1
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Demuth J, Kantor M, Kucera R, Miletin M, Novakova V. Comparison of Quenching Efficiencies in Long Triple-Labeled and Double-Labeled TaqMan Oligodeoxynucleotide Probes. Bioconjug Chem 2022; 33:788-794. [PMID: 35476400 DOI: 10.1021/acs.bioconjchem.2c00023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Although triple labeling of molecular beacons has been documented to improve quenching efficiencies and studies generally assume similar benefits at long TaqMan probes, a limited number of works have studied this issue in TaqMan probes. We therefore prepared a series of long triple-labeled oligodeoxynucleotide probes with 6-carboxyfluorescein as a fluorophore at the 5'-end and BlackBerry (BBQ-650) or azaphthalocyanine quenchers at the 3'-end and in the intrastrand position and systematically compared their quenching efficiencies with those of the corresponding double-labeled probes including important control probes. A model polymerase chain reaction (PCR) assay enabled the determination of the quenching efficiencies of static and Förster resonance energy transfer (FRET) quenching in the target probes. The type of probe had no effect on the static quenching ability. Importantly, FRET quenching of double-labeled probes with a quencher at the 3'-end showed a statistically insignificant difference from the control probe without any quencher, indicating the need to shift the quencher closer to the fluorophore in long probes. Shortening the distance between the fluorophore and the quencher played a key role in FRET quenching, whereas the introduction of an additional quencher only slightly improved the quenching efficiency. BBQ-labeled probes had lower quenching efficiencies than azaphthalocyanine probes. The methodologies and relationships described above seem, however, to be universal and applicable to any quencher.
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Affiliation(s)
- Jiri Demuth
- Faculty of Pharmacy in Hradec Kralove, Charles University, Ak. Heyrovskeho 1203, Hradec Kralove 50005, Czech Republic
| | - Michal Kantor
- Faculty of Pharmacy in Hradec Kralove, Charles University, Ak. Heyrovskeho 1203, Hradec Kralove 50005, Czech Republic
| | - Radim Kucera
- Faculty of Pharmacy in Hradec Kralove, Charles University, Ak. Heyrovskeho 1203, Hradec Kralove 50005, Czech Republic
| | - Miroslav Miletin
- Faculty of Pharmacy in Hradec Kralove, Charles University, Ak. Heyrovskeho 1203, Hradec Kralove 50005, Czech Republic
| | - Veronika Novakova
- Faculty of Pharmacy in Hradec Kralove, Charles University, Ak. Heyrovskeho 1203, Hradec Kralove 50005, Czech Republic
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2
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Kučera R, Sčensná A, Miletín M, Zimčík P. The chromatographic behaviour of new double-labelled oligodeoxynucleotide probes containing azaphthalocyanine dye as a quencher with respect to evaluation of their purity. Biomed Chromatogr 2020; 35:e5033. [PMID: 33226652 DOI: 10.1002/bmc.5033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 10/12/2020] [Accepted: 11/19/2020] [Indexed: 11/07/2022]
Abstract
The influence of experimental conditions on chromatographic behaviour of promising oligodeoxynucleotide double-labelled molecular probes containing an azaphthalocyanine macrocycle as a perspective dark quencher was studied. A recently introduced new stationary phase based on styrene-divinylbenzene copolymer was tested. The planar and hydrophobic structure of the azaphthalocyanine is considerably different from those of currently used fluorophores and quenchers. Thus, the most challenging issue was the separation of the double-labelled probe from its main impurity represented by a mono-labelled probe, containing only the azaphthalocyanine macrocycle. The absorbance measurement cannot simply determine this impurity, and its presence fundamentally compromises the biological assay. The commonly used gradient elution was not suitable and isocratic conditions seemed to be more appropriate. The azaphthalocyanine moiety influences the properties of the modified oligodeoxynucleotides substantially, and thus their chromatographic behaviour was determined predominantly by this quencher. Acetonitrile was the preferred organic solvent for the analysis of probes containing the azaphthalocyanine quencher and the effect of ion-pairing reagents was dependent on the probe structure. The temperature seemed to be an effective parameter for fine-tuning of the separation and mass transfer improvement. Generally, our findings could be helpful in method development for purity evaluation of double-labelled oligodeoxynucleotide probes and semipreparative methods.
