Polymethine dyes as spectral-fluorescent probes for biomacromolecules

Spectral-fluorescent study of substituted trimethine cyanine dyes in solutions and in complexes with DNA. Effects of aggregation, moderate heating, and decreasing pH

Trimethine cyanine dyes are widely used as probes for the detection, study and quantification of biomolecules. In particular, cationic trimethine cyanines noncovalently interact with DNA with growing fluorescence. However, their use is often limited by the tendency to self-association - to the formation of aggregates. Disubstituted trimethine cyanines with hydrophobic substituents are especially prone to aggregation. In this work, we studied the interaction of a number of substituted trimethine cyanines with DNA (in aqueous buffer solutions) and showed that their aggregation strongly interfered with their use as fluorescent probes for DNA. To eliminate this drawback, preliminary heating of dye solutions with DNA to 60-70 °C was used, followed by cooling to room temperature. Compared to the experiments without heating, an increase in the dye fluorescence intensity was observed due to the partial thermal decomposition of the aggregates and the interaction of the resulting monomers with DNA. To decompose aggregates, another method was also used - protonation of the dyes with amino substituents in buffer solutions with pH 5.0, which also led to growing the dye fluorescence intensity in the presence of DNA. Complexes of the dyes with DNA were modeled using molecular docking. Effective binding constants of the dyes to DNA and detection limits when using the dyes as probes for DNA (LOD and LOQ) were determined. It is shown that dye 3 with heating in neutral buffer and dye 1 in acidic buffer may be recommended as sensitive probes for DNA. It is concluded that the method of preliminary heating may be applied to dyes prone to aggregation, for improving their properties as biomolecular probes. Another possible means to reduce the interfering effects of dye aggregates is to use easily protonated dyes (with amino substituents) in slightly acidic media.

Shortwave infrared polymethine dyes for bioimaging: ultrafast relaxation dynamics and excited-state decay pathways

Excited-state relaxation in two prototypical shortwave infrared (SWIR) polymethine dyes developed for bioimaging, heptamethine chromenylium Chrom7 and flavylium Flav7, is studied by means of femtosecond transient absorption with broadband ultraviolet-to-SWIR probing complemented by steady-state and time-resolved fluorescence and phosphorescence measurements. The relaxation processes of the dyes in dichloromethane are resolved with sub-100 fs temporal resolution using SWIR, near-IR, and visible photoexcitation. Different population members of the ground-state inhomogeneous ensemble are found to equilibrate via skeletal deformation changes with time constants of 90 fs and either 230 fs (Chrom7) and 350 fs (Flav7) followed by slower evolution matching the 1-ps timescale of diffusive solvation dynamics. Molecules excited into high-lying singlet electronic states (Sn) by visible excitation repopulate with time constants of 400 fs (Chrom7) and 450 fs (Flav7) the corresponding first excited singlet S1 states, which decay within several hundreds of picoseconds in dichloromethane and chloroform solvents. Vibrational relaxation in S1 for both Chrom7 and Flav7 in dichloromethane occurs with time constants of 350 and 800 fs for excess of vibrational energy of ∼1000 and 10 000 cm-1 deposited by near-IR and visible excitation, respectively. Two competing non-radiative processes are present in S1: temperature-independent internal conversion, and thermally-activated twisting about a carbon-carbon bond of the conjugated chain, which is substantial at room temperature but essentially nonreactive, producing traces of isomer product. Intersystem crossing in S1, and thus the triplet quantum yield, is minor. The importance of absorption bands from the excited S1 state in applications requiring high-intensity excitation conditions is discussed.

Water-soluble chromenylium dyes for shortwave infrared imaging in mice

In vivo imaging using shortwave infrared light (SWIR, 1000-2000 nm) benefits from deeper penetration and higher resolution compared to using visible and near-infrared wavelengths. However, the development of biocompatible SWIR contrast agents remains challenging. Despite recent advancements, small molecule SWIR fluorophores are often hindered by their significant hydrophobicity. We report a platform for generating a panel of soluble and functional dyes for SWIR imaging by late-stage functionalization of a versatile fluorophore intermediate, affording water-soluble dyes with bright SWIR fluorescence in serum. Specifically, a tetra-sulfonate derivative enables clear video-rate imaging of vasculature with only 0.05 nmol dye, and a tetra-ammonium dye shows strong cellular retention for tracking of tumor growth. Additionally, incorporation of phosphonate functionality enables imaging of bone in awake mice. This modular design provides insights for facile derivatization of existing SWIR fluorophores to introduce both solubility and bioactivity towards in vivo bioimaging.

