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Hanczyc P. Role of Alkali Cations in DNA-Thioflavin T Interaction. J Phys Chem B 2024; 128:7520-7529. [PMID: 38833533 PMCID: PMC11317975 DOI: 10.1021/acs.jpcb.4c02417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 05/20/2024] [Accepted: 05/22/2024] [Indexed: 06/06/2024]
Abstract
This study investigates the role of alkali cations in modulating the interaction between deoxyribonucleic acid (DNA) and Thioflavin T (ThT) in dilute and condensed phases. The emission characteristics of ThT were analyzed in the presence of double-stranded DNA and G-quadruplex structures with a focus on the effects of four cations: sodium, potassium, calcium, and magnesium. The ThT emission in double-stranded DNA was influenced by direct DNA binding and steric hindrance within the hydration shell of DNA, which was modulated by the presence of alkali cations. Lasing spectroscopy experiments further highlighted ThT sensitivity to the spatial arrangement of water molecules in the DNA hydration shell. Lasing was exclusively observed in the presence of Mg2+ in the G-quadruplex structure, suggesting that the parallel propeller configuration of G4 provides an optimal environment for ThT light amplification. This study highlights the critical role of cations in DNA-dye interactions and reaffirms the significance of ThT in biophysical studies.
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Affiliation(s)
- P. Hanczyc
- Institute of Experimental
Physics, Faculty of Physics, University
of Warsaw, Pasteura 5, Warsaw 02-093, Poland
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2
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Takahashi M, Norden B. Linear Dichroism Measurements for the Study of Protein-DNA Interactions. Int J Mol Sci 2023; 24:16092. [PMID: 38003280 PMCID: PMC10671323 DOI: 10.3390/ijms242216092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/04/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Linear dichroism (LD) is a differential polarized light absorption spectroscopy used for studying filamentous molecules such as DNA and protein filaments. In this study, we review the applications of LD for the analysis of DNA-protein interactions. LD signals can be measured in a solution by aligning the sample using flow-induced shear force or a strong electric field. The signal generated is related to the local orientation of chromophores, such as DNA bases, relative to the filament axis. LD can thus assess the tilt and roll of DNA bases and distinguish intercalating from groove-binding ligands. The intensity of the LD signal depends upon the degree of macroscopic orientation. Therefore, DNA shortening and bending can be detected by a decrease in LD signal intensity. As examples of LD applications, we present a kinetic study of DNA digestion by restriction enzymes and structural analyses of homologous recombination intermediates, i.e., RecA and Rad51 recombinase complexes with single-stranded DNA. LD shows that the DNA bases in these complexes are preferentially oriented perpendicular to the filament axis only in the presence of activators, suggesting the importance of organized base orientation for the reaction. LD measurements detect DNA bending by the CRP transcription activator protein, as well as by the UvrB DNA repair protein. LD can thus provide information about the structures of protein-DNA complexes under various conditions and in real time.
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Affiliation(s)
- Masayuki Takahashi
- School of Life Science and Technology, Tokyo Institute of Technology, Oookayama, Meguro, Tokyo 152-8550, Japan
| | - Bengt Norden
- Department of Chemical and Biological Engineering, Chemistry, Chalmers University of Technology, 412 96 Gothenburg, Sweden;
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3
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Deng ZY, Hu Z, Feng HJ. Dynamic interplay between thionine and DNA under carbon ion irradiation: a real-time first-principles study. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2022; 51:025101. [PMID: 36327460 DOI: 10.1088/1361-648x/ac9fff] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
Understanding the interactions between deoxyribonucleic acid (DNA) and photosensitizer under ion irradiation benefits the development of aptasensors, DNA biosensors and cancer diagnosis. Using real-time time-depended density functional theory, by simulating high-energy C ion passing through DNA with poly(dG)·poly(dC) sequence and that with embedded thionine (3,7-diamino-5-phenothiazinium, TH), we compared the electronic stopping power (ESP), evolution of the structure and charge, and absorption spectrum. TH inserting leads the increase in space charge density, a larger electron de-excitation and a larger ESP, but the speed corresponding to the maximum ESP is almost same. When C ion passes through TH-DNA, the structure of TH slightly changes and there still exists noncovalent interaction between TH and DNA, but the absorption coefficient depends on the electron occupied state of TH when the ion passes through. These results indicate that at low radiation doses, TH still can be a DNA detector, although its response wavelength and intensity have been slightly changed, and provide a theoretical reference to improve the possible application of phenothiazine dye in DNA biosensor under ion irradiation.
