Influence of the Aggregation of Homo-N-Mer Cyanine Dyes on the Nucleic Acids Detection Sensitivity (original) (raw)
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Bioorganic & Medicinal Chemistry Letters, 1999
Spectral properties of newly synthesized cyanine dyes, namely 1-[6-(4-{6-[2,6-dimethyl-4-(3-methyl-2,3-dihydro-1,3benzothiazol-2-ylidenmethyl)-1-pyridiniumyl]hexanoyl}piperazino)-6-oxohexyl]-2,6-dimethyl-4-(3-ethyl-2,3-dihydro--1,3-benzothiazol-2-ylidenmethyl)pyridinium (K-6) (bichromophoric dye) and 1-[5-di(3-{5-[2,6-dimethyl-4-(3-methyl-2,3-dihydro-1,3-benzothiazol-2-ylidenmethyl)-1-pyridiniumyl]pentylcarboxamido}propyl) carbamoylpentyl]-2,6-dimethyl-4-(3-methyl-2,3-dihydro-1,3-benzothiazol-2-ylidenmethyl) pyridinium (K-T) (trichromophoric dye) in solutions in the presence of and without deoxyribonucleic acid (DNA) were studied within a wide concentration range. It has been established that absorption, as well as fluorescence of investigated dye solutions, without DNA are mainly determined by H-aggregates of dye molecules. On the contrary, the fluorescence of dye solutions in the presence of DNA gives an intrinsic dye molecular fluorescence. H-aggregates are broken because of binding dye molecules with DNA. It has been suggested that both K-T and K-6 molecules bind mainly with DNA via the interaction of two chromophores. As the ratio of the number of dye molecules to that of DNA base pairs increases with an increase in dye concentration, a formation of dye molecule H-aggregates on DNA molecules are observed. Such aggregates have a different structure than those formed in the solutions without DNA. On the grounds of the data obtained, it is concluded that it is possible to use a dye aggregation capable of obtaining higher values for fluorescence enhancement of the DNA stains.
6,6'-Disubstituted benzothiazole trimethine cyanines - new fluorescent dyes for DNA detection
Spectrochimica Acta Part A-molecular and Biomolecular Spectroscopy, 2006
The influence of methyl-, 2-hydroxyethyl-, dimethyl-, diethyl-and benzoyl-amino substituents in the 6,6 -positions of benzothiazole heterocycle of trimethine cyanines on their spectral-luminescent properties and behavior in presence of DNA, RNA and BSA was studied. It was shown that incorporation of 6,6 -substituents generally leads to the increase in dyes tendency to aggregation, resulting in the considerable decrease in the emission intensity of the disubstituted dyes as compared to the unsubstituted ones. Emission of the studied 6,6 -disubstited dyes in DNA presence is considerably more intensive than in presence of RNA, that points on the existing of DNA binding preference for the mentioned dyes. Insertion of benzoyl-amino groups into the 6,6 -positions permitted us to design the DNA-sensitive dyes on the basis of symmetric trimethine cyanines with unsubstituted polymethine chain, while typically such dyes slightly respond on the presence of biopolymers. 6,6 -Benzoyl-amino-disubstituted trimethine cyanines are proposed as efficient dyes for DNA detection.
Journal of Biochemical and Biophysical Methods, 2006
The series of recently synthesized monomeric and homodimeric cyanine dyes based on monomethine cyanine chromophore with oxazolo[4,5-b]pyridinium and quinoline end groups [Vassilev A, Deligeorgiev T, Gadjev N, Drexhage K-H. Synthesis of novel monomeric and homodimeric cyanine dyes based on oxazolo[4,5-b]pyridinium and quinolinium end groups for nucleic acid detection, Dyes Pigm 2005;66:135-142] were studied as possible fluorescent probes for nucleic acids detection. Significant fluorescence enhancement and intensity level (quantum yield up to 0.75) was observed for all the dyes in the presence of DNA. The oxazolo [4,5-b]pyridinium cyanines demonstrated high sensitivity as fluorescent stains for postelectrophoretic visualization of nucleic acids in agarose gels upon both VIS and UV transillumination, and the visualized band contained 0.8 ng of dsDNA.
Symmetric cyanine dyes for detecting nucleic acids
Biotechnic & Histochemistry, 2008
A novel approach to the design of sensitive fluorescent probes for nucleic acids detection is proposed. Suitable modifications of tri-and pentamethine cyanine dyes in the polymethine chain and/or in the heterocyclic residues can result in a significant decrease in unbound dye fluorescence intensity and an increase in dye emission intensity in the presence of DNA compared to the unsubstituted dye. The sharp enhancement in the fluorescence intensity upon dye interaction with double-stranded DNA permits the application of the modified tri-and pentamethine dyes as fluorescent probes in double-stranded DNA detection in homogeneous assays.