Bluer Phototruncation: Retro-Diels-Alder of Heptamethine Cyanine to Trimethine Cyanine through an Allene Hydroperoxide Intermediate

The photoconversion of heptamethine to pentamethine cyanines and of pentamethine to trimethine cyanines was recently reported. Here, we report mechanistic studies and initial experimental evidence for a previously unexplored 4-carbon truncation reaction that converts the simplest heptamethine cyanine to the corresponding trimethine cyanine. We propose a DFT-supported model describing a singlet oxygen (1O2)-mediated formation of an allene hydroperoxide intermediate and subsequent 4-carbon loss through a retro-Diels-Alder process. Fluorescence and mass spectrometry measurements provide evidence of this direct conversion process. This 4-carbon truncation reaction adds to a growing body of cyanine reactivity and may provide an optical tool leading to a substantial blue-shift (Δλem) of ∼200 nm.

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. We synthesized the asymmetric dicationic homodimeric monomethine cyanine dyes 1,1'-(1,3-phenylenebis(methylene))bis(4-((3-methylbenzo[d]thiazol-2(3H)-ylidene)methyl)pyridin-1-ium) bromide (Т1) and 1,1'-(1,3-phenylenebis(methylene))bis(4-((3-methylbenzo[d]thiazol-2(3H)-ylidene)methyl)quinolin-1-ium) bromide (M1) and tested their binding specificity, spectral characteristics, membrane penetration in living and fixed cells, cellular toxicity, and stability of fluorescent emission. Mesenchymal cells have diverse phenotypes and extensive proliferation and differentiation properties. We found dyes T1 and M1 to show high photochemical stability in living mesenchymal stem cells from apical papilla (SCAP) with a strong fluorescent signal when bound to nucleic acids. We found M1 to perform better than control fluorochrome (Hoechst 33342) for in vivo DNA visualization. T1, on the other hand, stains granular cellular structures resembling ribosomes in living cells and after permeabilization of the nuclear membrane stains the nucleoli and not the chromatin in the nucleus. This makes T1 suitable for the visualization of structures rich in RNA in living and fixed cells.

Photonics of Some Monomethine Cyanine Dyes in Solutions and in Complexes with Biomolecules

In search of new probes for biomolecules, the spectral fluorescent study of four monomethine cyanine dyes (MCD), both unsymmetrical and symmetrical, has been carried out in different organic solvents, in aqueous buffer solutions, and in the presence of DNA and HSA. The complexation of MCD with biomacromolecules leads to a steep growth of the fluorescence intensity. Complexes of MCD with dsDNA and HSA of various types were modeled in silico by molecular docking. Experiments on thermal dissociation of dsDNA in the presence of MCD showed the formation of intercalative complexes of MCD with DNA. Quenching of intrinsic fluorescence of HSA by MCD occurred with rate constants much higher than the diffusion limit, that is, in dye-HSA complexes. Effective constants of MCD complexation with the biomacromolecules were estimated. MCD 1 has the best characteristics as a possible fluorescent probe for dsDNA and can serve as a sensitive and selective probe for dsDNA in the presence of HSA. Photochemical properties of MCD complexed with DNA have been also studied. An increase in the quantum yield of the triplet states of MCD in complexes with DNA has been found, which may be important for using these dyes as potential candidates in photodynamic therapy.

Spectral-fluorescent and photochemical study of 6,6'-di(benzoylamino)trimethine cyanine dyes in solutions as possible probes for DNA

Spectral-fluorescent and photochemical properties of trimethine cyanine dyes T-304, T-306, and T-307, having substituents in 6,6'-positions, in various organic solvents, in aqueous buffer solutions, in the presence of surfactants and ethanol additives, and the effect on these properties of addition of DNA have been studied. Strong aggregation of the dyes in aqueous and aqueous buffer solutions has been shown. This is due to increased hydrophobicity of the dyes, which makes it difficult to use them as spectral-fluorescent probes for DNA. In the presence of DNA, trimethine cyanines partially form highly fluorescent complexes of dye monomers with the biomolecule, with slight decomposition of the initial aggregates and the formation of aggregates on DNA molecules. The formation of different types of dye-DNA complexes, i.e., intercalation and binding in the DNA grooves, was modeled by molecular docking. Dye-DNA complexes were also studied by circular dichroism spectroscopy and by thermal dissociation of DNA. To reveal selectivity of the dyes, their interaction with human serum albumin was briefly studied. The presence of moderate concentrations of nonionic surfactants does not lead to a significant decomposition of aggregates, but leads to a biphasic dependence of the fluorescence intensity on the DNA concentration. At the same time, ethanol additives (15%) lead to a more or less linear concentration dependence of the fluorescence intensity, which makes it possible to use these dyes as fluorescent probes for DNA. The effective binding constants of the dyes to DNA and the limits of DNA detection using the dyes in the presence of 15% ethanol were estimated. Photoisomerization and generation of the triplet states of T-304, T-306, and T-307 have been also studied. Along with the fluorescence growth, complexation with DNA leads to an increase in the yield of the triplet states of the dyes. This creates a prerequisite for using the dyes in targeted PDT. In the presence of DNA, the decay kinetics of the triplet states are biexponential, which indicates different types of dye complexes with DNA. The rate constants of oxygen quenching of the triplet states of the dyes bound to DNA are significantly lower than the diffusion-controlled values (taking into account the spin-statistical factor), which is explained by the shielding effect on the triplet molecules in complexes with DNA. The data obtained show that dyes T-304, T-306 and T-307, with addition of 15% ethanol, can be used as possible fluorescent probes for DNA.

