Selective molecular probes for G-quadruplex and G-quadruplex-duplex junctions: Cyanine dye interactions and structural insight.

There is growing interest in hybrid DNA structures, particularly G-quadruplex-duplex junctions, as potential ligand binding sites. In this work, we investigate the interaction of two cyanine dyes (R9 and 3b), which differ in hydrophilicity, with various DNA structures, including duplex DNA, parallel and antiparallel G-quadruplexes, and a G-quadruplex-duplex junction. We employed molecular spectroscopic techniques (UV-visible absorption, circular dichroism, fluorescence), nuclear magnetic resonance (NMR) spectroscopy, multivariate analysis, and molecular docking studies.

Bioaggregachromism of Asymmetric Monomethine Cyanine Dyes as Noncovalent Binders for Nucleic Acids.

Two new asymmetric monomethine cyanine dyes, featuring dimethoxy quinolinium or methyl quinolinium end groups and benzothiazole or methyl benzothiazole end groups were synthesized. The chemical structures of the two dyes-()-6,7-dimethoxy-1-methyl-4-((3-methylbenzo[d]thiazol-2(3H)-ylidene)methyl)quinolin-1-ium iodide () and ()-4-((3,5-dimethylbenzo[d]thiazol-2(3H)-ylidene)methyl)-1,2-dimethylquinolin-1-ium iodide ()-were confirmed through NMR spectroscopy and MALDI-TOF mass spectrometry. A new methodology was developed to study monocationic dyes in the absence of a matrix and cationizing compounds in MALDI-TOF mass experiments.

Aggregachromic Fluorogenic Asymmetric Cyanine Probes for Sensitive Detection of Heparin and Protamine.

The precise and fast detection of heparin, the most widely used anticoagulant, remains a significant challenge for assessing its use in a clinical setting. In this work, we adapt a well-established asymmetric cyanine fluorogenic platform for the purpose of ultrasensitive heparin detection in the presence of common interferant chemical species. Three analogous fluorescence probes are synthesized in order to optimize for the number of binding moieties.

Nanoconfined Chlorine-Substituted Monomethine Cyanine Dye with a Propionamide Function Based on the Thiazole Orange Scaffold-Use of a Fluorogenic Probe for Cell Staining and Nucleic Acid Visualization.

The development of fluorescence-based methods for bioassays and medical diagnostics requires the design and synthesis of specific markers to target biological microobjects. However, biomolecular recognition in real cellular systems is not always as selective as desired. A new concept for creating fluorescent biomolecular probes, utilizing a fluorogenic dye and biodegradable, biocompatible nanomaterials, is demonstrated.

Asymmetric Monomethine Cyanine Dyes with Hydrophobic Functionalities for Fluorescent Intercalator Displacement Assay.

A new green procedure has been applied for the synthesis and purification of asymmetric monomethine cyanine dyes. The photophysical properties of the newly synthesized compounds have been examined by combined application of spectroscopic and theoretical methods. The structural characteristics of the molecules and dimer formation were characterized by quantum chemical computation and juxtaposed to the aggregachromism in UV/Vis spectra.

Aggregation induced nucleic acids recognition by homodimeric asymmetric monomethyne cyanine fluorochromes in mesenchymal stem cells.

In the light of recent retrovirus pandemics, the issue of discovering new and diverse RNA-specific fluorochromes for research and diagnostics became of acute importance. The great majority of nucleic acid-specific probes either do not stain RNA or cannot distinguish between DNA and RNA. The versatility of polymethine dyes makes them suitable as stains for visualization, analysis, and detection of nucleic acids, proteins, and other biomolecules.

Styryl dyes with N-Methylpiperazine and N-Phenylpiperazine Functionality: AT-DNA and G-quadruplex binding ligands and theranostic agents.

New monomethine, unsymmetrical styryl dyes consisting of benzothiazole and N-methylpiperazine or N-phenylpiperazine scaffolds were synthesized, and their binding affinities for different ds-polynucleotides and G-quadruplex were studied. Substitution of piperazine unit with methyl or phenyl group strongly influenced their binding modes, binding affinities, spectroscopic responses and antiproliferative activities. Compounds with N-methylpiperazine substituents showed a significant preference for AT-DNA polynucleotides and demonstrated AT-minor groove binding, which manifested in strong fluorescence increase, significant double helix stabilization, and positive induced circular dichroism spectra.

Tetrathienothiophene Porphyrin as a Metal-Free Sensitizer for Room-Temperature Triplet-Triplet Annihilation Upconversion.

