1
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Ertl FJ, Kopanchuk S, Dijon NC, Veikšina S, Tahk MJ, Laasfeld T, Schettler F, Gattor AO, Hübner H, Archipowa N, Köckenberger J, Heinrich MR, Gmeiner P, Kutta RJ, Holliday ND, Rinken A, Keller M. Dually Labeled Neurotensin NTS 1R Ligands for Probing Radiochemical and Fluorescence-Based Binding Assays. J Med Chem 2024. [PMID: 39261089 DOI: 10.1021/acs.jmedchem.4c01470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
Abstract
The determination of ligand-receptor binding affinities plays a key role in the development process of pharmaceuticals. While the classical radiochemical binding assay uses radioligands, fluorescence-based binding assays require fluorescent probes. Usually, radio- and fluorescence-labeled ligands are dissimilar in terms of structure and bioactivity, and can be used in either radiochemical or fluorescence-based assays. Aiming for a close comparison of both assay types, we synthesized tritiated fluorescent neurotensin receptor ligands ([3H]13, [3H]18) and their nontritiated analogues (13, 18). The labeled probes were studied in radiochemical and fluorescence-based (high-content imaging, flow cytometry, fluorescence anisotropy) binding assays. Equilibrium saturation binding yielded well-comparable ligand-receptor affinities, indicating that all these setups can be used for the screening of new drugs. In contrast, discrepancies were found in the kinetic behavior of the probes, which can be attributed to technical differences of the methods and require further studies with respect to the elucidation of the underlying mechanisms.
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Affiliation(s)
- Fabian J Ertl
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraβe 31, D-93053 Regensburg, Germany
| | - Sergei Kopanchuk
- Institute of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia
| | - Nicola C Dijon
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, U.K
| | - Santa Veikšina
- Institute of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia
| | - Maris-Johanna Tahk
- Institute of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia
| | - Tõnis Laasfeld
- Institute of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia
| | - Franziska Schettler
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraβe 31, D-93053 Regensburg, Germany
| | - Albert O Gattor
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraβe 31, D-93053 Regensburg, Germany
| | - Harald Hübner
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich Alexander University, Nikolaus-Fiebiger-Straβe 10, D-91058 Erlangen, Germany
| | - Nataliya Archipowa
- Institute of Biophysics and Physical Biochemistry, Faculty of Biology and Preclinical Medicine, University of Regensburg, Universitätsstraβe 31, D-93053 Regensburg, Germany
| | - Johannes Köckenberger
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich Alexander University, Nikolaus-Fiebiger-Straβe 10, D-91058 Erlangen, Germany
| | - Markus R Heinrich
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich Alexander University, Nikolaus-Fiebiger-Straβe 10, D-91058 Erlangen, Germany
| | - Peter Gmeiner
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich Alexander University, Nikolaus-Fiebiger-Straβe 10, D-91058 Erlangen, Germany
| | - Roger J Kutta
- Institute of Physical and Theoretical Chemistry, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraβe 31, D-93053 Regensburg, Germany
| | - Nicholas D Holliday
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, U.K
| | - Ago Rinken
- Institute of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia
| | - Max Keller
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraβe 31, D-93053 Regensburg, Germany
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2
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Archipowa N, Wittmann L, Köckenberger J, Ertl FJ, Gleixner J, Keller M, Heinrich MR, Kutta RJ. Characterization of Fluorescent Dyes Frequently Used for Bioimaging: Photophysics and Photocatalytical Reactions with Proteins. J Phys Chem B 2023; 127:9532-9542. [PMID: 37903729 DOI: 10.1021/acs.jpcb.3c04484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Derivatives of the rhodamine-based dye 5-TAMRA (5-carboxy-tetramethylrhodamine) and the indocarbocyanine-type Cy3B (cyclized derivative of the cyanine dye Cy3), both representing important fluorophores frequently used for the labeling of biomolecules (proteins, nucleic acids) and bioactive compounds, such as receptor ligands, were photophysically investigated in aqueous solution, i.e., in neat phosphate-buffered saline (PBS) and in PBS supplemented with 1 wt % bovine serum albumin (BSA). The dyes exhibit comparable absorption (λabs,max: 550-569 nm) and emission wavelengths (λem,max: 580-582 nm), and similar S1 lifetimes (2.27-2.75 ns), and their excited state deactivation proceeds mainly via the lowest excited singlet state (triplet quantum yield ca. 1%). However, the probes show marked differences with respect to their fluorescence quantum yield and photostability. While 5-TAMRA shows a lower quantum yield (37-39%) than the Cy3B derivative (ca. 57%), its photostability is considerably higher compared to Cy3B. Generally, the impact of the protein on the photophysics is low. However, on prolonged illumination, both fluorescent dyes undergo a photocatalytic reaction with tryptophan residues of BSA mediated by sensitized singlet oxygen resulting in a tryptophan photoproduct with an absorption maximum around 330 nm. The overall results of this work will assist in choosing the right dye for the labeling of bioactive compounds, and the study demonstrates that experiments performed with 5-TAMRA or Cy3B-labeled compounds in a biological environment may be influenced by photochemical modification of experimentally relevant proteins at aromatic amino acid residues.