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Affiliation(s)
- Radim Kučera
- Faculty of Pharmacy in Hradec Králové, Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Charles University, Hradec Králové, Czech Republic
| | - Anna Sčensná
- Faculty of Pharmacy in Hradec Králové, Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Charles University, Hradec Králové, Czech Republic
| | - Miroslav Miletín
- Faculty of Pharmacy in Hradec Králové, Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Charles University, Hradec Králové, Czech Republic
| | - Petr Zimčík
- Faculty of Pharmacy in Hradec Králové, Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Charles University, Hradec Králové, Czech Republic
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3
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Demuth J, Miletin M, Machan M, Kantor M, Zimcik P, Novakova V. Synthesis and J-Dimer Formation of Tetrapyrazinoporphyrazines with Different Functional Groups for Potential Biomolecular Probe Applications. Chempluschem 2020; 85:527-537. [PMID: 32187858 DOI: 10.1002/cplu.202000026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/18/2020] [Indexed: 12/24/2022]
Abstract
Though tetrapyrazinoporphyrazines (TPyzPzs) are generally presented as universal dark quenchers for oligonucleotide probes, the availability of TPyzPzs bearing different functional groups suitable for attachment to 3', and 5' ends or intrastrand positions remains rather limited. Therefore, a synthetic route to hexa(bis(2-methoxyethyl)amino) or hexa(diethylamino) TPyzPzs functionalized by an azide, hydroxy, or carboxy group or their combinations was developed. Studies of self-assembly into J-dimers in nonpolar solvents and their stability upon titration with pyridine (association constants, KP values, ranging 0.32-12.7×102 M-1 ) revealed that smaller peripheral substituents and functionalization of TPyzPzs improves the stability of J-dimers. ΦΔ and ΦF were low for the monomers (ΦF <0.0001, ΦΔ <0.008, DMF) due to quenching by intramolecular charge transfer; however, they increased in nonpolar solvents and after self-assembly into J-dimer (up to ΦF =0.027, ΦΔ =0.28).
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Affiliation(s)
- Jiri Demuth
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis Faculty of Pharmacy in Hradec Kralove, Charles University, Akademika Heyrovskeho 1203, Hradec Kralove, Czech Republic
| | - Miroslav Miletin
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis Faculty of Pharmacy in Hradec Kralove, Charles University, Akademika Heyrovskeho 1203, Hradec Kralove, Czech Republic
| | - Matej Machan
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis Faculty of Pharmacy in Hradec Kralove, Charles University, Akademika Heyrovskeho 1203, Hradec Kralove, Czech Republic
| | - Michal Kantor
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis Faculty of Pharmacy in Hradec Kralove, Charles University, Akademika Heyrovskeho 1203, Hradec Kralove, Czech Republic
| | - Petr Zimcik
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis Faculty of Pharmacy in Hradec Kralove, Charles University, Akademika Heyrovskeho 1203, Hradec Kralove, Czech Republic
| | - Veronika Novakova
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis Faculty of Pharmacy in Hradec Kralove, Charles University, Akademika Heyrovskeho 1203, Hradec Kralove, Czech Republic
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4
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Demuth J, Miletin M, Kucera R, Ruzicka A, Havlinova Z, Libra A, Novakova V, Zimcik P. Self-assembly of azaphthalocyanine–oligodeoxynucleotide conjugates into J-dimers: towards biomolecular logic gates. Org Chem Front 2020. [DOI: 10.1039/c9qo01364d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Unique spatial self-assembly of azaphthalocyanine–oligonucleotide–fluorescein conjugates can be selectively dissociated by a complementary sequence or coordinating solvent and used for the development of biomolecular logic gates.
