Studies on the Spectral-Luminescent Properties of the Novel Homodimer Styryl Dyes in Complexes with DNA

Series of homodimer styryls containing on (p-dimethylaminostyryl) pyridinium residues that are connected with aliphatic linkage group was synthesized. Spectral luminescent properties of obtained dyes in free state and in nucleic acids presence were studied. It was shown that DNA binding affinity of the novel homodimers exceeds that of parent monomer (p-dimethylaminostyryl)pyridine iodide. For homodimers with the linkage 4–10 carbon atoms preference in binding to DNA than to RNA was observed. It could be concluded that parent monomer has different mechanisms of binding to nucleic acids than corresponding homodimer dye.     

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.     

Styryl Dyes as Two-Photon Excited Fluorescent Probes for DNA Detection and Two-Photon Laser Scanning Fluorescence Microscopy of Living Cells

Spectral-fluorescent properties of benzothiazole styryl monomer (Bos-3) and homodimer (DBos-21) dyes in presence of DNA were studied. The dyes enhance their fluorescence intensity in 2–3 orders of magnitude upon interaction with DNA. Studied styrylcyanines in DNA presence demonstrate rather high values of two-photon absorption (TPA) cross-section, which are comparable with the values of TPA cross section of the rhodamine dyes. An applicability of the styrylcyanines as probes for the fluorescence microscopy of living cells was studied. It was shown that both dyes are cell-permeable but homodimer dye DBos-21 produces noticeably brighter staining of HeLa cells comparing with monomer dye Bos-3. Molecules of DBos-21 initially bind to the nucleic acids- containing cell organelles (presumable mitochondria) and are able to penetrate into the cell nucleus. Thus, homodimer styryl DBos-21 dye is viewed as efficient stain for single-photon and two-photon excitation fluorescence imaging of living cells.     

The Mechanism of Benzothiazole Styrylcyanine Dyes Binding with dsDNA: Studies by Spectral-Luminescent Methods

In the presented work studies of the interaction mode of monomer and two homodimer benzothiazole styryl dyes containing spermine-like linkage/tail group with the double stranded (ds) DNA are reported. For these dyes, equilibrium constant of dye binding to DNA (K _b), as well as the number of dsDNA base pairs occupied by one bound dye molecule (n) were determined. The data obtained show that the presence of spermine-like group containing quaternary nitrogen (Bos-5) results in increase of K _b value as compared to this of unsubstituted analogue (Sbt). Besides, for the dimer dyes containing benzothiazole styryl chromophores, the K _b value is either five times higher (DBos-13) or almost the same (DBsu-10) as compared to this of corresponding monomer Sbt, depending on the position in the benzothiazole ring where the linker is attached. Moreover, the n values for both dimers are significantly different as well, pointing to the bis-intercalative binding mechanism for DBos-13 and for the groove-binding one for DBsu-10. The conclusion about the dimer dyes-dsDNA binding mechanisms is also supported by the study of the fluorescent response of these dyes on the presence of AT- and GC-containing polynucleotides.     

New Method for Covalent Fluorescent Biomolecule Labeling with Hemicyanine Dye

Fluorescent chromophore, alkylamino-(tetra-hydronaphthalenylidene)- benzothiazolium derivatives (HBTN dyes), are proposed as covalent labels for proteins via aliphatic amino groups. Spectral-luminescent properties of 3-methyl-2-{(E)-[7-(methylamino)-4,4a,5,6-tetra-hydronaphthalen-2(3H)-ylidene]methyl}-1,3-benzothiazol-3-ium chloride (HBTN, R=Me) and its predecessor, 2-[(E)-(7-methoxy-4,4a,5,6-tetrahydronaphthalen-2(3H)-ylidene)methyl]-3-methyl-1,3-benzothia-zol-3-ium chloride (ABTN), are studied for free dyes and in the presence of DNA and BSA. Considerable spectral-luminescent changes accompany the transformation of ABTN into HBTN that allows monitoring conjugation reaction. In presence of DNA and BSA the HBTN increases its emission in 15 and 4 times respectively and becomes strongly fluorescent. The conditions for labeling are developed and a model conjugate of HBTN dye with BSA is synthesized. It was shown that using of HBTN dye as a fluorescent label allows detection by eye of about 3 μg/band of BSA on polyacrylamide gel upon UV-irradiation.     