Solvent-Dependent Functional Aggregates of Unsymmetrical Squaraine Dyes on TiO2 Surface for Dye-Sensitized Solar Cells

Alkyl group wrapped donor-acceptor-donor (D-A-D) based unsymmetrical squaraine dyes SQ1, SQ5, and SQS4 were used to evaluate the effect of sensitizing solvents on dye-sensitized solar cell (DSSC) efficiency. A drastic change in DSSC efficiency was observed when the photo-anodes were sensitized in acetonitrile (bad solvent when considering dye solubility) and chloroform (good solvent) with an Iodolyte (I^-/I₃^-) electrolyte. The DSSC device sensitized with squaraine dyes in acetonitrile showed better photovoltaic performance with enhanced photocurrent generation and photovoltage compared to the device sensitized in chloroform. In a good sensitizing solvent, dyes with long hydrophobic alkyl chains are deleterious forming aggregates on the TiO₂ surface, which results in an incident photon-to-current conversion efficiency (IPCE) response mostly from monomeric and dimeric structures. Meanwhile, a bad sensitizing solvent facilitates the formation of well-packed self-assembled structures on the TiO₂ surface, which are responsible for a broad IPCE response and high device efficiencies. The photoanode sensitized in the bad sensitizing solvent showed enhanced V_OC values of 642, 675, and 699 mV; J_SC values of 6.38, 11.1, and 11.69 mA/cm²; and DSSC device efficiencies of 3.0, 5.63, and 6.13% for the SQ1, SQ5, and SQS4 dyes in the absence of a coadsorbent (chenodeoxycholic acid (CDCA)), respectively, which were further enhanced by CDCA addition. Meanwhile, the photoanode sensitized in the good sensitizing solvent showed relatively low photovoltaic V_OC values of 640, 652, and 650 mV; J_SC values of 5.78, 6.79, and 6.24 mA/cm²; and device efficiencies of 2.73, 3.35, and 3.20% for SQ1, SQ5, and SQS4 in the absence of CDCA, respectively, which were further varied with equivalents of CDCA. The best DSSC device efficiencies of 6.13 and 3.20% were obtained for SQS4 without CDCA, where the dye was sensitized in acetonitrile (bad) and chloroform (good) sensitizing solvents, respectively.

Photonics of Trimethine Cyanine Dyes as Probes for Biomolecules

Cyanine dyes are widely used as fluorescent probes in biophysics and medical biochemistry due to their unique photophysical and photochemical properties (their photonics). This review is focused on a subclass of the most widespread and studied cyanine dyes—trimethine cyanines, which can serve as potential probes for biomolecules. The works devoted to the study of the noncovalent interaction of trimethine cyanine dyes with biomolecules and changing the properties of these dyes upon the interaction are reviewed. In addition to the spectral-fluorescent properties, elementary photochemical properties of trimethine cyanines are considered, including: photoisomerization and back isomerization of the photoisomer, generation and decay of the triplet state, and its quenching by oxygen and other quenchers. The influence of DNA and other nucleic acids, proteins, and other biomolecules on these properties is covered. The interaction of a monomer dye molecule with a biomolecule usually leads to a fluorescence growth, damping of photoisomerization (if any), and an increase in intersystem crossing to the triplet state. Sometimes aggregation of dye molecules on biomolecules is observed. Quenching of the dye triplet state in a complex with biomolecules by molecular oxygen usually occurs with a rate constant much lower than the diffusion limit with allowance for the spin-statistical factor 1/9. The practical application of trimethine cyanines in biophysics and (medical) biochemistry is also considered. In conclusion, the prospects for further studies on the cyanine dye–biomolecule system and the development of new effective dye probes (including probes of a new type) for biomolecules are discussed.

Synthesis and characterization of polymethine dyes carrying thiobarbituric and carboxylic acid moieties

Polymethine dyes are prepared using a convenient synthesis and characterized by physicochemical and computational methods.

Photonics of meso-substituted carbocyanine dyes in solutions and in complexes with DNA