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Affiliation(s)
- Jiri Demuth
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis
- Charles University
- Faculty of Pharmacy in Hradec Králové
- 500 05 Hradec Kralove
- Czech Republic
| | - Miroslav Miletin
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis
- Charles University
- Faculty of Pharmacy in Hradec Králové
- 500 05 Hradec Kralove
- Czech Republic
| | - Radim Kucera
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis
- Charles University
- Faculty of Pharmacy in Hradec Králové
- 500 05 Hradec Kralove
- Czech Republic
| | - Ales Ruzicka
- Department of General and Inorganic Chemistry
- Faculty of Chemical Technology
- University of Pardubice
- Pardubice
- Czech Republic
| | - Zuzana Havlinova
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis
- Charles University
- Faculty of Pharmacy in Hradec Králové
- 500 05 Hradec Kralove
- Czech Republic
| | | | - Veronika Novakova
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis
- Charles University
- Faculty of Pharmacy in Hradec Králové
- 500 05 Hradec Kralove
- Czech Republic
| | - Petr Zimcik
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis
- Charles University
- Faculty of Pharmacy in Hradec Králové
- 500 05 Hradec Kralove
- Czech Republic
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5
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Wong RC, Lo PC, Ng DK. Stimuli responsive phthalocyanine-based fluorescent probes and photosensitizers. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2017.10.006] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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6
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Demuth J, Kucera R, Kopecky K, Havlínová Z, Libra A, Novakova V, Miletin M, Zimcik P. Efficient Synthesis of a Wide-Range Absorbing Azaphthalocyanine Dark Quencher and Its Application to Dual-Labeled Oligonucleotide Probes for Quantitative Real-Time Polymerase Chain Reactions. Chemistry 2018; 24:9658-9666. [PMID: 29683215 DOI: 10.1002/chem.201801319] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Indexed: 11/06/2022]
Abstract
Unsymmetrical dialkylamino-substituted zinc azaphthalocyanine (AzaPc) exhibits unique spectral and photophysical properties for dark quenchers of fluorescence in DNA hybridization probes. The panchromatic light absorption of AzaPc from 300 nm up to at least 700 nm and its lack of fluorescence make it an ideal candidate for a universal dark quencher. To prove this experimentally, oligodeoxyribonucleotide probes were labeled at the 3'-end by this AzaPc and at the 5'-end by a fluorophore used in the polymerase chain reaction (PCR)-that is, fluorescein, CAL Fluor Red 610, and Cy5. AzaPc showed a significantly higher quenching efficiency compared to the commercially available dark quenchers (BHQ-1, BHQ-2, BBQ-650) in a developed model of TaqMan PCR assay. The AzaPc-labeled probe proved to also be useful in a practical PCR assay for the quantification of the SLCO2B1 transporter gene expression. The constructed calibration curves indicated linearity in the range from 102 to 107 of target copies.
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Affiliation(s)
- Jiri Demuth
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Charles University, Faculty of Pharmacy in Hradec Kralove, Akademika Heyrovskeho 1203, Hradec Kralove, 500 05, Czech Republic
| | - Radim Kucera
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Charles University, Faculty of Pharmacy in Hradec Kralove, Akademika Heyrovskeho 1203, Hradec Kralove, 500 05, Czech Republic
| | - Kamil Kopecky
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Charles University, Faculty of Pharmacy in Hradec Kralove, Akademika Heyrovskeho 1203, Hradec Kralove, 500 05, Czech Republic
| | - Zuzana Havlínová
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Charles University, Faculty of Pharmacy in Hradec Kralove, Akademika Heyrovskeho 1203, Hradec Kralove, 500 05, Czech Republic.,Generi Biotech, Machkova 587, Hradec Kralove, 500 11, Czech Republic
| | - Antonín Libra
- Generi Biotech, Machkova 587, Hradec Kralove, 500 11, Czech Republic
| | - Veronika Novakova
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Charles University, Faculty of Pharmacy in Hradec Kralove, Akademika Heyrovskeho 1203, Hradec Kralove, 500 05, Czech Republic
| | - Miroslav Miletin
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Charles University, Faculty of Pharmacy in Hradec Kralove, Akademika Heyrovskeho 1203, Hradec Kralove, 500 05, Czech Republic
| | - Petr Zimcik
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Charles University, Faculty of Pharmacy in Hradec Kralove, Akademika Heyrovskeho 1203, Hradec Kralove, 500 05, Czech Republic
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7
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Novakova V, Donzello MP, Ercolani C, Zimcik P, Stuzhin PA. Tetrapyrazinoporphyrazines and their metal derivatives. Part II: Electronic structure, electrochemical, spectral, photophysical and other application related properties. Coord Chem Rev 2018. [DOI: 10.1016/j.ccr.2018.01.015] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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8
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Miletin M, Zimcik P, Novakova V. Photodynamic properties of aza-analogues of phthalocyanines. Photochem Photobiol Sci 2018; 17:1749-1766. [DOI: 10.1039/c8pp00106e] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Spectral and photophysical properties and in vitro photodynamic activity of aza-analogues of phthalocyanines are summarized.
