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Nagpal A, Tyagi N, Neelakandan PP. BODIPY-fused uracil: synthesis, photophysical properties, and applications. Photochem Photobiol Sci 2024; 23:365-376. [PMID: 38227134 DOI: 10.1007/s43630-023-00524-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 12/14/2023] [Indexed: 01/17/2024]
Abstract
Fluorescent nucleobase and nucleic acid analogs are important tools in chemical and molecular biology as fluorescent labelling of nucleobases has applications in cellular imaging and anti-tumor activity. Boron-dipyrromethene (BODIPY) dyes exhibiting high brightness and good photostability are extensively used as fluorescent labelling agents and as type II photosensitizers for photodynamic therapy. Thus, the combination of nucleobases and BODIPY to obtain new compounds with both anti-tumor activity and fluorescent imaging functions is the focus of our research. We synthesized two new nucleobase analogs 1 and 2 by fusing the BODIPY core directly with uracil which resulted in favorable photophysical properties and high emission quantum efficiencies particularly in organic solvents. Further, we explored the newly synthesized derivatives, which possessed good singlet oxygen generation efficiencies and bio-compatibility, as potential PDT agents and our results show that they exhibit in vitro anti-tumor activities.
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Affiliation(s)
- Ayushi Nagpal
- Institute of Nano Science and Technology, Knowledge City, Sector 81, Mohali, 140306, Punjab, India
| | - Nidhi Tyagi
- Institute of Nano Science and Technology, Knowledge City, Sector 81, Mohali, 140306, Punjab, India
| | - Prakash P Neelakandan
- Institute of Nano Science and Technology, Knowledge City, Sector 81, Mohali, 140306, Punjab, India.
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2
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Cell Uptake of Steroid-BODIPY Conjugates and Their Internalization Mechanisms: Cancer Theranostic Dyes. Int J Mol Sci 2023; 24:ijms24043600. [PMID: 36835012 PMCID: PMC9963437 DOI: 10.3390/ijms24043600] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/28/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023] Open
Abstract
Estradiol-BODIPY linked via an 8-carbon spacer chain and 19-nortestosterone- and testosterone-BODIPY linked via an ethynyl spacer group were evaluated for cell uptake in the breast cancer cell lines MCF-7 and MDA-MB-231 and prostate cancer cell lines PC-3 and LNCaP, as well as in normal dermal fibroblasts, using fluorescence microscopy. The highest level of internalization was observed with 11β-OMe-estradiol-BODIPY 2 and 7α-Me-19-nortestosterone-BODIPY 4 towards cells expressing their specific receptors. Blocking experiments showed changes in non-specific cell uptake in the cancer and normal cells, which likely reflect differences in the lipophilicity of the conjugates. The internalization of the conjugates was shown to be an energy-dependent process that is likely mediated by clathrin- and caveolae-endocytosis. Studies using 2D co-cultures of cancer cells and normal fibroblasts showed that the conjugates are more selective towards cancer cells. Cell viability assays showed that the conjugates are non-toxic for cancer and/or normal cells. Visible light irradiation of cells incubated with estradiol-BODIPYs 1 and 2 and 7α-Me-19-nortestosterone-BODIPY 4 induced cell death, suggesting their potential for use as PDT agents.
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Kaufmann J, Müller P, Andreadou E, Heckel A. Green‐Light Activatable BODIPY and Coumarin 5’‐Caps for Oligonucleotide Photocaging. Chemistry 2022; 28:e202200477. [PMID: 35420231 PMCID: PMC9322594 DOI: 10.1002/chem.202200477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Indexed: 12/02/2022]
Abstract
We synthesized two green‐light activatable 5’‐caps for oligonucleotides based on the BODIPY and coumarin scaffold. Both bear an alkyne functionality allowing their use in numerous biological applications. They were successfully incorporated in oligonucleotides via solid‐phase synthesis. Copper‐catalyzed alkyne‐azide cycloaddition (CuAAC) using a bisazide photo‐tether gave cyclic oligonucleotides that could be relinearized by activation with green light and were shown to exhibit high stability against exonucleases. Chemical ligation as another example for bioconjugation yielded oligonucleotides with an internal strand break site. Irradiation at 530 nm or 565 nm resulted in complete photolysis of both caging groups.
