Synthesis of new azaphthalocyanine dark quencher and evaluation of its quenching efficiency with different fluorophores

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

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.

The chromatographic behaviour of new double-labelled oligodeoxynucleotide probes containing azaphthalocyanine dye as a quencher with respect to evaluation of their purity

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.

Fluorescence properties and quantum-chemical modeling of tert-butyl-substituted porphyrazines: Structural and ionization effect

Synthesis and identification of tetrakis-[5,6-bis(4-tert-butylphenyl)pyrazino] porphyrazine, tetra-(4-tert-butyl)phthalocyanine and octakis-(4-tert-butylphenyl)porphyrazine were carried out. Spectrophotometric method was used to study the spectral, acidic and fluorescence properties of the synthesized compounds. It was determined that the synthesized tert-butyl-substituted porphyrazines exhibit a high sensitivity of fluorescence to the molecule ionization. To understand the features of the spectral properties the geometry optimization and an analysis of energy levels and localization of highest occupied and lowest unoccupied molecular orbitals of the studied compounds were performed on the basis of density functional theory with the BP86 functional and the def2-TZVP basis set. The effect of substituents in molecular fragments of the macrocycle on the acidic and electro-optical properties of the studied compounds is revealed. Materials with pH-tunable fluorescence were designed.

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

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, K_P values, ranging 0.32-12.7×10²  M^-1 ) revealed that smaller peripheral substituents and functionalization of TPyzPzs improves the stability of J-dimers. Φ_Δ and Φ_F were low for the monomers (Φ_F <0.0001, Φ_Δ <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 Φ_F =0.027, Φ_Δ =0.28).

Self-assembly of azaphthalocyanine–oligodeoxynucleotide conjugates into J-dimers: towards biomolecular logic gates

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.

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

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.

Photodynamic properties of aza-analogues of phthalocyanines

Spectral and photophysical properties and in vitro photodynamic activity of aza-analogues of phthalocyanines are summarized.

Photoelectrocatalytic degradation of partially hydrolyzed polyacrylamide using a novel particle electrode

Tetrapyrazinoporphyrazines and their metal derivatives (TPyzPzs) are the most widely studied class of phthalocyanines azaanalogues.

Systematic investigation of phthalocyanines, naphthalocyanines, and their aza-analogues. Effect of the isosteric aza-replacement in the core

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.

Fluorescence quenchers for hydrazone and oxime orthogonal bioconjugation

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.

Multi-path quenchers: efficient quenching of common fluorophores

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.