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Affiliation(s)
- Miroslav Miletin
- Faculty of Pharmacy in Hradec Kralove
- Charles University
- Hradec Kralove 50005
- Czech Republic
| | - Petr Zimcik
- Faculty of Pharmacy in Hradec Kralove
- Charles University
- Hradec Kralove 50005
- Czech Republic
| | - Veronika Novakova
- Faculty of Pharmacy in Hradec Kralove
- Charles University
- Hradec Kralove 50005
- Czech Republic
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9
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Llamas EM, Tome JPC, Rodrigues JMM, Torres T, Madder A. Porphyrin-based photosensitizers and their DNA conjugates for singlet oxygen induced nucleic acid interstrand crosslinking. Org Biomol Chem 2017. [DOI: 10.1039/c7ob01269a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Porphyrin-based photosensitisers and their DNA conjugates have been evaluated for interstrand crosslink generation using furan containing oligonucleotides and red light.
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Affiliation(s)
- Eva M. Llamas
- Department of Organic and Macromolecular Chemistry
- Ghent University
- 9000 Ghent
- Belgium
- Departamento de Química Orgánica
| | - João P. C. Tome
- Centro de Química Estrutural
- Departamento de Engenharia Química
- Instituto Superior Técnico
- Universidade de Lisboa
- 1049-001 Lisboa
| | - João M. M. Rodrigues
- Centro de Química Estrutural
- Departamento de Engenharia Química
- Instituto Superior Técnico
- Universidade de Lisboa
- 1049-001 Lisboa
| | - Tomás Torres
- Departamento de Química Orgánica
- Universidad Autónoma de Madrid
- 28049 Madrid
- Spain
- Imdea-Nanoscience
| | - Annemieke Madder
- Department of Organic and Macromolecular Chemistry
- Ghent University
- 9000 Ghent
- Belgium
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10
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Wang D, Li H, Wu G, Guo R, Li L, Zhao C, Liu F, Wang Y. Photoelectrocatalytic degradation of partially hydrolyzed polyacrylamide using a novel particle electrode. RSC Adv 2017. [DOI: 10.1039/c7ra11658f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Tetrapyrazinoporphyrazines and their metal derivatives (TPyzPzs) are the most widely studied class of phthalocyanines azaanalogues.
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Affiliation(s)
- Dejun Wang
- College of Chemical Engineering
- China University of Petroleum (East China)
- Qingdao
- P. R China
- State Key Laboratory of Petroleum Pollution Control
| | - Hui Li
- Qingdao Technical College
- Qingdao
- P. R China
| | - Guangrui Wu
- College of Chemical Engineering
- China University of Petroleum (East China)
- Qingdao
- P. R China
- State Key Laboratory of Petroleum Pollution Control
| | - Rui Guo
- College of Chemical Engineering
- China University of Petroleum (East China)
- Qingdao
- P. R China
- State Key Laboratory of Petroleum Pollution Control
| | - Lin Li
- College of Chemical and Environmental Engineering
- Shandong University of Science and Technology
- Qingdao
- P. R China
| | - Chaocheng Zhao
- College of Chemical Engineering
- China University of Petroleum (East China)
- Qingdao
- P. R China
- State Key Laboratory of Petroleum Pollution Control
| | - Fang Liu
- College of Chemical Engineering
- China University of Petroleum (East China)
- Qingdao
- P. R China
- State Key Laboratory of Petroleum Pollution Control
| | - Yongqiang Wang
- College of Chemical Engineering
- China University of Petroleum (East China)
- Qingdao
- P. R China
- State Key Laboratory of Petroleum Pollution Control
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11
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Tetrapyrazinoporphyrazines and their metal derivatives. Part I: Synthesis and basic structural information. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2015.09.006] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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12
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Machacek M, Kollár J, Miletin M, Kučera R, Kubát P, Simunek T, Novakova V, Zimcik P. Anionic hexadeca-carboxylate tetrapyrazinoporphyrazine: synthesis and in vitro photodynamic studies of a water-soluble, non-aggregating photosensitizer. RSC Adv 2016. [DOI: 10.1039/c5ra25881b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Photodynamic activity of hexadeca-carboxylate tetrapyrazinoporphyrazine is largely influenced by intracellular pH and its interaction with serum proteins.