Spectral-fluorescent and photochemical properties (photoisomerization and generation of the triplet state) of meso-substituted cationic carbocyanine dyes, 3,3'-di-(β-hydroxyethyl)-5,5'-dimethoxy-9-ethylthiacarbocyanine iodide (K1) and 3,3'-di-(β-hydroxyethyl)-9-methylthiacarbocyanine iodide (K2), have been studied in solutions and in the presence of DNA. In solutions, on passing from acetonitrile to dioxane, a growth of fluorescence of the dyes is observed due to a shift of the equilibrium of cis/trans isomers toward the fluorescent trans-isomer. Upon flash photolysis of dye solutions in dioxane, the formation and subsequent decay of the cis-photoisomers of the dyes are observed. In aqueous solutions, the interaction with DNA leads to the formation of noncovalent complexes of K1 and K2 with DNA, which is accompanied by a significant increase in the fluorescence intensity. The results of the molecular docking experiments showed the possibility of several types of binding, which was confirmed by the data obtained from other experiments. The effects of temperature and additions of NaCl on the stability of the dye-DNA complexes were studied. The spectral-fluorescent data were used to estimate the binding constants of the dyes with DNA and other characteristics of the dyes that are important for their use as probes. Upon flash photolysis of the dyes in complexes with DNA, photoisomerization is not observed, but the quantum yield of intersystem crossing to the triplet state increases. The decay of the triplet states occurs by a two-exponential law. The rate constants for quenching of the triplet states of the dyes complexed with DNA by oxygen were found to be lower than the expected values for diffusion-controlled quenching (taking into account the spin statistical factor 1/9), which is explained by the steric factor of complexation.

Conjugating pyrene onto PNA-based fluorescent probes for improved detection selectivity toward double-stranded siRNA

We report on the design of new siRNA-binding fluorescent probes with the improved detection selectivity toward intact double-stranded siRNAs over single-stranded forms by the conjugation of pyrene unit into thiazole orange base surrogate-carrying peptide nucleic acid (PNA) that can simultaneously recognize the 3'-overhang and double-stranded sequences of target siRNAs.

Polymethine Dyes as Probes for Detecting the SARS-COV-2 Coronavirus: In silico Molecular Docking Study

The noncovalent interaction between various polymethine dyes (45 compounds in total) and a spike protein (S), one of the main structural component of the SARS-CoV-2 coronavirus, is studied in silico (molecular docking) to develop effective probes to detect the virus. The interaction energies and the spatial configurations of the complexes of the dye molecules with S are found. We showed that cationic polymethine dyes and neutral squarylium dyes do not form stable complexes with S. Some anionic dyes having negative total energies E_tot may be recommended for practical research.

Novel (Phenothiazinyl)Vinyl-Pyridinium Dyes and Their Potential Applications as Cellular Staining Agents

We report here the synthesis and structural characterization of novel cationic (phenothiazinyl)vinyl-pyridinium (PVP) dyes, together with optical (absorption/emission) properties and their potential applicability as fluorescent labels. Convective heating, ultrasound irradiation and mechanochemical synthesis were considered as alternative synthetic methodologies proficient for overcoming drawbacks such as long reaction time, nonsatisfactory yields or solvent requirements in the synthesis of novel dye (E)-1-(3-chloropropyl)-4-(2-(10-methyl-10H-phenothiazin-3-yl)vinyl)pyridin-1-ium bromide 3d and its N-alkyl-2-methylpyridinium precursor 1c. The trans geometry of the newly synthesized (E)-4-(2-(7-bromo-10-ethyl-10H-phenothiazin-3-yl)vinyl)-1-methylpyridin-1-ium iodide 3b and (E)-1-methyl-4-(2-(10-methyl-10H-phenothiazin-3-yl)vinyl)pyridin-1-ium tetrafluoroborate 3a′ was confirmed by single crystal X-ray diffraction. A negative solvatochromism of the dyes in polar solvents was highlighted by UV-Vis spectroscopy and explanatory insights were supported by molecular modeling which suggested a better stabilization of the lowest unoccupied molecular orbitals (LUMO). The photostability of the dye 3b was investigated by irradiation at 365 nm in different solvents, while the steady-state and time-resolved fluorescence properties of dye 3b and 3a′ in solid state were evaluated under one-photon excitation at 485 nm. The in vitro cytotoxicity of the new PVP dyes on B16-F10 melanoma cells was evaluated by WST-1 assay, while their intracellular localization was assessed by epi-fluorescence conventional microscopy imaging as well as one- and two-photon excited confocal fluorescence lifetime imaging microscopy (FLIM). PVP dyes displayed low cytotoxicity, good internalization inside melanoma cells and intense fluorescence emission inside the B16-F10 murine melanoma cells, making them suitable staining agents for imaging applications.

Near-Infrared Fluorescent Probes with Rotatable Polyacetylene Chains for the Detection of Amyloid-β Plaques

The plaques of accumulated β-amyloid (Aβ) in the parenchymal brain are accepted as an important biomarker for the early diagnosis of Alzheimer's disease (AD). Many near-infrared (NIR) probes, which were based on the D-π-A structure and bridged by conjugated double bonds, had been reported and displayed a high affinity to Aβ plaques. Considering the isomerization caused by the polyethylene chain, however, the conjugated polyacetylene chain is a better choice for developing new NIR Aβ probes. Hence, in this report, a new series of NIR probes with naphthyl or phenyl rings and different numbers of conjugated triple bonds were designed, synthesized, and evaluated as NIR probes for Aβ plaques. Upon interaction with Aβ aggregates, these probes displayed a significant increase in fluorescence intensity (45- to 360-fold) and a high to moderate affinity (6.05-56.62 nM). Among them, probe 22b displayed excellent fluorescent properties with a 183-fold increase in fluorescence intensity and an emission maximum at 650 nm after incubated with Aβ aggregates. Furthermore, 22b had a high affinity to Aβ aggregates (K_d = 12.96 nM) and could efficiently detect the Aβ plaques in brain sections from both transgenic mice and AD patients in vitro. In summary, this work may lead to a new direction in the development of novel NIR probes for the detection of Aβ plaques.