An Investigation of Tricarbocyanines “Stains-All” and “iso-Stains-All” as Fluorescent Nucleic Acids Probes

Luminescent properties of carbocyanine dyes Stains-All and its isomer iso-Stains-All were studied in the presence of nucleic acids. Both dyes show sufficient fluorescent intensity increase in the presence of DNA and RNA and may be used as fluorescent probes for nucleic acids (NA) detection in homogeneous assays. It was supposed that Stains-All and iso-Stains-All bind with nucleic acids through different interaction modes.     

Fluorescence Characteristics of Variously Charged Asymmetric Monomethine Cyanine Dyes in the Presence of Nucleic Acids

Three asymmetric monomethine cyanine dyes bearing one, two, and three positive charges have been synthesized, and their absorption and fluorescence characteristics in the presence of nucleic acids were studied. The maxima of their longest wavelength absorption band lie between 500 and 520 nm. The dyes do not show fluorescence of their own in TE buffer (pH = 7.5), but become strongly fluorescent (Q_F = 0.2–0.6) on binding to double-stranded DNA. The fluorescence maxima of the investigated dye-dsDNA complexes are in the region of 530–550 nm. The influence of the dye/DNA ratio on both the position and intensity of the fluorescence maxima of the complexes is investigated.     

Mono and Trimethine Cyanines Cyan 40 and Cyan 2 as Probes for Highly Selective Fluorescent Detection of Non-canonical DNA Structures

Two of earlier reported dsDNA sensitive cyanine dyes??monomethine Cyan 40 and meso-substituted trimethine Cyan 2 were studied for their ability to interact with non-canonical DNA conformations. These dyes were characterized by spectral-luminescent methods in the presence of G-quadruplex, triplex and dsDNA motifs. We have demonstrated that Cyan 2 binds strongly and preferentially to triple- and quadruple-stranded DNA forms that results in a strong enhancement of the dye fluorescence, as compared to dsDNA, while Cyan 40 form fluorescent complexes preferentially only with the triplex form. Highly fluorescent complexes of Cyan 2 with DNA triplexes and G-quadruplexes and Cyan 40 with DNA triplexes are very stable and do not dissociate during gel electrophoresis, leading to preferential staining of the above DNA forms in gels. The data presented point to the intercalation mechanism of the Cyan 2 binding to G4-DNA, while the complexes of Cyan 40 and Cyan 2 with triplex DNA are believed to be formed via groove binding mode. The Cyan dyes can provide a highly sensitive method for detection and quantification of non-canonical structures in genome.     

Studies of Benzothiazole and Benzoselenazole Squaraines as Fluorescent Probes for Albumins Detection

Series of squaraine benzothiazole and benzoselenazole dyes were studied as possible fluorescent probes for the detection of proteins, particularly albumins. It was shown that majority of the studied squaraines give significant fluorescent response on the human serum albumin (HSA) and bovine serum albumin presence. For squaraine dyes with N-hexyl pendent groups (P-1, P-2, P-3, P-5) about 100−540-fold fluorescence intensity increase upon albumins addition was observed. At the same time in presence of other proteins, namely insulin, avidin from hen egg white, immunoglobulin G (IgG), carbonic anhydrase fluorescence enhancement values were considerably lower —up to 43 times in IgG presence. It was noted that generally, squaraines with long N-hexyl pendent groups demonstrate higher emission increase values upon proteins addition comparing with their analogues with short N-ethyl tails. It was shown that fluorescence intensity enhancement for benzothiazole squaraine dye P-3, relates linearly to the HSA concentration over the wide range—from 0.2 to 500 μg/ml. Together with noticeable selectivity of this dye to albumins, existence of wide dynamic range gives possibility to propose P-3 dye as probe for HSA quantification.     

A Comparison of the Singlet-Singlet and Triplet-Triplet Spectra of Some Typical Symmetrical Cyanine Dyes

The triplet-triplet (T-T) spectra of twelve symmetrical cyanine dyes have been recorded, using flash photolysis in the presence of triplet state sensitizers. Three sets of dyes have been studied, each set comprising four members which differ from one another by the length of the bridge joining two identical nuclei (quinoline or benzthiazole); the internuclear linking is made by one =CH-, or by a chain composed of three, five, or seven such groups. Excluding the shortest member of each set, the remaining nine dyes are found to follow a common trend: the wavenumber of the 0-0 vibrational peak of the most intense T-T absorption band is linearly related to that of the 0-0 peak of the first singlet-singlet absorption band.     

