Synthesis and J‐Dimer Formation of Tetrapyrazinoporphyrazines with Different Functional Groups for Potential Biomolecular Probe Applications

Demuth, Jiří; Miletín, Miroslav; Machan, Matej; Kantor, Michal; Zimčík, Petr; Novakova, Veronika

doi:10.1002/cplu.202000026

Cited by 2 publications

(3 citation statements)

References 45 publications

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“…Commercially available BBQ or AzaPc quenchers (prepared according to the literature , ) were introduced into the desired positions of ODN probes based on known methods, purified by high-performance liquid chromatography (HPLC) (Figure S1), and properly characterized (Figures S2–S10). Notably, Huisgen azide–alkyne 1,3-dipolar cycloaddition was found to be optimal for labeling at both the intrastrand and 3′-end positions.…”

Section: Resultsmentioning

confidence: 99%

“…The mass spectra of the oligonucleotide probes were obtained using a MALDI-TOF Bruker AutoFlex II mass spectrometer. Compounds A 1 and A 2 were prepared according to published procedures. , The solid phase modified by AzaPc A 2 was prepared according to a previously described method …”

Section: Experimental Sectionmentioning

confidence: 99%

“…Compounds A 1 and A 2 were prepared according to published procedures. 22,23 The solid phase modified by AzaPc A 2 was prepared according to a previously described method. 17 Synthesis of ODNs.…”

Section: ■ Conclusionmentioning

confidence: 99%

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Comparison of Quenching Efficiencies in Long Triple-Labeled and Double-Labeled TaqMan Oligodeoxynucleotide Probes

et al. 2022

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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 Forster 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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confidence: 99%

Section: Experimental Sectionmentioning

confidence: 99%

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Comparison of Quenching Efficiencies in Long Triple-Labeled and Double-Labeled TaqMan Oligodeoxynucleotide Probes

et al. 2022

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Consequences of isosteric replacement of benzene for pyrazine in phthalocyanines

Novakova

2022

J. Porphyrins Phthalocyanines

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Tetrapyrazinoporphyrazines (TPyzPzs) likely represent the most investigated group of azaanalogs of phthalocyanines. This review highlights the author’s contributions in this field and summarizes the most important features of these interesting macrocycles with the aim of emphasizing the differences from the parent phthalocyanines. In particular, uniqueness in synthesis, spectral, photophysical and electrochemical properties are discussed. Thanks to systematic investigation of intramolecular charge transfer with TPyzPzs as electron acceptors, detailed structure-activity relationships of this ultrafast quenching process have been disclosed. This opened the door for the use of TPyzPzs as fluorescence sensors and quenchers in oligodeoxynucleotide probes, the latter being unique for TPyzPzs, which have not been investigated with phthalocyanines. These two applications seem to be much more suitable for TPyzPzs than photodynamic therapy, where the phthalocyanines typically have superior in vitro activities.

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Synthesis and J‐Dimer Formation of Tetrapyrazinoporphyrazines with Different Functional Groups for Potential Biomolecular Probe Applications

Cited by 2 publications

References 45 publications

Comparison of Quenching Efficiencies in Long Triple-Labeled and Double-Labeled TaqMan Oligodeoxynucleotide Probes

Comparison of Quenching Efficiencies in Long Triple-Labeled and Double-Labeled TaqMan Oligodeoxynucleotide Probes

Consequences of isosteric replacement of benzene for pyrazine in phthalocyanines

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