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Affiliation(s)
- Miloslav Machacek
- Department of Biochemical Sciences
- Faculty of Pharmacy in Hradec Kralove
- Charles University in Prague
- Hradec Kralove
- Czech Republic
| | - Jan Kollár
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis
- Faculty of Pharmacy in Hradec Kralove
- Charles University in Prague
- Hradec Kralove
- Czech Republic
| | - Miroslav Miletin
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis
- Faculty of Pharmacy in Hradec Kralove
- Charles University in Prague
- Hradec Kralove
- Czech Republic
| | - Radim Kučera
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis
- Faculty of Pharmacy in Hradec Kralove
- Charles University in Prague
- Hradec Kralove
- Czech Republic
| | - Pavel Kubát
- J. Heyrovský Institute of Physical Chemistry
- v.v.i
- Academy of Sciences of the Czech Republic
- 182 23 Praha 8
- Czech Republic
| | - Tomas Simunek
- Department of Biochemical Sciences
- Faculty of Pharmacy in Hradec Kralove
- Charles University in Prague
- Hradec Kralove
- Czech Republic
| | - Veronika Novakova
- Department of Biophysics and Physical Chemistry
- Faculty of Pharmacy in Hradec Kralove
- Charles University in Prague
- Hradec Kralove
- Czech Republic
| | - Petr Zimcik
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis
- Faculty of Pharmacy in Hradec Kralove
- Charles University in Prague
- Hradec Kralove
- Czech Republic
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13
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Wang D, Huang J, Li K, Zhang C, Du Y, Yang P. A robust and efficient visible light driven photocatalyst for hydrogen evolution based on ruthenium dye N3 covalently immobilized on reduced graphene oxide. RSC Adv 2016. [DOI: 10.1039/c6ra03542f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
A robust and efficient photocatalyst based on ruthenium dye N3 covalently immobilized on reduced graphene oxide was used for photocatalytic hydrogen evolution.
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Affiliation(s)
- Dandan Wang
- College of Chemistry, Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
- China
| | - Jie Huang
- College of Chemistry, Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
- China
- Key Laboratory of Nano-Bio Interface
| | - Kezhen Li
- College of Chemistry, Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
- China
| | - Chunyong Zhang
- College of Chemistry, Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
- China
| | - Yukou Du
- College of Chemistry, Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
- China
| | - Ping Yang
- College of Chemistry, Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
- China
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14
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Patel PL, Rana NK, Patel MR, Kozuch SD, Sabatino D. Nucleic Acid Bioconjugates in Cancer Detection and Therapy. ChemMedChem 2015; 11:252-69. [PMID: 26663095 DOI: 10.1002/cmdc.201500502] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 11/23/2015] [Indexed: 12/28/2022]
Abstract
Nucleoside- and nucleotide-based chemotherapeutics have been used to treat cancer for more than 50 years. However, their inherent cytotoxicities and the emergent resistance of tumors against treatment has inspired a new wave of compounds in which the overall pharmacological profile of the bioactive nucleic acid component is improved by conjugation with delivery vectors, small-molecule drugs, and/or imaging modalities. In this manner, nucleic acid bioconjugates have the potential for targeting and effecting multiple biological processes in tumors, leading to synergistic antitumor effects. Consequently, tumor resistance and recurrence is mitigated, leading to more effective forms of cancer therapy. Bioorthogonal chemistry has led to the development of new nucleoside bioconjugates, which have served to improve treatment efficacy en route towards FDA approval. Similarly, oligonucleotide bioconjugates have shown encouraging preclinical and clinical results. The modified oligonucleotides and their pharmaceutically active formulations have addressed many weaknesses of oligonucleotide-based drugs. They have also paved the way for important advancements in cancer diagnosis and treatment. Cancer-targeting ligands such as small-molecules, peptides, and monoclonal antibody fragments have all been successfully applied in oligonucleotide bioconjugation and have shown promising anticancer effects in vitro and in vivo. Thus, the application of bioorthogonal chemistry will, in all likelihood, continue to supply a promising pipeline of nucleic acid bioconjugates for applications in cancer detection and therapy.
