O. I. Tolmachev

Fluorescent Properties of Pentamethine Cyanine Dyes with Cyclopentene and Cyclohexene Group in Presence of Biological Molecules

A series of pentamethine cyanine dyes with cyclohexene or cyclopentene group in polymethyne chain, assumed as DNA groove-binders, were studied as fluorescent probes for nucleic acids as well as for native and denatured proteins. It was revealed that the presence of methyl or dimethyl substituent in 5 position of the cyclohexene group hinders the formation of dye–DNA fluorescent complex, while the methyl substituent in 2 position leads to the increasing of the dye–DNA complex fluorescence intensity. The dyes SL-251, SL-1041, and SL-1046 containing methyl group in the 2 position of the cyclic group, are reported as bright DNA-sensitive dyes. The study of the dyes DNA-binding specificity demonstrated significant AT-preference that points to the groove-binding interaction mode. At the same time, the dyes SL-251, SL-377, and SL-957 with the 2-methyl substituted cyclohexene group were shown to be sensitive fluorescent dyes both for nonspecific (in SDS presence) proteins detection and for native BSA.

Novel fluorescent trimethine cyanine dye 7519 for amyloid fibril inhibition assay

Abstract Fluorescence spectroscopy was used to study the ability of dye 7519 to follow the transition of monomeric insulin into fibrils and applicability of the dye to the insulin aggregation inhibition assay. The commercially available classic amyloid stain, thioflavin T, was used as the reference dye. For selecting potential inhibitors, the QSAR approach was applied. Dye 7519 appeared to be suitable for monitoring insulin aggregation into fibrils in vitro. The properties of the dye allowed us to test it as a potential probe in the screening assay of potential inhibitors of insulin fibrillization. One hundred forty-four flavonoids were tested as potential inhibitors of amyloid fibril formation using the quantitative structure activity relationship approach. Among them, 10 candidates with high indexes of inhibition were selected for tests in vitro using dye 7519 and the reference amyloid dye thioflavine T. Using dye 7519 fluorescence, we found that two compounds had inhibitory effects on insulin amyloid formation. These results agree with inhibition data using the thioflavine T assay. Our studies demonstrated that the fluorescent cyanine dye 7519 is a sensitive probe for quantitative detection of insulin amyloid formation and can be applied to screen agents capable of affecting aggregation of amyloid proteins.

Tri- and pentamethine cyanine dyes for fluorescent detection of α-synuclein oligomeric aggregates

The pathogenesis of Parkinson’s disease that is the second most common neurodegenerative disease is associated with formation of different aggregates of α-synuclein (ASN), namely oligomers and amyloid fibrils. Current research is aimed on the design of fluorescent dyes for the detection of oligomeric aggregates, which are considered to be toxic and morbific spices. Fluorescent properties of series of benzothiazole trimethine and pentamethine cyanines were characterized in free state and in presence of monomeric, oligomeric and fibrilar ASN. The dyes with wide aromatic systems and bulky phenyl and alkyl substituents that are potentially able to interact with hydrophobic regions of oligomeric aggregates were selected for the studies. For majority of studied dyes noticeable changes in fluorescence characteristics were shown in the presence of fibrillar or oligomeric ASN, while the dyes slightly responded on the presence of monomeric protein. For pentamethine cyanine SL-631 and trimethine cyanine SH-299 certain specificity to oligomeric aggregates over fibrils was observed. Using these dyes at 10−6 M concentration permits the detection of oligomeric ASN in the concentrations range of at least 0.2–2 microM. Pentamethine cyanine SL-631 is proposed as dye for fluorescent detection of oligomeric aggregates of ASN, while trimethine cyanine SH-299 is shown to be a sensitive probe both on oligomeric and fibrillar ASN. It is proposed that wide aromatic system of SL-631 pentamethine dye molecule could better fix on the less dense and structured oligomeric formation, while less bulky and more “crescent-shape” molecule of trimethine dye SH-299 could easier enter into the groove of beta-pleated structure.

New Approach for Fluorescent Peptide Labeling with Pyrylium Cyanine Dyes

New approach for fluorescent peptide labeling with cyanine dyes utilizing the reaction of pyrylium salts with aliphatic aminogroup is proposed. The reaction of two pyrylium cyanines dye acids was investigated. Lysocyme was used as a model peptide for conjugation. The proposed method can be used as a simple and convenient alternative for the known procedures because it does not require preparation of the unstable amino-reactive intermediates from a carboxyl- or sulfo-derivative of cyanine dyes.