Optically excited triplet states of organic molecules serve as an energy pool for the subsequent processes, either photon energy downhill, such as room temperature phosphorescence, or photon energy uphill process-the triplet-triplet annihilation upconversion (TTA-UC). Manifestation of a high intersystem crossing coefficient is an unavoidable requirement for triplet state formation, following the absorption of a single photon. This requirement is even more inevitable if the excitation light is non-coherent, with moderate intensity and extremely low spectral power density, when compared with the light parameters of 1 Sun (1.

Fluorescence sensing technology for the rapid detection of haze-forming proteins in white wine.

The methods currently available for determining haze proteins in wine are time-consuming, expensive, and often not sufficiently accurate. The latter may lead to bentonite over-fining of a wine, which might strip wine phenolics and aroma compounds, or wine under-fining, which increases the risk of protein instability. In this work, an efficient and rapid fluorescence-based technology to detect haze-forming proteins in white wines was developed.

Polycationic Monomeric and Homodimeric Asymmetric Monomethine Cyanine Dyes with Hydroxypropyl Functionality-Strong Affinity Nucleic Acids Binders.

New analogs of the commercial asymmetric monomethine cyanine dyes thiazole orange (TO) and thiazole orange homodimer (TOTO) with hydroxypropyl functionality were synthesized and their properties in the presence of different nucleic acids were studied. The novel compounds showed strong, micromolar and submicromolar affinities to all examined DNA ds-polynucleotides and poly rA-poly rU. The compounds studied showed selectivity towards GC-DNA base pairs over AT-DNA, which included both binding affinity and a strong fluorescence response.

Precious metal-free molecular machines for solar thermal energy storage.

Four benzothiazolium crown ether-containing styryl dyes were prepared through an optimized synthetic procedure. Two of the dyes ( and ) having substituents in the 5-position of the benzothiazole ring are newly synthesized compounds. They demonstrated a higher degree of photoisomerization and a longer life time of the higher energy forms in comparison with the known analogs.

Halogen-containing thiazole orange analogues - new fluorogenic DNA stains.

Novel asymmetric monomeric monomethine cyanine dyes , which are analogues of the commercial dsDNA fluorescence binder thiazole orange (), have been synthesized. The synthesis was achieved by using a simple, efficient and environmetally benign synthetic procedure to obtain these cationic dyes in good to excellent yields. Interactions of the new derivatives of with dsDNA have been investigated by absorption and fluorescence spectroscopy.

New fluorogenic dyes for analysis of cellular processes by flow cytometry and confocal microscopy.

Fluorescent microscopy and fluorescent imaging by flow cytometry are two of the fastest growing areas in the medical and biological research. Innovations in fluorescent chemistry and synthesis of new dye probes are closely related to the development of service equipment such as light sources, and detection techniques. Among compounds known as fluorescent labels, the cyanine-based dyes have become widely used since they have high excitation coefficients, narrow emission bands and high fluorescence upon binding to nucleic acids.

Fluorescence study of the membrane effects of aggregated lysozyme.

The last decade has seen unprecedented upsurge of interest in the structural and toxic properties of particular type of protein aggregates, amyloid fibrils, associated with a number of pathological states. In the present study fluorescence spectroscopy technique has been employed to gain further insight into the membrane-related mechanisms of amyloid toxicity. To this end, erythrocyte model system composed of liposomes and hemoglobin was subjected to the action of oligomeric and fibrillar lysozyme.

Probing the structural properties of DNA/RNA grooves with sterically restricted phosphonium dyes: screening of dye cytotoxicity and uptake.

To explore in greater detail the recently reported rare kinetic differentiation between homo-polymeric and alternating AT-DNA sequences by using sterically restricted phosphonium dyes that form dimers within the DNA minor groove, new analogues were prepared in which the quinolone phosphonium moiety was kept constant, while the size and hydrogen bonding properties of the rest of the molecule were varied. Structure-activity relationship studies revealed that a slight increase in length by an additional methylene unit results in loss of kinetic AT selectivity, but yielded an AT-selective fluorescence response. These DNA/RNA-groove-bound dyes combine very low cytotoxicity with efficient cellular uptake and intriguingly specific fluorescent marking of mitochondria.

Novel fluorescent dyes for single DNA molecule techniques.

To answer the demands of scientific and medical imaging issues, the family of nucleic acid fluorescent dyes is constantly enlarging. Most of the developed dyes reveal high qualities in bulk solution assays but are inefficient to produce a strong and sufficiently stable signal to enable the application of single-molecule techniques. Therefore, we tested 12 novel monomeric and homodimeric cyanine dyes for potential single DNA molecule imaging.