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Affiliation(s)
- Pradeepkumar L Patel
- Sun Pharmaceutical Industries Inc., Analytical Research and Development, 270 Prospect Plains Road, Cranbury, NJ, 08512, USA
| | - Niki K Rana
- Department of Chemistry and Biochemistry, Seton Hall University, 400 South Orange Avenue, South Orange, NJ, 07079, USA
| | - Mayurbhai R Patel
- Department of Chemistry and Biochemistry, Seton Hall University, 400 South Orange Avenue, South Orange, NJ, 07079, USA
| | - Stephen D Kozuch
- Department of Chemistry and Biochemistry, Seton Hall University, 400 South Orange Avenue, South Orange, NJ, 07079, USA
| | - David Sabatino
- Department of Chemistry and Biochemistry, Seton Hall University, 400 South Orange Avenue, South Orange, NJ, 07079, USA.
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15
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Novakova V, Reimerova P, Svec J, Suchan D, Miletin M, Rhoda HM, Nemykin VN, Zimcik P. Systematic investigation of phthalocyanines, naphthalocyanines, and their aza-analogues. Effect of the isosteric aza-replacement in the core. Dalton Trans 2015; 44:13220-33. [DOI: 10.1039/c5dt01863c] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of zinc complexes of phthalocyanines, naphthalocyanines and their aza-analogs was studied and compared using UV-vis and MCD spectra, molecular calculations, and photophysical and electrochemical measurements.
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Affiliation(s)
- Veronika Novakova
- Department of Biophysics and Physical Chemistry
- Faculty of Pharmacy in Hradec Kralove
- Charles University in Prague
- Hradec Kralove
- Czech Republic
| | - Petra Reimerova
- Department of Biophysics and Physical Chemistry
- Faculty of Pharmacy in Hradec Kralove
- Charles University in Prague
- Hradec Kralove
- Czech Republic
| | - Jan Svec
- Department of Pharmaceutical Chemistry and Drug Control
- Faculty of Pharmacy in Hradec Kralove
- Charles University in Prague
- Hradec Kralove
- Czech Republic
| | - Daniel Suchan
- Department of Pharmaceutical Chemistry and Drug Control
- Faculty of Pharmacy in Hradec Kralove
- Charles University in Prague
- Hradec Kralove
- Czech Republic
| | - Miroslav Miletin
- Department of Pharmaceutical Chemistry and Drug Control
- Faculty of Pharmacy in Hradec Kralove
- Charles University in Prague
- Hradec Kralove
- Czech Republic
| | - Hannah M. Rhoda
- Department of Chemistry & Biochemistry
- University of Minnesota Duluth
- Duluth
- USA
| | - Victor N. Nemykin
- Department of Chemistry & Biochemistry
- University of Minnesota Duluth
- Duluth
- USA
| | - Petr Zimcik
- Department of Pharmaceutical Chemistry and Drug Control
- Faculty of Pharmacy in Hradec Kralove
- Charles University in Prague
- Hradec Kralove
- Czech Republic
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16
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Novakova V, Miletin M, Filandrová T, Lenčo J, Růžička A, Zimcik P. Role of steric hindrance in the Newman-Kwart rearrangement and in the synthesis and photophysical properties of arylsulfanyl tetrapyrazinoporphyrazines. J Org Chem 2014; 79:2082-93. [PMID: 24548285 DOI: 10.1021/jo402791c] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Conditions for the Newman-Kwart rearrangement of phenols into thiophenols were investigated in relation to the bulkiness of substituents at the 2 and 6 positions of the starting phenol derivative with an emphasis on eliminating side reactions. Thiophenols with different 2,6-disubstitution patterns (including hydrogen, methyl, isopropyl or tert-butyl groups) were used for the synthesis of 5,6-bis(arylsulfanyl)pyrazine-2,3-dicarbonitriles that underwent cyclotetramerization leading to the corresponding zinc tetrapyrazinoporphyrazines (TPyzPz), aza-analogues of phthalocyanines. Several methods for the cyclotetramerization were attempted to