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Affiliation(s)
- Nataliya Archipowa
- Institute of Biophysics and Physical Biochemistry, Faculty of Biology and Preclinical Medicine, University of Regensburg, D-93053 Regensburg, Germany
| | - Lukas Wittmann
- Institute of Physical and Theoretical Chemistry, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Johannes Köckenberger
- Department of Chemistry and Pharmacy, Molecular and Clinical Pharmacy, Friedrich-Alexander-University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, D-91058 Erlangen, Germany
| | - Fabian J Ertl
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Jakob Gleixner
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Max Keller
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Markus R Heinrich
- Department of Chemistry and Pharmacy, Molecular and Clinical Pharmacy, Friedrich-Alexander-University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, D-91058 Erlangen, Germany
| | - Roger Jan Kutta
- Institute of Physical and Theoretical Chemistry, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
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3
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Müller C, Gleixner J, Tahk MJ, Kopanchuk S, Laasfeld T, Weinhart M, Schollmeyer D, Betschart MU, Lüdeke S, Koch P, Rinken A, Keller M. Structure-Based Design of High-Affinity Fluorescent Probes for the Neuropeptide Y Y 1 Receptor. J Med Chem 2022; 65:4832-4853. [PMID: 35263541 DOI: 10.1021/acs.jmedchem.1c02033] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The recent crystallization of the neuropeptide Y Y1 receptor (Y1R) in complex with the argininamide-type Y1R selective antagonist UR-MK299 (2) opened up a new approach toward structure-based design of nonpeptidic Y1R ligands. We designed novel fluorescent probes showing excellent Y1R selectivity and, in contrast to previously described fluorescent Y1R ligands, considerably higher (∼100-fold) binding affinity. This was achieved through the attachment of different fluorescent dyes to the diphenylacetyl moiety in 2 via an amine-functionalized linker. The fluorescent ligands exhibited picomolar Y1R binding affinities (pKi values of 9.36-9.95) and proved to be Y1R antagonists, as validated in a Fura-2 calcium assay. The versatile applicability of the probes as tool compounds was demonstrated by flow cytometry- and fluorescence anisotropy-based Y1R binding studies (saturation and competition binding and association and dissociation kinetics) as well as by widefield and total internal reflection fluorescence (TIRF) microscopy of live tumor cells, revealing that fluorescence was mainly localized at the plasma membrane.