Fluorescence study of lipid bilayer interactions of Eu(III) coordination complexes.

The interaction between Eu(III) tris-β-diketonato coordination complexes (EC), displaying antitumor activity, and lipid vesicles composed of zwitterionic lipid phosphatidylcholine has been studied using fluorescence spectroscopy techniques. To characterize EC-membrane binding, several fluorescent probes, including pyrene, Prodan and 1,6-diphenyl-1,3,5-hexatriene, have been employed. It has been found that EC display effective partitioning into lipid phase, giving rise to structural modifications of both polar and nonpolar lipid bilayer regions, viz.

A novel squarylium dye for monitoring oxidative processes in lipid membranes.

A novel squaraine probe SQ-1 has been found to be appropriate for monitoring the peroxidation processes in membrane systems. Formation of free radicals was triggered by methemoglobin (metHb) or cytochrome c (cyt c) binding to the model lipid membranes composed of zwitterionic lipid phosphatidylcholine (PC) and anionic lipid cardiolipin (CL). Protein association with the lipid vesicles was followed by drastic quenching of SQ-1 fluorescence.

Structure-fluorescence contrast relationship in cyanine DNA intercalators: toward rational dye design.

The fluorescence enhancement mechanisms of a series of DNA stains of the oxazole yellow (YO) family have been investigated in detail using steady-state and ultrafast time-resolved fluorescence spectroscopy. The strong increase in the fluorescence quantum yield of these dyes upon DNA binding is shown to originate from the inhibition of two distinct processes: 1) isomerisation through large-amplitude motion that non-radiatively deactivates the excited state within a few picoseconds and 2) formation of weakly emitting H-dimers. As the H-dimers are not totally non-fluorescent, their formation is less efficient than isomerisation as a fluorescent contrast mechanism.

Fluorescence study of protein-lipid complexes with a new symmetric squarylium probe.

The novel symmetric squarylium derivative SQ-1 has been synthesized and tested for its sensitivity to the formation of protein-lipid complexes. SQ-1 binding to the model membranes composed of zwitterionic lipid phosphatidylcholine (PC) and its mixtures with anionic lipid cardiolipin (CL) in different molar ratios was found to be controlled mainly by hydrophobic interactions. Lysozyme (Lz) and ribonuclease A (RNase) exerted an influence on the probe association with lipid vesicles resulting presumably from the competition between SQ-1 and the proteins for bilayer free volume and modification of its properties.

A green synthesis of isatoic anhydrides from isatins with urea-hydrogen peroxide complex and ultrasound.

The oxidation of isatins at room temperature, using the cheap and environmentally friendly urea-hydrogen peroxide complex and ultrasonic irradiation, has been investigated. The ultrasonic irradiation dramatically reduces the reaction time. With easy and reproducible reaction procedures, different isatoic anhydrides were obtained in excellent yield and with high purity.

Evaluation of the cytotoxic and pro-apoptotic activities of Eu(III) complexes with appended DNA intercalators in a panel of human malignant cell lines.

A series of 8 europium (III) tris-beta-diketonates with common formula Eu(L)(3)Int, where L is acetyl acetone, thenoyltrifluoroacetone, benzoylacetone, dibenzoylmethane and Int is 1,10-phenanthroline or 2,2'-bipyridine, together with an analog without intercalating moiety (Eu(III)(acetyl acetone)(3)(H(2)O)(2)) were tested for cytotoxic activity in a panel of human tumor cell lines, using the MTT-dye reduction assay. The panel consisted of the leukemias HL-60, BV-173, SKW-3, K-562, LAMA-84 and the urinary bladder carcinoma 5637. The tested europium complexes with appended intercalator moieties exhibited profound cytotoxic effects with IC(50) values lower or comparable to those of the referent drug cis-DDP, whereby the 1,10-phenanthroline bearing compounds were invariably more active than the corresponding 2,2'-bipyridine analogs.

Ultrafast excited-state dynamics of DNA fluorescent intercalators: new insight into the fluorescence enhancement mechanism.

The excited-state dynamics of the DNA bisintercalator YOYO-1 and of two derivatives has been investigated using ultrafast fluorescence up-conversion and time-correlated single photon counting. The free dyes in water exist in two forms: nonaggregated dyes and intramolecular H-type aggregates, the latter form being only very weakly fluorescent because of excitonic interaction. The excited-state dynamics of the nonaggregated dyes is dominated by a nonradiative decay with a time constant of the order of 5 ps associated with large amplitude motion around the monomethine bridge of the cyanine chromophores.