eliminate problematic side reactions. Magnesium butoxide was found as the most suitable cyclotetramerization agent and afforded TPyzPzs in reasonable yields of approximately 30% under mild conditions. The varying arrangements of the peripheral substitutions resulting from the different bulkiness of the substituents were demonstrated by the X-ray structures of the pyrazine-2,3-dicarbonitriles. The prepared zinc arylsulfanyl TPyzPzs showed an absorption maximum at a Q-band over 650 nm, fluorescence quantum yields between 0.078 and 0.20, and singlet oxygen quantum yields ranging 0.58-0.69. TPyzPzs with isopropyl groups were found to be the best derivatives in this series as they combined facile cyclotetramerization, no aggregation, and good photophysical properties, which makes them potentially suitable for photodynamic therapy.
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Affiliation(s)
- Veronika Novakova
- Department of Biophysics and Physical Chemistry, ‡Department of Pharmaceutical Chemistry and Drug Control, and ⊥Department of Biochemical Sciences, Faculty of Pharmacy, Faculty of Pharmacy in Hradec Kralove, Charles University in Prague , Heyrovskeho 1203, 500 05, Hradec Kralove, Czech Republic
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Guzaev AP. Solid-phase supports for oligonucleotide synthesis. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2013; Chapter 3:3.1.1-3.1.60. [PMID: 23775808 DOI: 10.1002/0471142700.nc0301s53] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
This unit attempts to provide a reasonably complete inventory of over 280 solid supports available to oligonucleotide chemists for preparation of natural and 3'-modified oligonucleotides. Emphasis is placed on non-nucleosidic solid supports. The relationship between the structural features of linkers and their behavior in oligonucleotide synthesis and deprotection is discussed wherever the relevant observations are available.
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Chevalier A, Massif C, Renard PY, Romieu A. Bioconjugatable Azo-Based Dark-Quencher Dyes: Synthesis and Application to Protease-Activatable Far-Red Fluorescent Probes. Chemistry 2012; 19:1686-99. [DOI: 10.1002/chem.201203427] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Indexed: 11/08/2022]
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Crisalli P, Hernández AR, Kool ET. Fluorescence quenchers for hydrazone and oxime orthogonal bioconjugation. Bioconjug Chem 2012; 23:1969-80. [PMID: 22913527 PMCID: PMC3447104 DOI: 10.1021/bc300344b] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
We describe the synthesis and properties of new fluorescence quenchers containing aldehyde, hydrazine, and aminooxy groups, allowing convenient bioconjugation as oximes or hydrazones. Conjugation to oligonucleotides proceeded in high yield with aniline as catalyst. Kinetics studies of conjugation show that, under optimal conditions, a hydrazine or aminooxy quencher can react with aldehyde-modified DNA to form a stable hydrazone or oxime adduct in as little as five minutes. The resulting quencher-containing DNAs were assessed for their ability to quench the emission of fluorescein in labeled complements and compared to the commercially available dabcyl and Black Hole Quencher 2 (BHQ2), which were conjugated as phosphoramidites. Results show that the new quenchers possess slightly different absorbance properties compared to dabcyl and are as efficient as the commercial quenchers in quenching fluorescein emission. Hydrazone-based quenchers were further successfully incorporated into molecular beacons and shown to give high signal to background ratios in single nucleotide polymorphism detection in vitro. Finally, aminooxy and hydrazine quenchers were applied to quenching of an aldehyde-containing fluorophore associated with living cells, demonstrating cellular quenching within one hour.