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Affiliation(s)
- Janik Kaufmann
- Institute for Organic Chemistry and Chemical Biology Goethe University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt Germany
| | - Patricia Müller
- Institute for Organic Chemistry and Chemical Biology Goethe University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt Germany
| | - Eleni Andreadou
- Institute for Organic Chemistry and Chemical Biology Goethe University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology Goethe University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt Germany
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Deore PS, Manderville RA. Ratiometric fluorescent sensing of the parallel G-quadruplex produced by PS2.M: implications for K + detection. Analyst 2020; 145:1288-1293. [PMID: 31895357 DOI: 10.1039/c9an02122a] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Fluorescent ligands that selectively bind to a specific G-quadruplex (GQ) topology (antiparallel, hybrid or parallel) are highly sought after for aptasensor development and nanodevice construction. The coumarin-benzothiazole hybrid (BnBtC) is an internal charge transfer (ICT) ratiometric fluorescent probe, which displays two well-resolved emission bands at ∼450 nm for the coumarin component and ∼650 nm for the ICT band. The red ICT emission of BnBtC displays turn-on responses to protic solvent polarity and upon binding GQ structures, especially those produced by the hemin binding aptamer (PS2.M). In the present work, BnBtC was found to exhibit enhanced ICT emission upon binding the parallel GQ topology of PS2.M that is selectively produced in the presence of K+. This ability to discriminate K+ from other cationic metal ions through a turn-on ratiometric fluorescent response demonstrates the potential utility of the BnBtC probe for biosensor applications.
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Affiliation(s)
- Prashant S Deore
- Departments of Chemistry & Toxicology, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
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Gray MD, Deore PS, Chung AJ, Van Riesen AJ, Manderville RA, Prabhakar PS, Wetmore SD. Lighting Up the Thrombin-Binding Aptamer G-Quadruplex with an Internal Cyanine-Indole-Quinolinium Nucleobase Surrogate. Direct Fluorescent Intensity Readout for Thrombin Binding without Topology Switching. Bioconjug Chem 2020; 31:2596-2606. [PMID: 33156614 DOI: 10.1021/acs.bioconjchem.0c00530] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Fluorescent nucleobases represent an important class of molecular reporters of nucleic acid interactions. In this work, the advantages of utilizing a noncanonical fluorescent nucleobase surrogate for monitoring thrombin binding by the 15-mer thrombin binding aptamer (TBA) is presented. TBA folds into an antiparallel G-quadruplex (GQ) with loop thymidine (T) residues interacting directly with the protein in the thrombin-TBA complex. In the free GQ, T3 is solvent-exposed and does not form canonical base-pairs within the antiparallel GQ motif. Upon thrombin binding, T3 interacts directly with a hydrophobic protein binding pocket. Replacing T3 with a cyanine-indole-quinolinium (4QI) hemicyanine dye tethered to an acyclic 1,2-propanediol linker is shown to have minimal impact on GQ stability and structure with the internal 4QI displaying a 40-fold increase in emission intensity at 586 nm (excitation 508 nm) compared to the free dye in solution. Molecular dynamics (MD) simulations demonstrate that the 4QI label π-stacks with T4 and T13 within the antiparallel GQ fold, which is supported by strong energy transfer (ET) fluorescence from the GQ (donor) to the 4QI label (acceptor). Thrombin binding to 4QI-TBA diminishes π-stacking interactions between 4QI and the GQ structure to cause a turn-off emission intensity response with an apparent dissociation constant (Kd) of 650 nM and a limit of detection (LoD) of 150 nM. These features highlight the utility of internal noncanonical fluorescent surrogates for monitoring protein binding by GQ-folding aptamers in the absence of DNA topology switching.
