022, People's Republic of China
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11
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ACHYUTHAN KE, McCLAIN JL, ZHOU Z, WHITTEN DG, BRANCH DW. Spectroscopic Analyses of the Noncovalent Self-Assembly of Cyanines upon Various Nucleic Acid Scaffolds. ANAL SCI 2009; 25:469-74. [DOI: 10.2116/analsci.25.469] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
| | - Jaime L. McCLAIN
- Biosensors and Nanomaterials Department, Sandia National Laboratories
| | - Zhijun ZHOU
- Department of Chemical and Nuclear Engineering, University of New Mexico
| | - David G. WHITTEN
- Department of Chemical and Nuclear Engineering, University of New Mexico
| | - Darren W. BRANCH
- Biosensors and Nanomaterials Department, Sandia National Laboratories
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Zhou Z, Tang Y, Whitten DG, Achyuthan KE. New high-throughput screening protease assay based upon supramolecular self-assembly. ACS APPLIED MATERIALS & INTERFACES 2009; 1:162-170. [PMID: 20355768 DOI: 10.1021/am800091h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
We previously demonstrated that the supramolecular self-assembly of cyanines could be useful for developing fluorescent enzymatic assays. We took that concept a step further by synthesizing a covalent adduct of the tetrapeptide Asp-Glu-Val-Asp (DEVD) and a cyanine (DEVD-cyanine). The DEVD-cyanine due to its canonical sequence was recognized and hydrolyzed by the proteases, Caspase-3 and -7 in 96- or 384-microwell plate reactions. The catalytically liberated cyanine self-assembled upon scaffolds of carboxymethylamylose (CMA), carboxymethylcellulose (CMC), or a mixture of CMA and CMC resulting in a J aggregate exhibiting bright fluorescence at a 470 nm emission wavelength (optimum signal/background using excitation wavelengths of 415-440 nm). The fluorescence intensity increased with enzyme and substrate concentrations or reaction time and exhibited classical saturation profiles of a rectangular hyperbola. Saturation of the reaction was at 30 U/mL (1 microg/mL) Caspase-3 and 250 microM DEVD-cyanine. The reaction kinetics was linear between 1 and 20 min and saturated at 60 min. The affinity constant (Km) for DEVD-cyanine was approximately 23 microM, similar to those of previously reported values for other DEVD substrates of Caspase-3. Maximal fluorescence emission was observed by using a mixture of CMA and CMC scaffolds at 65 and 35 microM, respectively. The reaction kinetics of Caspase-7 executed in a 384-well plate was similar to the reaction kinetics of Caspase-3 conducted in a 96-well plate. We believe that this is the first demonstration of a cyanine liberated from a covalent adduct due to protease action, leading to supramolecular self-assembly and the detection of protease activity.
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Affiliation(s)
- Zhijun Zhou
- Department of Chemical and Nuclear Engineering, The University of New Mexico, Albuquerque, New Mexico 87131, USA
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Nath A, Fernández C, Lampe JN, Atkins WM. Spectral resolution of a second binding site for Nile Red on cytochrome P4503A4. Arch Biochem Biophys 2008; 474:198-204. [PMID: 18395506 DOI: 10.1016/j.abb.2008.03.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2008] [Revised: 03/11/2008] [Accepted: 03/15/2008] [Indexed: 11/30/2022]
Abstract
Nile Red is sequentially metabolized by cytochrome P4503A4 to the N-monoethyl and N-desethyl products, which typifies the metabolism of many amine containing drugs. Sequential metabolism of a single substrate results in complex kinetics that confound predictive models of drug clearance. As a fluorescent model for drugs which undergo sequential metabolism, Nile Red provides the opportunity to monitor drug-CYP interactions wherein the fluorescent properties of Nile Red could, in principle, be exploited to determine individual rate and equilibrium constants for the individual reactions. Previously, it was shown that Nile Red binds at the active site and fluoresces (K(D) approximately 50nM) with maximum emission at approximately 620nm, but it was unclear whether a red-shifted emission, at approximately 660nm, consisted of only free Nile Red or Nile Red bound at a second site on the protein. Here, equilibrium binding studies, including 'reverse titrations' spanning low ratios of CYP3A4/Nile Red, indicate two binding sites for Nile Red with a contribution to the 'red emission' greater than can be accounted for by free Nile Red. Singular value decomposition affords basis spectra for both spectral components and fits well to the experimentally determined concentration dependence of Nile Red emission. In addition, the red spectral component, with an apparent K(D)=2.2muM, is selectively eliminated by titration with the known allosteric effectors of CYP3A4, alpha-napthoflavone and testosterone. Furthermore, the double mutant L2311F/D214E, previously demonstrated to perturb a peripheral allosteric site, lacks the red-emitting Nile Red binding site, but retains the blue-emitting site. Together these data indicate that a second Nile Red site competes with other effectors of CYP3A4 at a site that results in Nile Red emission at 660nm.
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Affiliation(s)
- Abhinav Nath
- Department of Medicinal Chemistry, University of Washington, Box 357610, Seattle, WA 98195-7610, USA
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