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Affiliation(s)
- Pete Crisalli
- Department of Chemistry, Stanford University Stanford, California 94305-5080, USA
| | - Armando R. Hernández
- Department of Chemistry, Stanford University Stanford, California 94305-5080, USA
| | - Eric T. Kool
- Department of Chemistry, Stanford University Stanford, California 94305-5080, USA
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Ali H, van Lier JE. An easy route for the synthesis of pyrazine-2,3-dicarbonitrile 5,6-bis-substituted derivatives using a palladium catalyst. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2012.06.102] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Vachova L, Novakova V, Kopecky K, Miletin M, Zimcik P. Effect of intramolecular charge transfer on fluorescence and singlet oxygen production of phthalocyanine analogues. Dalton Trans 2012; 41:11651-6. [PMID: 22832706 DOI: 10.1039/c2dt31403g] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Intramolecular charge transfer (ICT) was studied on a series of magnesium, metal-free and zinc complexes of unsymmetrical tetrapyrazinoporphyrazines and tribenzopyrazinoporphyrazines bearing two dialkylamino substituents (donors) and six alkylsulfanyl or aryloxy substituents (non-donors). The dialkylamino substituents were responsible for ICT that deactivated excited states and led to considerable decrease of fluorescence and singlet oxygen quantum yields. Photophysical and photochemical properties were compared to corresponding macrocycles that do not bear any donor centers. The data showed high feasibility of ICT in the tetrapyrazinoporphyrazine macrocycle and significantly lower efficiency of this deactivation process in the tribenzopyrazinoporphyrazine type molecules. Considerable effect of non-donor peripheral substituents on ICT was also described. The results imply that tetrapyrazinoporphyrazines may be more suitable for development of new molecules investigated in applications based on ICT.
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Affiliation(s)
- Lenka Vachova
- Department of Pharmaceutical Chemistry and Drug Control, Faculty of Pharmacy in Hradec Kralove, Charles University in Prague, Heyrovskeho 1203, 50005, Hradec Kralove, Czech Republic
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Loakes D. Nucleotides and nucleic acids; oligo- and polynucleotides. ORGANOPHOSPHORUS CHEMISTRY 2012. [DOI: 10.1039/9781849734875-00169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- David Loakes
- Medical Research Council Laboratory of Molecular Biology, Hills Road Cambridge CB2 2QH UK
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Crisalli P, Kool ET. Multi-path quenchers: efficient quenching of common fluorophores. Bioconjug Chem 2011; 22:2345-54. [PMID: 22034828 DOI: 10.1021/bc200424r] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Fluorescence quenching groups are widely employed in biological detection, sensing, and imaging. To date, a relatively small number of such groups are in common use. Perhaps the most commonly used quencher, dabcyl, has limited efficiency with a broad range of fluorophores. Here, we describe a molecular approach to improve the efficiency of quenchers by increasing their electronic complexity. Multi-Path Quenchers (MPQ) are designed to have multiple donor or acceptor groups in their structure, allowing for a multiplicity of conjugation pathways of varied length. This has the effect of broadening the absorption spectrum, which in turn can increase quenching efficiency and versatility. Six such MPQ derivatives are synthesized and tested for quenching efficiency in a DNA hybridization context. Duplexes placing quenchers and fluorophores within contact distance or beyond this distance are used to measure quenching via contact or FRET mechanisms. Results show that several of the quenchers are considerably more efficient than dabcyl at quenching a wider range of common fluorophores, and two quench fluorescein and TAMRA as well as or better than a Black Hole Quencher.
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Affiliation(s)
- Pete Crisalli
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA
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Novakova V, Miletin M, Kopecky K, Franzová Š, Zimcik P. Synthesis of Unsymmetrical Alkyloxy/Aryloxy-azaphthalocyanines Based on a Transetherification Reaction. European J Org Chem 2011. [DOI: 10.1002/ejoc.201100689] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Kopecky K, Novakova V, Miletin M, Kučera R, Zimcik P. Synthesis of new azaphthalocyanine dark quencher and evaluation of its quenching efficiency with different fluorophores. Tetrahedron 2011. [DOI: 10.1016/j.tet.2011.06.038] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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