Study on the spectral behavior of four fluorescent dyes and their interactions with nucleic acid by the luminescence method

The spectral characteristics of four fluorescent dyes: tetrabromofluorescein (TBF), tetrachlorotetrabromofluorescein (TTF), lissamine rhodamine RB 200 (LSR) and methylene violet (MV) were studied by fluorescence and paper substrate room temperature phosphorescence (PS-RTP) methods. The factors affected the luminescence were investigated including pH value, paper substrate and drying conditions, etc. The fluorescence polarizations and PS-RTP lifetimes of these compounds were obtained. The intensity of fluorescence and phosphorescence of TBF and TTF increased in the presence of DNA. Contrarily, that of LSR and MV decreased. The fluorescence quenching and polarization studies indicate that TTF, LSR and MV intercalate into DNA base pairs. In addition, the interaction of TBF with DNA is the comprehensive interaction of two modes: intercalation and groove binding. It was also found that ionic strength could affect the binding of fluorescent dyes and DNA.     

Influence of the Aggregation of Homo-N-Mer Cyanine Dyes on the Nucleic Acids Detection Sensitivity

Novel benzothiazolopyridinium homo-n-mer cyanine dyes are proposed for nucleic acid fluorescent detection. Dependence of the sensitivity of detection in solution from the dye molecules/DNA base pairs ratio was studied. It was shown that the presence of the dye excess could significantly decrease the detection limit. We believe this could be explained by the formation of the dye aggregates on DNA surface.     

A New Fluorescence Resonance Energy Transfer Pair and Its Application to Oligonucleotide Labeling and Fluorescence Resonance Energy Transfer Hybridization Studies

We describe two new fluorescence resonance energy transfer (FRET) compatible labels, their covalent linkage to oligonucleotides, and their use as donor and acceptor, respectively, in FRET hybridization studies. The dyes belong to the cyanine dyes, and water solubility is imparted by a phosphonate which represents a new solubilizing group in DNA labels. They were linked to amino-modified synthetic oligonucleotides via oxysuccinimide (OSI) esters. The studies performed include binding assays, determinations of molecular distances, homogeneous competitive assays, and limits of detection, which are in the order of 5 pmol/L for a 15-mer.     

Spectroscopic study of interaction of styrylcyanine dye Sbt and its derivatives with bovine serum albumin

The spectral-fluorescent characteristics of styrylcyanine dye Sbt ((E)-2-(4-(dimethylamino) styryl)-3-methylbenzo[d]thiazol-3-ium iodide) and homodimers, dyes conjugated with two chromophores in aqueous solutions without and in the presence of bovine serum albumin (BSA), are studied. It is established that in the presence of BSA for dyes Dbt-5 and Dbt-10, an increase of the absorptivity, a slight broadening and the emergence of new band on the short wavelength range with λ_max=410 nm is observed; also hypsochromic shift of the absorption and fluorescence at 30 nm and 7 nm, respectively for the dye D-183 is observed. The intensity of the fluorescence emission fundamental band in all the studied dyes in the presence of BSA increases by 3.5 to 55 times. The binding constant (K) and number of binding sites (N) of studied dyes with BSA are determined. The dependence of the binding constants with BSA from the dipole moment of dye molecules is identified, which shows that in addition to the electrostatic attraction forces between molecules of styrylcyanine dyes with BSA, hydrophobic interactions are essential. It is shown that the aggregation of dye affects the processes of interaction of the dyes with the BSA.     

Novel,Monomeric Cyanine Dyes as Reporters for DNA Helicase Activity

The dimeric cyanine dyes, YOYO-1 and TOTO-1, are widely used as DNA probes because of their excellent fluorescent properties. They have a higher fluorescence quantum yield than ethidium homodimer, DAPI and Hoechst dyes and bind to double-stranded DNA with high affinity. However, these dyes are limited by heterogeneous staining at high dye loading, photocleavage of DNA under extended illumination, nicking of DNA, and inhibition of the activity of DNA binding enzymes. To overcome these limitations, seven novel cyanine dyes (Cyan-2, DC-21, DM, DM-1, DMB-2OH, SH-0367, SH1015-OH) were synthesized and tested for fluorescence emission, resistance to displacement by Mg²⁺, and the ability to function as reporters for DNA unwinding. Results show that Cyan-2, DM-1, SH-0367 and SH1015-OH formed highly fluorescent complexes with dsDNA. Of these, only Cyan-2 and DM-1 exhibited a large fluorescence enhancement in buffers, and were resistant to displacement by Mg²⁺. The potential of these two dyes to function as reporter molecules was evaluated using continuous fluorescence, DNA helicase assays. The rate of DNA unwinding was not significantly affected by either of these two dyes. Therefore, Cyan-2 and DM-1 form the basis for the synthesis of novel cyanine dyes with the potential to overcome the limitations of YOYO-1 and TOTO-1.     