Discovery of a size-record breaking green-emissive fluorophore: small, smaller, HINA

Astonishingly, 3-hydroxyisonicotinealdehyde (HINA) is despite its small size a green-emitting push–pull fluorophore in water (QY of 15%) and shows ratiometric emission response to biological relevant pH differences (pK_a2 ∼ 7.1). Moreover, HINA is the first small-molecule fluorophore reported that possesses three distinctly emissive protonation states. This fluorophore can be used in combination with metal complexes for fluorescent-based cysteine detection in aqueous media, and is readily taken up by cells. The theoretical description of HINA's photophysics remains challenging, even when computing Franck–Condon profiles via coupled-cluster calculations, making HINA an interesting model for future method development.

Astonishingly, 3-hydroxyisonicotinealdehyde (HINA) is despite its small size a green-emitting push–pull fluorophore in water (QY of 15%) and shows ratiometric emission response to biological relevant pH differences (pK_a2 ∼ 7.1).

ICG-loaded gold nano-bipyramids with NIR activatable dual PTT-PDT therapeutic potential in melanoma cells

A great amount of effort is directed towards the progress of cancer treatment approaches aspiring to develop non-invasive, targeted and highly efficient therapies. In this context, Photothermal (PTT) and Photodynamic (PDT) Therapies were proven as promising. This work aims to integrate the therapeutic activities of two near-infrared (NIR) photoactive biomaterials - gold nano-bipyramids (AuBPs) and Indocyanine Green (ICG) - into one single targeted hybrid nanosystem able to operate as dual PTT-PDT agent with higher efficiency compared with each one alone. Firstly, different aspect ratio' AuBPs were systematically investigated in water solution for their intrinsic ability to efficiently generate toxic reactive oxygen species, namely oxygen singlet (¹O₂), under NIR laser irradiation, as this effect is less investigated in literature. Interestingly, the photodynamic activity of AuBPs measured by monitoring the photooxidation of 9,10-Anthracenediyl-bis(methylene)dimalonic acid (ABDA) - a well-known ¹O₂ sensor, is important, counting for 30 % decrease in ABDA optical absorbance for the most active AuBPs, well-correlating with the previously determined photothermal conversion efficiency. Furthermore, ICG was successfully grafted onto the Poly-lactic acid (PLA) coating of plasmonic nanoparticles and, consequently, the as-designed fully integrated hybrid nanosystem shows improved PTT-PDT performance in solution. Specifically, by triggering simultaneous PTT-PDT activities, the ¹O₂ amount is doubled, while the heating monitoring shows higher and faster increase in temperature compared to AuBPs alone. Finally, the efficiency of the combined PTT-PDT therapeutic activity was validated in vitro against B16-F10 cell line by covalent conjugation of the nanosystem with Folic Acid, which ensures the cellular recognition by overexpression of folate receptor.

Fluorimetric and CD Recognition between Various ds-DNA/RNA Depends on a Cyanine Connectivity in Cyanine-guanidiniocarbonyl-pyrrole Conjugate

Two novel isosteric conjugates of guanidiniocarbonyl-pyrrole and 6-bromo-TO (thiazole orange) were prepared, differing only in linker connectivity to cyanine (benzothiazole nitrogen vs. quinoline nitrogen). The quinoline analog was significantly more susceptible to aggregation in an aqueous medium, which resulted in induced circular dichroism (ICD; λ = 450-550 nm) recognition between A-T(U) and G-C basepair containing polynucleotides. The benzothiazole-isostere showed pronounced (four-fold) fluorimetric selectivity toward ds-RNA in comparison to any ds-DNA, at variance to its quinoline-analogue fluorescence being weakly selective to GC-DNA. Preliminary screening on human tumor and normal lung cell lines showed that both dyes very efficiently enter living cells and accumulate in mitochondria, causing moderate cytotoxic effects, and thus could be considered as lead compounds toward novel theragnostic mitochondrial dyes.

Protein Discrimination Using a Fluorescence-Based Sensor Array of Thiacarbocyanine-GUMBOS

Sensitive and selective detection of proteins from complex samples has gained substantial interest within the scientific community. Early and precise detection of key proteins plays an important role in potential clinical diagnosis, treatment of different diseases, and proteomic research. In the study reported here, six different compounds belonging to a group of uniform materials based on organic salts (GUMBOS) have been synthesized using three thiacarbocyanine (TC) dyes and employed as fluorescent sensors. Fluorescence properties of micro- and nanoaggregates of these TC-based GUMBOS formed in phosphate buffer solutions are studied in the absence and presence of seven proteins. Fluorescence response patterns of these TC-based GUMBOS were analyzed by linear discriminant analysis (LDA). The constructed LDA model allowed discrimination of these seven proteins at various concentrations with 100% accuracy. The sensing and discrimination abilities of these TC-based GUMBOS were further evaluated in mixtures of two major proteins, i.e., human serum albumin and hemoglobin. Fluorescence response patterns of these mixtures were analyzed by LDA. This model allowed discrimination of various mixtures with 100% accuracy. Moreover, spiked urine samples were prepared and the responses of these sensors were collected and analyzed by LDA. Remarkably, discrimination of these seven proteins was also achieved with 100% accuracy.