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Affiliation(s)
- Zun-Yi Deng
- School of Physics, Northwest University, Xi'an 710127, People's Republic of China
| | - Zhihua Hu
- School of Physics, Northwest University, Xi'an 710127, People's Republic of China
| | - Hong-Jian Feng
- School of Physics, Northwest University, Xi'an 710127, People's Republic of China
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4
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Wang J, Yang Q, Liu H, Chen Y, Jiang W, Wang Y, Zeng H. A nanomaterial-free and thionine labeling-based lateral flow immunoassay for rapid and visual detection of the transgenic CP4-EPSPS protein. Food Chem 2022; 378:132112. [PMID: 35033711 DOI: 10.1016/j.foodchem.2022.132112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 12/14/2021] [Accepted: 01/06/2022] [Indexed: 12/28/2022]
Abstract
Nanomaterial-based lateral flow immunoassays (LFIAs) have been widely used for the on-site detection of genetically modified components. However, the practical applications are often limited by the complex matrix, such as in red samples. In this study, a thionine (Thi) labeling-based LFIA was developed for the first time to detect CP4-EPSPS protein. The optimal labeling concentration of Thi was 0.5 mg/mL, and the antibody could be rapidly coupled to Thi in 10 min. The visual limit of detection (vLOD) levels for transgenic soybean, sugar beet, and cotton containing the CP4-EPSPS protein reached 0.05%, 0.1%, and 0.1%, respectively, and had no interference from other proteins. After storage at 4 °C for three months, the LFIA sensitivity remained unchanged and showed good stability. This method could be used to screen and detect a variety of transgenic crops containing the CP4-EPSPS protein, and the results were consistent with the current standard assay. This study pioneered the development of an immunochromatographic method using Thi as a marker and applied it to the detection of the CP4-EPSPS protein in herbicide-tolerant transgenic crops. This provides a new method for the rapid immunoassay of Thi as a dye and has good prospects for practical application.
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Affiliation(s)
- Jinbin Wang
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China; Crops Ecological Environment Security Inspection and Supervision Center (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai 201106, China
| | - Qianwen Yang
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China; School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China
| | - Hua Liu
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China; Crops Ecological Environment Security Inspection and Supervision Center (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai 201106, China
| | - Yifan Chen
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China; Crops Ecological Environment Security Inspection and Supervision Center (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai 201106, China
| | - Wei Jiang
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China; Crops Ecological Environment Security Inspection and Supervision Center (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai 201106, China
| | - Yu Wang
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China; School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China
| | - Haijuan Zeng
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China; Crops Ecological Environment Security Inspection and Supervision Center (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai 201106, China.
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5
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Sochacka J, Pacholczyk M, Jeleń M, Morak-Młodawska B, Pluta K. Interaction of new tri-, tetra-, and pentacyclic azaphenothiazine derivatives with calf thymus DNA: Spectroscopic and molecular docking studies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 262:120105. [PMID: 34245970 DOI: 10.1016/j.saa.2021.120105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/03/2021] [Accepted: 06/21/2021] [Indexed: 06/13/2023]
Abstract
Azaphenothiazines (AZA), modified phenothiazine derivatives, have been reported to exhibit a wide spectrum of biological activities, including anticancer activities, but the mechanisms of their interactions with biomolecules are not fully recognized. In this work, the mode of interaction of selected AZA with calf thymus DNA was investigated using UV-Vis absorption, fluorescence spectroscopy (competition experiment with ethidium bromide, quenching of fluorescence) and molecular docking. The investigated AZA represent dipyrido[3,4-b;3'4'-e][1,4]thiazine, quino[3,2-b]benzo[1,4]thiazine and diquino[3,2-b;2',3'-e][1,4]thiazine possessing tricyclic, tetracyclic and pentacyclic ring system with the additional N,N-dimethylaminopropyl group at the nitrogen atom in the 1,4 thiazine ring. The results obtained from spectroscopic studies showed that AZA bind to DNA by insertion of a fragment of the fused rings system between the base pair stack in the double helix of DNA. In addition, the number of rings in the AZA structures seemed to be related to the strength of the interaction, because pentacyclic AZA (binding constant Kb = 6.31 × 106 L/mol) demonstrated 10-fold higher affinity towards DNA than the tetracyclic AZA and about 100-fold higher affinity than that of tricyclic AZA. The molecular docking results showed that the binding mode of AZA to DNA helix was an intercalation mode with the partial insertion of one planar part of the AZA structure (the pyridine or quinoline ring) into the neighboring bases of one of the DNA chains with additional hydrogen bonding with the minor groove through the positively charged N,N-dimethylaminopropyl group. Chemical potential (μ), chemical hardness (ƞ), electronegativity (χ) and the value of electrons transferred from one system to another (ΔN) calculated from the HOMO and LUMO energies by the density functional theory method indicated that AZA acted as the electron acceptors to the DNA bases.