Development of a quantitative structure activity relations (QSAR) model to guide the design of fluorescent dyes for detecting amyloid fibrils

Abstract Quantitative structure activity relationship (QSAR) studies were performed on a set of polymethine compounds to develop new fluorescent probes for detecting amyloid fibrils. Two different approaches were evaluated for developing a predictive model: part least squares (PLS) regression and an artificial neural network (ANN). A set of 60 relevant molecular descriptors were selected by performing principal component analysis on more than 1600 calculated molecular descriptors. Through QSAR analysis, two predictive models were developed. The final versions produced an average prediction accuracy of 72.5 and 84.2% for the linear PLS and the non-linear ANN procedures, respectively. A test of the ANN model was performed by using it to predict the activity, i.e., staining or non-staining of amyloid fibrils, using 320 compounds. The five candidates whose greatest activities were selected by the ANN model underwent confirmation of their predicted properties by empirical testing. The results indicated that the ANN model potentially is useful for facilitating prediction of activity of untested compounds as dyes for detecting amyloid fibrils.

Research on the growth of dye film in vacuum in situ

Organic film deposition in vacuum is fast developing scientific and industrial domain. We developed installation for deposition of organic films equipped with optical spectrometer for measurements in situ. We are developing new dyes aimed for application in waveguide sensor, nonlinear optics and studying film organisation during deposition. Fluorinated azo-dyes and azomethine dyes were synthesized at University of Applied Sciences Wildau and at the Institute of Organic Chemistry, Kyiv. Compounds were evaporated at a pressure of 10-3 Pa using resistive heated crucible. Glass and glass covered with polytetrafluoroethylene (PTFE) film are used as substrates. The films were studied with Polytec and StellarNet spectrometers and an atomic force microscope. Optical spectra of the dye films revealed, that some compounds were decomposed during evaporation. Several kinds of dyes were evaporated and deposited without decomposition. Some deposited films formed H-aggregates and other types of aggregates. AFM images of dye films showed that their morphology depends on the chemical structure of the compounds and on the nature of the substrate on which the film was grown.

Effect of Concentration on Isomerization of Rhodanine Derivatives of Merocyanine Dyes in Polar Solvents

Rhodanine derivatives of merocyanine dyes with residues of 1,3,3-trimethyl-3H-indole and 3-ethylbenzothiazoline have been found to possess two molecular forms in diluted solutions of polar solvents such as dimethylformamide, dimethyl sulfoxide, and N-methylpyrrolidinone. The first molecular form was observed to prevail at low concentrations of the dyes, normally up to 10−5 M. The second one prevails at higher concentrations and is displayed through a new band in the electronic absorption spectrum, which is red-shifted with respect to the absorption band of the first form. No similar effect was found for these dyes by use of nonpolar solvents or upon alkyl-substitution of the molecules at nitrogen atom in the rhodanine moiety. We assign the above two forms to different molecular isomers and the analogous spectral changes were shown to take place by light or heat influence which correspond to a typical isomerization effect for the related merocyanine dyes. It is discussed that the isomer transformation is facilitated by the increased mobility of the proton bonded to the nitrogen atom of the rhodanine moiety in the polar environment and the increased amount of dye-dye collisions.

Enigma of the second harmonic generation in oriented film of symmetric squaraine

Second harmonic generation (SHG) in the oriented film of symmetric squaraine (Sq) was studied. Oriented Sq film on aligned polytetrafluoroethylyne (PTFE) sublayer prepared by vacuum deposition with subsequent rubbing using a cloth has been obtained. However, the mechanisms of orientation and SHG are still not clear. Methyl and ethyl substituted hydroxyl-Sq (OHSq) compounds formed oriented films with dichroic ratio of 8 on PTFE layer but with dichroic ratio of 1,5 on Teflon AF. Second layer deposition of Me-OHSq on Et-OHSq or of Et-OHSq on Me-OHSq led to an increase of the film dichroic ratio. Only the film, where Me-OHSq was first layer, exhibits an increase of SHG signal after deposition of second layer. Small differences in bi-layered OHSq films structure was detected by X-Ray diffraction (XRD) spectra.