Cyanine dyes

Cyanine dyes are characterized by an odd number 2n + 3 of π-centers and 2n + 4 π-electrons (where n is the number of vinyl groups –CH = CH–). This special feature has a marked impact on their electronic structure and thus their equilibrium structure in the electronic ground state as well their color and electronic spectrum, respectively. Their first technical application was the use as spectral sensitizers in silver halide photography. Today they have numerous of applications in digital optical data storage, Computer-to-Plate lithographic printing plates, bio-analysis and medical diagnostics.

Probing of Nucleic Acid Structures, Dynamics, and Interactions With Environment-Sensitive Fluorescent Labels

Fluorescence labeling and probing are fundamental techniques for nucleic acid analysis and quantification. However, new fluorescent probes and approaches are urgently needed in order to accurately determine structural and conformational dynamics of DNA and RNA at the level of single nucleobases/base pairs, and to probe the interactions between nucleic acids with proteins. This review describes the means by which to achieve these goals using nucleobase replacement or modification with advanced fluorescent dyes that respond by the changing of their fluorescence parameters to their local environment (altered polarity, hydration, flipping dynamics, and formation/breaking of hydrogen bonds).

The guanidiniocarbonylpyrrole-fluorophore conjugates as theragnostic tools for dipeptidyl peptidase III monitoring and inhibition

Study of seven new guanidiniocarbonylpyrrole (GCP)-fluorophore conjugates interactions with dipeptidyl peptidase III (DPP III) showed that all compounds bind strongly (K_s ≈ µM) to enzyme active site, but with very different fluorimetric response (varying from quenching to strong increase), dependent on the fluorophore type and intramolecular pre-organisation of molecule. Positively charged lysine side chain improved significantly compound solubility but diminished fluorescence increase upon DPP III binding and completely abolished inhibitory effect on DPP III activity, whereas linker-neutral analogues showed stronger emission increase and were efficient enzyme inhibitors. By far the best fluorimetric response and inhibitive properties showed cyanine-GCP analogue, thus being promising lead compound for both enzyme sensing and bio-activity inhibiting (theragnostic) studies of DPP III in the future.Communicated by Ramaswamy H. Sarma.

Spectral-fluorescent study of the interaction of polymethine dye probes with biological surfactants - bile salts

Spectral-fluorescent properties of polymethine dye probes anionic 3,3'-di(sulfopropyl)-4,5,4',5'-dibenzo-9-ethylthiacarbocyanine-betaine (DEC) and cationic 3,3',9-trimethylthiacarbocyanine iodide (Cyan 2) in the presence of biological surfactants, bile salts sodium cholate (NaC), sodium deoxycholate (NaDC) and sodium taurocholate (NaTC), as well as sodium dodecyl sulfate (SDS), have been studied in a wide range of surfactant concentrations. When a surfactant is introduced into a solution of DEC, changes of the spectral-fluorescent properties are observed due to decomposition of dye dimers into cis-monomers and cis-trans conversion of the resulting monomers. In the presence of SDS, both processes occur in parallel, caused by noncovalent interaction of dye monomers with micelles, and mainly occur near the critical micelle concentration (CMC). In contrast, upon the introduction of increasing concentrations of bile salts, decomposition of dye dimers into the monomers begins at lower concentrations than cis-trans conversion. The former process is almost completed at concentrations close to CMC of secondary micelles (CMC2), while the latter process occurs even at concentrations of bile salts much higher than CMC2. Hence, DEC can serve as a probe that permits estimating the value of CMC2 and is indicative of reorganization of secondary micelles upon an increase in bile salt concentration. Aggregation of DEC and Cyan 2 on bile salts is also observed. Since it is observed at relatively low concentrations of bile salts (<CMC2), the aggregation probably occurs on monomeric molecules of bile salts and their small associates and primary micelles. Decomposition of the aggregates formed begins at concentrations of bile salts above CMC2 (that is, upon the interaction with secondary micelles).