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Affiliation(s)
- Micaela D Gray
- Department of Chemistry & Toxicology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Prashant S Deore
- Department of Chemistry & Toxicology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Andrew J Chung
- Department of Chemistry & Toxicology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Abigail J Van Riesen
- Department of Chemistry & Toxicology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Richard A Manderville
- Department of Chemistry & Toxicology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Preethi Seelam Prabhakar
- Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4
| | - Stacey D Wetmore
- Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4
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Rigotti T, Asenjo‐Pascual J, Martín‐Somer A, Milán Rois P, Cordani M, Díaz‐Tendero S, Somoza Á, Fraile A, Alemán J. Boron Dipyrromethene (BODIPY) as Electron‐Withdrawing Group in Asymmetric Copper‐Catalyzed [3+2] Cycloadditions for the Synthesis of Pyrrolidine‐Based Biological Sensors. Adv Synth Catal 2020. [DOI: 10.1002/adsc.201901465] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Thomas Rigotti
- Department of Organic Chemistry (module 01)Universidad Autonoma de Madrid, Cantoblanco 28049 Madrid Spain
| | - Juan Asenjo‐Pascual
- Department of Organic Chemistry (module 01)Universidad Autonoma de Madrid, Cantoblanco 28049 Madrid Spain
| | - Ana Martín‐Somer
- Department of Chemistry (module 13)Universidad Autonoma de Madrid, Cantoblanco 28049 Madrid Spain
| | | | | | - Sergio Díaz‐Tendero
- Department of Chemistry (module 13)Universidad Autonoma de Madrid, Cantoblanco 28049 Madrid Spain
- Institute for Advanced Research in Chemical Sciences (IAdChem)Universidad Autónoma de Madrid 28049 Madrid Spain
- Condensed Matter Physics Center (IFIMAC)Universidad Autónoma de Madrid, Cantoblanco 28049 Madrid Spain
| | | | - Alberto Fraile
- Department of Organic Chemistry (module 01)Universidad Autonoma de Madrid, Cantoblanco 28049 Madrid Spain
- Institute for Advanced Research in Chemical Sciences (IAdChem)Universidad Autónoma de Madrid 28049 Madrid Spain
| | - José Alemán
- Department of Organic Chemistry (module 01)Universidad Autonoma de Madrid, Cantoblanco 28049 Madrid Spain
- Institute for Advanced Research in Chemical Sciences (IAdChem)Universidad Autónoma de Madrid 28049 Madrid Spain
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Brandes B, Hoenke S, Fischer L, Csuk R. Design, synthesis and cytotoxicity of BODIPY FL labelled triterpenoids. Eur J Med Chem 2020; 185:111858. [DOI: 10.1016/j.ejmech.2019.111858] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 11/02/2019] [Accepted: 11/04/2019] [Indexed: 12/21/2022]
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Deore PS, Gray MD, Chung AJ, Manderville RA. Ligand-Induced G-Quadruplex Polymorphism: A DNA Nanodevice for Label-Free Aptasensor Platforms. J Am Chem Soc 2019; 141:14288-14297. [PMID: 31436972 DOI: 10.1021/jacs.9b06533] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
G-Quadruplexes (GQs) serve as popular recognition elements for DNA aptasensors and are incorporated into a DNA nanodevice capable of controlled conformational changes to activate a sensing mechanism. Herein we highlight the utility of a GQ-GQ nanodevice fueled by GQ-specific ligands as a label-free aptasensor detection strategy. The concept was first illustrated utilizing the prototypical polymorphic human telomeric repeat sequence (H-Telo22, d[AG3(T2AG3)3]) that can undergo ligand-induced topology changes between antiparallel, parallel, or hybrid GQ structures. The H-Telo22-ligand interactions served as a model of the GQ-GQ nanodevice. The utility of the device in a real aptasensor platform was then highlighted utilizing the ochratoxin A (OTA) binding aptamer (OTABA) that folds into an antiparallel GQ in the absence and presence of target OTA. Three cationic fluorogenic ligands served as GQ-specific light-up probes and as potential fuel for the GQ-GQ nanodevice by producing an inactive GQ topology (parallel or hybrid) of OTABA. Our findings demonstrate efficient OTA-mediated dye displacement with excellent emission sensitivity for OTA detection when the fluorogenic dyes induce a topology change in OTABA (parallel or hybrid). However, when the fluorogenic dye fails to induce a conformational change in the antiparallel fold of OTABA, subsequent additions of OTA to the aptamer-dye complex results in poor dye displacement with weak emission response for OTA detection. These results are the first to exemplify a ligand-induced GQ-GQ nanodevice as an aptasensor mechanism and demonstrate diagnostic applications for topology-specific GQ binders.
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Affiliation(s)
- Prashant S Deore
- Departments of Chemistry and Toxicology , University of Guelph , Guelph , Ontario N1G 2W1 , Canada
| | - Micaela D Gray
- Departments of Chemistry and Toxicology , University of Guelph , Guelph , Ontario N1G 2W1 , Canada
| | - Andrew J Chung
- Departments of Chemistry and Toxicology , University of Guelph , Guelph , Ontario N1G 2W1 , Canada
| | - Richard A Manderville
- Departments of Chemistry and Toxicology , University of Guelph , Guelph , Ontario N1G 2W1 , Canada
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Deore PS, Manderville RA. Aptamer-induced thermofluorimetric protein stabilization and G-quadruplex nucleic acid staining by SYPRO orange dye. NEW J CHEM 2019. [DOI: 10.1039/c9nj00188c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Serendipitously discovered nucleic acid staining by SYPRO Orange dye utilized to demonstrate proteins thermal stabilization (increase in melting temperature,Tm) as a function of increased DNA aptamer binding affinity (decrease in dissociation constant,Kd).
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Affiliation(s)
- Prashant S. Deore
- Departments of Chemistry & Toxicology
- University of Guelph
- Guelph
- Canada
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