Optimized Dyes for Protein and Nucleic Acid Detection
Springer Series on Fluorescence, 2011
Fluorescent homogeneous detection is widely used in modern biomedical techniques for analysis and quantification of nucleic acids and proteins. This method is based on the ability of low-fluorescent dye to bind noncovalently with target biomolecule with significant increase of dye's emission intensity. A wide range of probes for homogeneous detection developed during last decades are reviewed here. Series of cyanine dyes were developed for using in visualization of nucleic acids in living cells and detection of amplification products in real-time PCR. Besides, the cyanines, and triphenylmethane dyes that are able to detect certain nucleic acid structures (double stranded, triplex, and quadruplex DNA) and styrylcyanine dyes for two-photon excited fluorescent detection and imaging of DNA are described. Dyes applied for nonspecific proteins detection belong to different classes, among them are complexes of Ru 2+ , merocyanines, and trimethine cyanines. Moreover, cyanine dyes sensitive to amyloid b-pleated protein formations and albumin-specific squaraine dyes are discussed here.
Synthesis and fluorescence characteristics of novel asymmetric cyanine dyes for DNA detection
Journal of Photochemistry and Photobiology A: Chemistry, 2011
Sixteen new asymmetric monomethine cyanine dyes have been synthesized and their spectral characteristics and interaction with double stranded DNA have been investigated. The dyes absorb in the region 453-519 nm and have molar absorptivities in the range 37.900-93.100 l M −1 cm −1 . The dyes do not have intrinsic fluorescence, but in the presence of dsDNA they exhibited a significant enhancement in fluorescence. The most pronounced increase was found for D9, D10, D12 and D16 allowing the recommendation of these dyes as the most sensitive DNA markers. Thermodynamic analysis of cyanine-DNA complexation was carried out using the McGhee & von Hippel non-cooperative excluded site model, and binding parameters have been derived. A hypothesis describing the DNA-dye binding mode has been proposed.
Intercalating Cyanine Dyes for Nucleic Acid Detection
Recent Patents on Materials Sciencee, 2009
The intercalating non-covalent binding fluorescent cyanine dyes for nucleic acid detection are reviewed and the patent literature for the last two decades (since their discovery) is included. The synthetic methods for the preparation of unsymmetrical cyanine dyes that are useful as nucleic acid probes are presented. Most of the specific applications of such fluorescent cyanine dyes are reviewed and these include flow cytometry, PCR reactions, sequencing, hybridization, gel electrophoresis, capillary gel electrophoresis, liquid chromatography, quantification of DNA and RNA in solution, disinfection of blood products, diagnosis of different infections and diseases, melting curve analysis, covalent labeling for oligonucleotides and the application of such labeled nucleotides in clinical assays, staining and assessing the viability of the cells, chromosome staining etc. The outlook for current and future developments in this area is also outlined.
Spectrochimica Acta Part A-molecular and Biomolecular Spectroscopy, 2001
Absorption, fluorescence emission and excitation spectra of benzothiazole cyanine dyes -thiazole orange (TO) and 7-methyl-6-(3-methyl-2,3-dihydro-1,3-benzothiazol-2-ylidenmethyl) [1,3] dioxolo [4%,5%:4,5] benzo [d] [1,3] thiazolium methylmethosulfate (Cyan 13) -were investigated over a wide concentration range. The dyes form aggregates with a 'sandwich'-like structure in water solution. At low dye to DNA concentrations ratios, Cyan 13 and TO monomers appear to interact with the DNA. On increasing the dye to DNA concentrations ratio, free dye molecules aggregate with the DNA-bound ones. The spectra of the free dye aggregates and the aggregates formed on the DNA, are characterized by an anomalously large (more than 100 nm) Stokes shift. This suggests, that the y-electron systems of the aggregates undergo substantial changes in excited state, compared to those of the monomers. The formation of aggregates consisting of the free and DNA-bound dye molecules can be explained using the half-intercalation model of the interaction of the cyanine dye monomers with the DNA.
Spectroscopic Studies of α,γ-Disubstituted Trimethine Cyanine: New Fluorescent Dye for Nucleic Acids
2002
Spectral properties of 3-methyl-2-{3-[3-methyl-1,3-benzothiazolo-2(3H )-ylidene]-1,4-cylopentadien-1-yl}-1,3-benzothiazolo-3-ium tosylate (Cyan-Cpentd) in a free state and in the complexes with nucleic acids and synthetic polynucleotides have been investigated by absorption and fluorescence spectroscopy. Significant fluorescence intensity enhancement of dye-nucleic acids complexes is observed. For the first time Cyan-Cpentd is proposed as a new probe for nucleic acid detection. Binding mechanism of Cyan-Cpentd is discussed in view of the NA-ligand interaction models.