Isomerization and Properties of Isomers of Carbocyanine Dyes

One of the important features of polymethine (cyanine) dyes is isomerization about one of C–C bonds of the polymethine chain. In this review, spectral properties of the isomers, photoisomer-ization and thermal back isomerization of carbocyanine dyes, mostly meso-substituted carbocy-anine dyes, are considered. meso-Alkyl-substituted thiacarbocyanine dyes are present in polar solvents mainly as cis isomers and, hence, exhibit no photoisomerization, whereas in nonpolar solvents, in which the dyes are in the trans form, photoisomerization takes place. In contrast, the meso-substituted dyes 3,3′-dimethyl-9-phenylthiacarbocyanine and 3,3′-diethyl-9-(2-hydroxy-4-methoxyphenyl)thiacarbocyanine occur as trans isomers and exhibit photoisomerization in both polar and nonpolar solvents. The behavior of these dyes may be ex-plained by the fact that the phenyl ring of the substituent in their molecules can be twisted at some angle, removing the substituent from the plane of the molecule and reducing its steric ef-fect on the conformation of the trans isomer. In some cases, photoisomerization of cis isomers of meso-substituted carbocyanine dyes is also observed (for some meso-alkyl-substituted dyes com-plexed with DNA and chondroitin-4-sulfate; for 3,3′-diethyl-9-methoxythiacarbocyanine in moderate polarity solvents). The cycle photoisomerization–thermal back isomerization of cya-nine dyes can be used in various systems of information storage and deserves further investiga-tion using modern research methods.

Isomerization and Properties of Isomers of Carbocyanine Dyes

One of the important features of polymethine (cyanine) dyes is isomerization around one of C–C bonds of the polymethine chain. In this review, spectral properties of the isomers, photoisomerization and thermal back isomerization of carbocyanine dyes, mostly meso-substituted carbocyanine dyes, are considered. meso-Alkyl-substituted thiacarbocyanine dyes are present in polar solvents mainly as cis isomers and, hence, exhibit no photoisomerization, whereas in nonpolar solvents, in which the dyes are in the trans form, photoisomerization takes place. In contrast, the meso-substituted dyes 3,3′-dimethyl-9-phenylthiacarbocyanine and 3,3′-diethyl-9-(2-hydroxy-4-methoxyphenyl)thiacarbocyanine occur as trans isomers and exhibit photoisomerization in both polar and nonpolar solvents. The behavior of these dyes may be explained by the fact that the phenyl ring of the substituent in their molecules can be twisted at some angle, removing the substituent from the plane of the molecule and reducing its steric effect on the conformation of the trans isomer. In some cases, photoisomerization of cis isomers of meso-substituted carbocyanine dyes is also observed (for some meso-alkyl-substituted dyes complexed with DNA and chondroitin-4-sulfate; for 3,3′-diethyl-9-methoxythiacarbocyanine in moderate polarity solvents). The cycle photoisomerization–thermal back isomerization of cyanine dyes can be used in various systems of information storage and deserves further investigation using modern research methods.

Fluorimetric Detection of G-Quadruplex DNA in Solution and Adsorbed on Surfaces with a Selective Trinuclear Cyanine Dye

Quadruplex DNA, which is a relevant target for anticancer therapies, may alter its conformation because of interactions with interfaces. In pursuit of a versatile methodology to probe adsorption-induced conformational changes, the interaction between a fluorescent [2.2.2]heptamethinecyanine dye and quadruplex DNA (G4-DNA) was studied in solution and on surfaces. In solution, the cyanine dye exhibits a strong light-up effect upon the association with G4-DNA without interference from double-stranded DNA. In addition, a terminal π-stacking as a binding mode between the cyanine dye and G4-DNA is concluded using NMR spectroscopy. To unravel the effects of adsorption on the conformation of quadruplex-DNA, G4-DNA, and double-stranded and single-stranded DNA were adsorbed to positively charged poly(allylamine) hydrochloride (PAH) surfaces, both in planar and in constrained 55 nm diameter aluminum oxide nanopore formats. All DNA forms showed a very strong affinity to the PAH surfaces as shown by surface plasmon resonance and reflectometric interference spectroscopy. The significant increase of the fluorescence emission intensity of the cyanine light-up probe observed exclusively for surface immobilized G4-DNA affords evidence for the adsorption of G4-DNA on PAH with retained quadruplex conformation.

Influence of the interaction with DNA on the spectral-fluorescent and photochemical properties of some meso-substituted polymethine dyes

Spectral-fluorescent and photochemical properties of meso-substituted thiacarbocyanine dyes 3,3'-dimethyl-9-phenylthiacarbocyanine and 3,3'-diethyl-9-(2-hydroxy-4-methoxyphenyl)thiacarbocyanine in solutions and their interaction with DNA were studied. The dyes form noncovalent complexes with DNA, which is accompanied by changes in the absorption spectra and an increase in the fluorescence intensity of the dyes. The data obtained suggest that the dyes are in the form of trans-isomers both in solvents of different polarity and in complexes with DNA. It was shown that the interaction of the dyes with DNA is a complex process involving monomeric dye molecules and aggregates of the dyes. The primary photochemical processes of the dyes in solutions and in complexes with DNA were studied by flash photolysis technique. Upon flash photoexcitation in solutions, the formation and decay of the photoisomers of the dyes were observed, with no generation of the triplet states. In the complex with DNA, no signal of photoisomers was detected; in the absence of oxygen, the formation of the triplet state of the dyes was observed. The decay kinetics of the triplet state of the dyes were two-exponential. The process of quenching of the triplet state of the dyes by oxygen in a complex with DNA was studied, the respective quenching rate constants were estimated, being lower than the diffusion-controlled value.