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Affiliation(s)
- Christoph Müller
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Jakob Gleixner
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Maris-Johanna Tahk
- Institute of Chemistry, Faculty of Bioorganic Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia
| | - Sergei Kopanchuk
- Institute of Chemistry, Faculty of Bioorganic Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia
| | - Tõnis Laasfeld
- Institute of Chemistry, Faculty of Bioorganic Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia
| | - Michael Weinhart
- Institute of Inorganic Chemistry, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Dieter Schollmeyer
- Department of Chemistry, Johannes-Gutenberg-University Mainz, Düsbergweg 10-14, 55099 Mainz, Germany
| | - Martin U Betschart
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany
| | - Steffen Lüdeke
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany
| | - Pierre Koch
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Ago Rinken
- Institute of Chemistry, Faculty of Bioorganic Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia
| | - Max Keller
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
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4
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Li Y, Zhang N, Wang H, Zhao Q. Fluorescence Anisotropy-Based Signal-Off and Signal-On Aptamer Assays Using Lissamine Rhodamine B as a Label for Ochratoxin A. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:4277-4283. [PMID: 32182058 DOI: 10.1021/acs.jafc.0c00549] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Ochratoxin A (OTA), a common mycotoxin, has attracted great concern as many foodstuffs can suffer from OTA contamination; OTA causes harmful effects on human and animals. Rapid and sensitive detection of OTA is demanded in many fields for agricultural product quality, food safety, and health. Aptamer fluorescence polarization/anisotropy (FP/FA) assays integrate advantages of nucleic acid aptamers (e.g., easy preparation, high stability, and low cost) and FP/FA analysis (e.g., high sensitivity, rapidity, simplicity, and robustness). Here, we report the preparation of lissamine rhodamine B labeled OTA and developed competitive aptamer fluorescence anisotropy (FA) assays for OTA with signal-off or signal-on responses by using this fluorescently labeled probe. In the signal-off FA assay, the binding between the fluorescent probe and aptamer gave a large FA signal due to molecular volume increase, and the fluorescent probe was displaced from the aptamer in the presence of OTA target, causing FA to decrease. To further enhance the FA change in the signal-off assay, large-sized streptavidin was conjugated on the aptamer, and this assay allowed for a detection limit of 2.5 nM and a more remarkable FA decrease. Furthermore, we found that the fluorescent probe could interact with Tween 20, which caused the fluorescent probe to show a higher FA value than that of the aptamer-fluorescent probe complex. A signal-on FA assay was achieved in the binding buffer containing 0.1% Tween 20, with a detection limit of 10 nM. Signal-off and signal-on FA methods both were selective and enabled detection of OTA spiked in red wine samples, showing capability for target analysis in complex sample matrix.
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Affiliation(s)
- Yapiao Li
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ning Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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5
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Byun WG, Lim D, Park SB. Discovery of Small-Molecule Modulators of Protein-RNA Interactions by Fluorescence Intensity-Based Binding Assay. Chembiochem 2019; 21:818-824. [PMID: 31587454 DOI: 10.1002/cbic.201900467] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 10/04/2019] [Indexed: 12/18/2022]
Abstract
Protein-RNA interactions mediate various cellular processes, the dysregulation of which has been associated with a list of diseases. Thus, novel experimental tools for monitoring protein-RNA interactions are highly desirable to identify new chemical modulators of these therapeutic targets. In this study, we constructed simple fluorescence intensity-based protein-RNA binding assays by testing multiple environment-sensitive organic fluorophores. We selected the oncogenic interaction between Lin28 and the let-7 microRNA and the important immunomodulatory Roquin-Tnf CDE interaction as representative targets. We adapted this assay to high-throughput screening for the identification of pyrazolyl thiazolidinedione-type molecules as potent small-molecule inhibitors of protein-microRNA interactions. We clearly showed the structure-activity relationships of this new class of Lin28-let-7 interaction inhibitors, and confirmed that cellular mature let-7 microRNAs and their target genes could be modulated upon treatment with the pyrazolyl thiazolidinedione-type inhibitor. We expect that our simple and adaptable screening approach can be applied for the development of various assay systems aimed at the identification of bioactive small molecules targeting protein-RNA interactions.