沢吨染料的光化漂白动力学及全息特性研究

研究了以三乙醇胺作为引发剂,五种沢吨染料的光化漂白过程.实验结果表明五种染料的光化漂白速率大小顺序是藻红B(ErB)＞曙红Y(EY)＞孟加拉玫瑰红B(RsB)＞罗丹明B(RoB)＞荧光素(F).并研究了曝光强度及染料浓度对漂白过程的影响,以及这五种染料的全息记录性能.     

Detection of <Emphasis Type="Italic">Bifidobacterium</Emphasis> Species-specific 16S rDNA Based on QD FRET Bioprobe

Fluorescence resonance energy transfer (FRET) that consists of quantum dot as donors and organic fluorophore dyes as acceptors has been a very important method to detect biomolecules such as nucleic acids. In this work, we established a new FRET detection system of Bifidobacterium species-specific 16S rDNA using QD—ROX FRET bioprobe, in which 525 nm QD-DNA conjugation consisted of the carboxyl-modified QD and the amino-modified DNA in the presence of EDC. Both ROX-DNA and the conjugation above could hybridize with the target DNA after forming the QD—ROX bioprobe. When the hybridization made the distance between the QD and ROX to meet FRET effect needed, 525 nm QD fluorescence intensity decreased and ROX fluorescence intensity increased. In the control, there was no notable change of fluorescence intensities without target DNA. It is very clear that the change of the QD and ROX fluorescence intensities provide the good base and guaranty for this rapid and simple detection system.     

Locating of Nucleic Acid Intercalators in Yeast Cells by Image Analysis Combined Fluorescence Microscopy

Intracellular distribution in the intact (not fixed) Saccharomyces cerevisiae cells of the nucleic acid intercalators (NAI) was studied using fluorescence microscopy combined with computer image analysis (ImageJ software, NIH, USA). Three NAI—the anthracycline anticancer drug doxorubicin (DR) along with the nucleic acid dyes ethidium (E) and 4′,6-diamidino-2-phenylindole (DAPI)—were used. Staining pattern and ImageJ quantitative analysis data provided evidence that all three NAI were located in the nuclei and in the mitochondria. DR and E, in contrast to DAPI, may be bound to not only DNA, but to the mitochondrial membranes as well. Experiments on the combined application of DR+DAPI and E+DAPI have shown potential competition of DAPI with DR and E for binding sites in the nuclear and mitochondrial DNA. With the approach presented herein, the yeast cells of S. cerevisiae can be used as a model for locating intracellular sites of the fluorescing nucleic acid intercalators. This model may be of help in designing new DNA-targeted drugs and in preliminary studies of their interaction with eukaryotic cells.     

Spectroscopic Study of the Interaction of Styrylcyanine Dyes Sbo,Sil and Their Derivatives with Bovine Serum Albumin

The spectral-luminescent characteristics of newly synthesized styrylcyanine dyes on the base of dyes Sbo ((E)-2-(4-(dimethylamino)styryl)-3-methylbenzo[d]oxazol-3-ium iodide) and Sil ((E)-2-(4-(dimethylamino)styryl)-1,3,3-trimethyl-3H-indolium perchlorate) in aqueous solutions without and in the presence of bovine serum albumin (BSA) were studied. It was established that the absorption spectra of dyes Tol-6, Dbo-10 and Dil-10 with increasing amount of BSA appear new bands with λ_max = 505 nm, λ_max = 512 nm and λ_max = 566 nm, respectively, whose intensity increases in proportion to the amount of albumin. The intensity of the glow of the main band of fluorescence in the presence of BSA sharply increases. The binding constant (K) and the number of binding sites (N) of studied dyes with BSA were determined. The dependence of binding constants with BSA on the dipole moment of dye molecules was determined, which indicates that besides electrostatic forces of attraction between molecules styrylcyanine dyes with BSA, hydrophobic interactions are essential.     

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.