Fine Structure in Electronic Spectra of Cyanine Dyes: Are Sub-Bands Largely Determined by a Dominant Vibration or a Collection of Singly Excited Vibrations?

This work critically examines attempts to model the fine structure apparent in electronic spectra of cyanine dyes and their analogues. Numerous computational studies reported over the past decade attribute the origin of sub‐bands and their relative intensities to vibronic transitions in which the relevant electronic transition is coupled, irrespective of symmetry, with a collection of vibrations. It is contended that this type of approach is not supported by experimental evidence. An argument is reiterated for a more appropriate model that adheres closely to fundamental principles and fits the data. It stipulates that essentially just one symmetric vibration, carbon–carbon bond stretching of the cyanine polymethine chain, dominates the coupling and is responsible for the observed fine structure. Furthermore, it is pointed out that the intensities of the sub‐bands are readily explained by means of the Franck–Condon principle.

Spectral-fluorescent study of the interaction of the polymethine dye probe Cyan 2 with chondroitin-4-sulfate

The noncovalent interaction of the polymethine dye probe 3,3',9-trimethylthiacarbocyanine iodide (Cyan 2) with chondroitin-4-sulfate (C4S) in buffer solutions with different pH and in water in the absence of buffers has been studied by spectral-fluorescent methods. It has been shown that in all media studied, at relatively high concentrations, the dye is bound to C4S mainly as a monomer, which is accompanied by a steep rise of fluorescence (the intermediate formation of dye aggregates on the biopolymer is also observed). From the dependence of the fluorescence quantum yield on the concentration of C4S, the parameters of binding of the dye monomer to C4S were obtained: the effective binding constant K, the number of the monomeric C4S units n per one dye monomer bound to C4S, and the fluorescence quantum yield of the bound dye monomer Φ_fb. The dependence of Φ_fb (and K) on рН of the medium is not monotonic: it has a minimum in the region of neutral pH and a growth in the regions of acid and basic pH. This can be explained by changing the charge of a C4S macromolecule as a function of pH and related conformational alterations in the biopolymer, which can affect the rigidity of a dye molecule and the energy of its interaction with the biopolymer.

Lysine linkage in abasic site-binding ligand-thiazole orange conjugates for improved binding affinity to orphan nucleobases in DNA/RNA hybrids

Introduction of lysine linkage in the conjugate between abasic site-binding ligands and thiazole orange significantly improved the binding affinity for target orphan adenine or uracil nucleobase in DNA/RNA hybrids.

Mechanistic aspects of thioflavin-T self-aggregation and DNA binding: evidence for dimer attack on DNA grooves

Thioflavin-T (TFT) is a fluorescent marker widely employed in biomedical research but the mechanism of its binding to polynucleotides has been poorly understood. This paper presents a study of the mechanisms of TFT self-aggregation and binding to DNA. Relaxation kinetics of TFT solutions show that the cyanine undergoes dimerization followed by dimer isomerisation. The interaction of TFT with DNA has been investigated using static methods, such as spectrophotometric and spectrofluorometric titrations under different conditions (salt content, temperature), fluorescence quenching, viscometric experiments and the T-jump relaxation method. The combined use of these techniques enabled us to show that the TFT monomer undergoes intercalation between the DNA base pairs and external binding according to a branched mechanism. Moreover, it has also been observed that, under dye excess conditions, the TFT dimer binds to the DNA grooves. The molecular structures of intercalated TFT and the groove-bound TFT dimer are obtained by performing QM/MM MD simulations.

Elaboration of an unexplored substitution site in synthetic bacteriochlorins

The ability to introduce substituents at designated sites about the perimeter of synthetic bacteriochlorins – analogs of bacteriochlorophylls of bacterial photosynthesis – remains a subject of ongoing study. Here, the self-condensation of a dihydrodipyrrin-dioxolane affords a 5-[2-(trimethylsiloxy)ethoxy]bacteriochlorin. Like a 5-methoxybacteriochlorin, the latter undergoes regioselective bromination at the 15-position, directed by the distal 5-alkoxy group. On the other hand, attempted bromination of a bacteriochlorin bearing a 5-(2-hydroxyethoxy) group resulted in intramolecular ether formation with the adjacent β-pyrroline position to give an annulated dioxepine ring (confirmed by single-crystal X-ray structural analysis). The hydroxyethoxy group at the 5-position can be derivatized by acylation. In addition, the installation of auxochromes (methoxycarbonyl, phenylethynyl) at the β-pyrrole rings causes a substantial bathochromic shift of the long-wavelength absorption band (812 nm) and companion fluorescence emission band (821 nm). Taken together, the modification of the 5-substituent complements existing methods for installing a single substituent on the bacteriochlorin macrocycle.