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Affiliation(s)
- Jolanta Sochacka
- Department of General and Inorganic Chemistry, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, Jagiellońska 4, 41-200 Sosnowiec, Poland.
| | - Marcin Pacholczyk
- Silesian University of Technology, Department of Systems Biology and Engineering, Faculty of Automatic Control, Electronics and Computer Science, Akademicka 16, 44-100 Gliwice, Poland
| | - Małgorzata Jeleń
- Department of Organic Chemistry, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, Jagiellońska 4, 41-200 Sosnowiec, Poland
| | - Beata Morak-Młodawska
- Department of Organic Chemistry, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, Jagiellońska 4, 41-200 Sosnowiec, Poland
| | - Krystian Pluta
- Department of Organic Chemistry, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, Jagiellońska 4, 41-200 Sosnowiec, Poland
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6
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Solomon ML, Abendroth JM, Poulikakos LV, Hu J, Dionne JA. Fluorescence-Detected Circular Dichroism of a Chiral Molecular Monolayer with Dielectric Metasurfaces. J Am Chem Soc 2020; 142:18304-18309. [PMID: 33048539 DOI: 10.1021/jacs.0c07140] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Strong enhancement of molecular circular dichroism (CD) has the potential to enable efficient asymmetric photolysis, a method of chiral separation that has conventionally been impeded by insufficient yield and low enantiomeric excess. Here, we study experimentally how predicted enhancements in optical chirality density near resonant silicon nanodisks boost CD. We use fluorescence-detected circular dichroism (FDCD) spectroscopy to measure indirectly the differential absorption of circularly polarized light by a monolayer of optically active molecules functionalized to silicon nanodisk arrays. Importantly, the molecules and nanodisk antennas have spectrally coincident resonances, and our fluorescence technique allows us to deconvolute absorption in the nanodisks from the molecules. We find that enhanced FDCD signals depend on nanophotonic resonances, in good agreement with simulated differential absorption and optical chirality density, while no signal is detected from molecules adsorbed on featureless silicon surfaces. These results verify the potential of nanophotonic platforms to be used for asymmetric photolysis with lower energy requirements.
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Affiliation(s)
- Michelle L Solomon
- Materials Science and Engineering, Stanford University, 496 Lomita Mall, Stanford, California 94305, United States
| | - John M Abendroth
- Materials Science and Engineering, Stanford University, 496 Lomita Mall, Stanford, California 94305, United States
| | - Lisa V Poulikakos
- Materials Science and Engineering, Stanford University, 496 Lomita Mall, Stanford, California 94305, United States.,Mechanical and Aerospace Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Jack Hu
- Materials Science and Engineering, Stanford University, 496 Lomita Mall, Stanford, California 94305, United States
| | - Jennifer A Dionne
- Materials Science and Engineering, Stanford University, 496 Lomita Mall, Stanford, California 94305, United States
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7
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García-Mendiola T, Requena-Sanz S, Martínez-Periñán E, Bravo I, Pariente F, Lorenzo E. Influence of carbon nanodots on DNA-Thionine interaction. Application to breast cancer diagnosis. Electrochim Acta 2020. [DOI: 10.1016/j.electacta.2020.136522] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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8
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Electropolymerization of thionine as a stable film along with carbon nanotube for sensitive detection of tetracycline antibiotic drug. IRANIAN POLYMER JOURNAL 2020. [DOI: 10.1007/s13726-020-00788-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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9
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Purwanto MGM, Weisz K. NMR studies on oligonucleotide - Methylene blue conjugates targeting double-helical nucleic acids. Biophys Chem 2019; 257:106314. [PMID: 31862498 DOI: 10.1016/j.bpc.2019.106314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 11/30/2019] [Accepted: 12/03/2019] [Indexed: 10/25/2022]
Abstract
Methylene blue (MB) - nucleic acid interactions are of considerable interest due to the photosensitizing activity of the dye with potential applications in medicine and biotechnology. Covalent attachment of the MB to an oligonucleotide through a flexible heptamethylene linker enabled a positioning of the dye moiety to specific sites through triplex formation with a target duplex. NMR studies demonstrated interactions of MB with the nucleic acids. In sequences with the MB moiety facing the triplex-duplex junction with an alternating CG duplex overhang next to a T·A·T triple-helical tract, proton resonances experienced severe linebroadening upon MB binding and point to kinetically labile complexes with exchange among different binding modes. For sequences with the MB moiety facing a terminal T·A·T base triad of the triplex tract, structural heterogeneity decreased when compared to a triplex without MB attached to the third strand. Also, the thermal stability of the latter construct increased significantly in the presence of MB, indicating external end stacking as predominant binding mode. Without any obvious disruptions of sequential imino-imino NOE contacts within the triplex and duplex tracts, a most favorable intercalation between T·A·T base triples or CG base pairs is not supported by the present data under our experimental conditions.