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Affiliation(s)
- Wan Gi Byun
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, South Korea
| | - Donghyun Lim
- Department of Biophysics and Chemical Biology, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, South Korea
| | - Seung Bum Park
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, South Korea.,Department of Biophysics and Chemical Biology, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, South Korea
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6
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Li Y, Zhao Q. Aptamer Structure Switch Fluorescence Anisotropy Assay for Small Molecules Using Streptavidin as an Effective Signal Amplifier Based on Proximity Effect. Anal Chem 2019; 91:7379-7384. [PMID: 31079453 DOI: 10.1021/acs.analchem.9b01253] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Fluorescence polarization/anisotropy (FP/FA) approaches are appealing for targets sensing in homogeneous solution due to simplicity, reproducibility and sensitivity. Taking advantage of aptamers, aptamer structure switch FA methods are unique for small molecule detection based on the competition between aptamer-target binding and the hybridization of aptamer and complementary DNA (cDNA). However, usually small FA change is generated in these aptamer assays that only rely on size change caused by hybridization of an oligonucleotide because of the rapid local rotation of fluorophores and small mass change. Here we describe a simple and general aptamer structure switch FA assay for small molecules by employing a large-sized streptavidin (SA) as an effective signal amplifier based on proximity effect to reduce local rotation of fluorophore. In this design, the SA-labeled cDNA hybridizes with fluorescein (FAM)-labeled aptamer, drawing FAM close to SA and bringing a much higher FA value due to restricted local rotation of FAM. Small molecule-aptamer probe binding causes displacement of the SA-labeled cDNA and great decrease of FA. The closeness of SA to FAM in the duplex is key for this proposed strategy to produce large FA changes in target detection. Our method enabled to detect 60 pM aflatoxin B1 (AFB1), 1 nM ochratoxin A (OTA), and 0.5 μM adenosine triphosphate (ATP), respectively. This aptamer FA method combines the merits of aptamers and FA analysis, and it is promising in applications of detection of small molecules with good sensitivity.
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Affiliation(s)
- Yapiao Li
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing 100085 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Qiang Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing 100085 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
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7
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NIR-Fluorescent Multidye Silica Nanoparticles with Large Stokes Shifts for Versatile Biosensing Applications. J Fluoresc 2019; 29:293-305. [PMID: 30613851 DOI: 10.1007/s10895-018-02339-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 12/26/2018] [Indexed: 02/07/2023]
Abstract
We have synthesized and characterized of a series of single and multidye copolymerized nanoparticles with large to very large Stokes shifts (100 to 255 nm) for versatile applications as standalone or multiplexed probes in biological matrices. Nanoparticles were prepared via the Stöber method and covalently copolymerized with various combinations of three dyes, including one novel aminocyanine dye. Covalently encapsulated dyes exhibited no significant leakage from the nanoparticle matrix after more than 200 days of storage in ethanol. Across multiple batches of nanoparticles with varying dye content, the average yields and average radii were found to be highly reproducible. Furthermore, the batch to batch variability in the relative amounts of dye incorporated was small (relative standard deviations <2.3%). Quantum yields of dye copolymerized nanoparticles were increased 50% to 1000% relative to those of their respective dye-silane conjugates, and fluorescence intensities were enhanced by approximately three orders of magnitude. Prepared nanoparticles were surface modified with polyethylene glycol and biotin and bound to streptavidin microspheres as a proof of concept. Under single wavelength excitation, microsphere-bound nanoparticles displayed readily distinguishable fluorescence signals at three different emission wavelengths, indicating their potential applications to multicolor sensing. Furthermore, nanoparticles modified with polyethylene glycol and biotin demonstrated hematoprotective qualities and reduced nonspecific binding of serum proteins, indicating their potential suitability to in vivo imaging applications.
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8
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Wasin T, Enomoto K, Sakurai T, Padalkar VS, Cheng HL, Tang MT, Horio A, Sakamaki D, Omichi M, Saeki A, Kikuchi K, Hori Y, Chiba A, Saito Y, Kamiya T, Sugimoto M, Seki S. Fabrication of “Clickable” Polyfluorene Nanowires with High Aspect Ratio as Biological Sensing Platforms. ACS Sens 2016. [DOI: 10.1021/acssensors.6b00070] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Tuchinda Wasin
- Department
of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
- International
College, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Kazuyuki Enomoto
- International
College, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Tsuneaki Sakurai
- Department
of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Vikas S. Padalkar
- Department
of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Hoi Lok Cheng
- International
College, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Michael T. Tang
- International
College, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Akifumi Horio
- Department
of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Daisuke Sakamaki
- Department
of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Masaaki Omichi
- Department
of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
| | - Akinori Saeki
- Department
of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
| | - Kazuya Kikuchi
- Department
of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
- Department
of Material and Life Science, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
| | - Yuichiro Hori
- Department
of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
- Department
of Material and Life Science, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
| | - Atsuya Chiba
- Quantum
Beam Science
Research Directorate (QuBS), National Institutes for Quantum and Radiological
Science and Technology (QST), 1233,
Watanuki-machi, Takasaki, Gunma 370-1292, Japan
| | - Yuichi Saito
- Quantum
Beam Science
Research Directorate (QuBS), National Institutes for Quantum and Radiological
Science and Technology (QST), 1233,
Watanuki-machi, Takasaki, Gunma 370-1292, Japan
| | - Tomihiro Kamiya
- Quantum
Beam Science
Research Directorate (QuBS), National Institutes for Quantum and Radiological
Science and Technology (QST), 1233,
Watanuki-machi, Takasaki, Gunma 370-1292, Japan
| | - Masaki Sugimoto
- Quantum
Beam Science
Research Directorate (QuBS), National Institutes for Quantum and Radiological
Science and Technology (QST), 1233,
Watanuki-machi, Takasaki, Gunma 370-1292, Japan
| | - Shu Seki
- Department
of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
- International
College, Osaka University, Toyonaka, Osaka 560-0043, Japan
- Department
of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
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9
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You Y, Tataurov AV, Owczarzy R. Measuring thermodynamic details of DNA hybridization using fluorescence. Biopolymers 2011; 95:472-86. [PMID: 21384337 PMCID: PMC3082624 DOI: 10.1002/bip.21615] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2010] [Revised: 01/31/2011] [Accepted: 02/21/2011] [Indexed: 11/11/2022]
Abstract
Modern real-time PCR systems make it easy to monitor fluorescence while temperature is varied for hundreds of samples in parallel, permitting high-throughput studies. We employed such system to investigate melting transitions of ordered nucleic acid structures into disordered random coils. Fluorescent dye and quencher were attached to oligonucleotides in such a way that changes of fluorescence intensity with temperature indicated progression of denaturation. When fluorescence melting data were compared with traditional ultraviolet optical experiments, commonly used dye/quencher combinations, like fluorescein and tetramethylrhodamine, showed substantial discrepancies. We have therefore screened 22 commercially available fluorophores and quenchers for their ability to reliably report annealing and melting transitions. Dependence of fluorescence on temperature and pH was also investigated. The optimal performance was observed using Texas Red or ROX dyes with Iowa Black RQ or Black Hole quenchers. These labels did not alter two-state nature of duplex melting process and provided accurate melting temperatures, free energies, enthalpies, and entropies. We also suggest a new strategy for determination of DNA duplex thermodynamics where concentration of a dye-labeled strand is kept constant and its complementary strand modified with a quencher is added at increasing excess. These methodological improvements will help build predictive models of nucleic acid hybridization. © 2011 Wiley Periodicals, Inc. Biopolymers 95: 472–486, 2011.
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Affiliation(s)
- Yong You
- Department of Molecular Genetics and Biophysics, Integrated DNA Technologies, Coralville, IA, USA
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10
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Nardo L, Bondani M, Andreoni A. DNA-ligand binding mode discrimination by characterizing fluorescence resonance energy transfer through lifetime measurements with picosecond resolution. Photochem Photobiol 2008; 84:101-10. [PMID: 18173709 DOI: 10.1111/j.1751-1097.2007.00204.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe a method for distinguishing between minor groove binders and base intercalators that is based on measurements of the fluorescence lifetime of a donor (D) in the presence of an acceptor (A). The D-A pair is separated by a short double helix DNA with which the ligands interact. By plotting the D fluorescence lifetime as a function of the ligand-to-base pair concentration ratio we find a clear signature that distinguishes between the two binding mechanisms: minor groove binding induces an asymptotic decrease of the D fluorescence lifetime, while intercalation gives a monotonically increasing lifetime and the appearance of an additional short lifetime. We assayed Quinacrine, Hoechst and 4'-6'diamidine-2-phenyl indole, which in control experiments performed on oligodeoxyribonucleotides (oligos) lacking the A are demonstrated not to interfere with the D fluorescence. The changes in fluorescence lifetimes measured in the case of dual-labeled oligos are thus caused by structural changes in the DNA that modify the D-A distance. The appearance of the short-lived transient in the fluorescence decay of Ds attached to dual-labeled oligos upon binding of an intercalator can be interpreted as denaturation.
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Affiliation(s)
- Luca Nardo
- Dipartimento di Fisica e Matematica, Universita' degli Studi dell'Insubria, Como, Italy.
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