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Affiliation(s)
| | - Klaus Weisz
- University of Surabaya, Faculty of Biotechnology, Surabaya, Indonesia; University of Greifswald, Institute of Biochemistry, 17489 Greifswald, Germany.
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10
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Tiravia M, Sabuzi F, Cirulli M, Pezzola S, Di Carmine G, Cicero DO, Floris B, Conte V, Galloni P. 3,7-Bis(N
-methyl-N
-phenylamino)phenothiazinium Salt: Improved Synthesis and Aggregation Behavior in Solution. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900504] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Martina Tiravia
- Department of Chemical Science and Technologies; University of Rome Tor Vergata; Via della Ricerca Scientifica snc 00133 Rome Italy
| | - Federica Sabuzi
- Department of Chemical Science and Technologies; University of Rome Tor Vergata; Via della Ricerca Scientifica snc 00133 Rome Italy
| | - Martina Cirulli
- Department of Chemical Science and Technologies; University of Rome Tor Vergata; Via della Ricerca Scientifica snc 00133 Rome Italy
- School of Biological and Chemical Sciences; Queen Mary University of London; Mile End Road E1 4NS London United Kingdom
| | - Silvia Pezzola
- BT-InnoVaChem srl; Via della Ricerca Scientifica snc 00133 Rome Italy
| | - Graziano Di Carmine
- Department of Chemical and Pharmaceutical Sciences; University of Ferrara; Via L. Borsari 4 44121 Ferrara Italy
| | - Daniel Oscar Cicero
- Department of Chemical Science and Technologies; University of Rome Tor Vergata; Via della Ricerca Scientifica snc 00133 Rome Italy
| | - Barbara Floris
- Department of Chemical Science and Technologies; University of Rome Tor Vergata; Via della Ricerca Scientifica snc 00133 Rome Italy
| | - Valeria Conte
- Department of Chemical Science and Technologies; University of Rome Tor Vergata; Via della Ricerca Scientifica snc 00133 Rome Italy
| | - Pierluca Galloni
- Department of Chemical Science and Technologies; University of Rome Tor Vergata; Via della Ricerca Scientifica snc 00133 Rome Italy
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11
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Tuite EM, Nordén B. Structural Heterogeneity in Polynucleotide-Facilitated Assembly of Phenothiazine Dyes. J Phys Chem B 2018; 122:2891-2899. [PMID: 29481085 DOI: 10.1021/acs.jpcb.7b12835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The assembly of stacked dyes on DNA is of interest for electron transfer, light harvesting, sensing, and catalysis applications. A combination of UV/vis absorption, linear dichroism (LD), and circular dichroism (CD) was applied to characterize thoroughly the aggregation with DNA of the phenothiazine dyes methylene blue, azure B, and thionine. Aggregates of each dye with [poly(dG-dC)]2, [poly(dA-dT)]2, and calf thymus DNA were explored at high dye:DNA binding ratios, where excess dye groove-binds after all intercalation sites are filled. The organization of the aggregates (dimers, trimers, and multimers) with polydeoxynucleotides displays a structural diversity that depends on DNA sequence, extent of methylation of dye exocyclic amine groups, and ionic strength. The dyes typically form right-handed H-aggregates having negative LD, consistent with stepped stacking along the minor groove. However, aggregates in some dye:DNA aggregates show left-handed chirality or positive LD, indicating unusual modes of aggregation such as formation of adventitious dimers between intercalated and minor groove bound dye. In terms of sequence-dependence, methylene blue shows more extensive aggregation with [poly(dA-dT)]2, while thionine aggregates more with [poly(dG-dC)]2. Azure B has distinctive behavior that is unlike either other dyes. Thus, although these phenothiazine dyes possess a common tricyclic framework, the organization of their polynucleotide-facilitated aggregates depends sensitively on the extent of methylation of the exocyclic amines.
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Affiliation(s)
- Eimer M Tuite
- School of Chemistry , Bedson Building , Newcastle University , Newcastle upon Tyne , NE1 7RU , U.K
| | - Bengt Nordén
- Department of Chemical and Biological Engineering , Chalmers University of Technology , Gothenburg S-41296 , Sweden
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