Interaction of cyanine dyes with nucleic acids. XVII. Towards an aggregation of cyanine dyes in solutions as a factor facilitating nucleic acid detection

Spectral properties of newly synthesized cyanine dyes, namely 1-[6-(4-[6-[2,6-dimethyl-4-(3-methyl-2,3-dihydro-1,3-benzothiazol- 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]pro pyl) carbamoylpentyl]-2,6-dimethyl-4-(3-methyl-2,3-dihydro-1,3-benzo thiazol-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.     

Interaction of cyanine dyes with nucleic acids. XVIII. Formation of the carbocyanine dye J-aggregates in nucleic acid grooves.

Spectral properties of carbocyanine dye 3-methyl-2-[3-methyl-2-(3-methyl-2,3-dihydro-1,3-benzothiazole-2-iliden)-1- butenyl]-1,3-benzothiazole-3-il iodide (Cyan betaiPr) in water solution, as well as in the presence of different types of double stranded DNA have been studied. While in water solution of 'free' dye Cyan betaiPr stays mainly in monomeric form, in the presence of DNA the dye molecules form J-aggregates. The molecular structure of these J-aggregates causes the Davydov splitting of their absorption band, corresponding to the first electronic transition. A study of site-specificity showed that in the presence of poly (dA/dT) the majority of Cyan betaiPr molecules form J-aggregates, while in the presence of poly (dGC/dGC) dye molecules stay mainly in monomeric form and in presence of chicken erythrocytes DNA both J-aggregate and monomeric forms of dye are present. We suppose that Cyan betaiPr molecules aggregate in DNA groove, which serves as a template for J-aggregate forming. An increase of ionic strength of solution leads to the release of dye molecules from DNA grooves and prevents J-aggregates formation.     

Interaction of cyanine dyes with nucleic acids: XXVI. Intercalation of the trimethine cyanine dye cyan 2 into double-stranded DNA: study by spectral luminescence methods

The interaction between double-stranded (ds) DNA and the cyanine dye Cyan 2 has been studied with spectral luminescence methods. Binding constant values have been determined by fluorescence titration and dye distribution in the two-phase system ethyl acetate-water (3.6 x 10(4) and 1.5 x 10(4) M(-1), respectively). Cyan 2 exhibits a small specificity for guanine-cytosine (GC) sequences in total DNA and synthetic polydeoxynucleotides poly(dA/dT) and poly(dGdC/dGdC). The DNA complexes with Cyan 2 are stable at high-ionic strength solution when NaCl is added. The dye molecule complexed with DNA is apparently shielded from the anionic quencher--iodide ion. The negative linear dichroism of the visible absorption band of aligned Cyan 2-DNA complexes indicates that the bound dye lies almost perpendicularly to the DNA helix axis. The linear dichroism of the absorption band at 260 nm suggests a considerable change in the DNA B-form. The results are consistent with an intercalative binding interaction between Cyan 2 and ds DNA.     

Interactions of cyanine dyes with nucleic acids. XXIV. Aggregation of monomethine cyanine dyes in presence of DNA and its manifestation in absorption and fluorescence spectra.

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 pi-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.     

花菁-脱氧核糖核酸的共振光散射光谱及其分析应用

研究了一种苯并噻唑阳离子花菁与脱氧核糖核酸(DNA)作用的共振光散射光谱,在pH 6.0的六次甲基四胺-HCl缓冲介质中,痕量DNA的加入使花菁在590nm的共振光散射强度显著增强。在最佳实验条件下,增强的共振光散射强度与DNA浓度具有良好的线性关系,据此建立了一种测定DNA的共振光散射光谱法。方法的线性范围为:小牛胸腺DNA(CT DNA),0～20μg/mL,鱼精子DNA(FS DNA),0～15μg/mL;检出限分别为0.005μg/mL和0.008μg/mL。该方法已用于合成样品中DNA的测定。     

Free Radicals: XXVII. Synthesis of 2,6-Diphenyl-4-[p-(2,6-diphenyl-4-pyridyl)phenyl]pyranyl

Starting with 2,6-diphenyl-4-(p-tolyl)pyridine a synthesis of 2,6-diphenyl-4-[p-(2,6-diphenyl-4-pyridyl)phenyl]pyrylium perchlorate was performed. By reduction of the latter the corresponding radical was obtained. The radical was shown to be unstable with respect to oxygen.     

Bischromophoric styrylpyridinium dyes. Spectroscopic properties of 1,3-bis-[4-(p-N,N-dialkylaminostyryl)pyridinyl]propane dibromides

The photophysical properties of newly synthesized bischromophoric solvatochromic stilbazolium dyes, 1,3-bis-[4-(p-N,N-dialkylaminostyryl)pyridinyl]propane dibromides (C1-C9), were studied in a series of solvents and their spectroscopic properties were compared with structurally related, monochromophoric styrylpyridinium dyes (SP1-SP9). The position of the UV-vis absorption spectra maximum of novel dyes is only slightly solvent polarity dependent in contrast to the fluorescence spectra that show pronounced solvatochromic effect demonstrated by a large Stokes shifts. The influence of the solvent on absorption and emission spectra, and the solvatochromic properties observed for both ground and first excited states for all the dyes were used for the evaluation of their excited state dipole moments. The ground state dipole moments of both mono- and bischromophoric dyes were established by applying ab initio calculations. The calculations and measurements unexpectedly show that the bischromophoric dyes are characterized by ground state dipole moments being equal to about half of that characterizing their monomeric equivalents, while the excited state dipole moments of bischromophoric dyes are about 10-25% higher in comparison to their monomeric equivalents.     

Polyamides incorporating phosphine oxide groups. III. Polymerisation of bis[4-(2-aminoethyl)aminophenyl]-phenylphosphine oxide with dicarboxylic acids

The new polymerisation monomer bis[4-(2-aminoethyl)aminophenyl]-phenylphosphine oxide (p-BAPPO) was prepared in good yield by the nucleophilic substitution reaction between bis(4-fluorophenyl)phenylphosphine oxide and a large excess of 1,2-diaminoethane. Five novel polyamides, incorporating phosphine oxide groups within the polymer backbone were synthesised by the condensation reaction of p-BAPPO with a series of aromatic and aliphatic dicarboxylic acids. The thermal properties of these polymers were investigated by differential scanning calorimetry and thermogravimetric analysis. Glass transition temperatures in the 180–215°C range were recorded. Although we observed their thermooxidative stabilities (5% weight loss > 345°C) to be lower by 40–70°C than those previously found for wholly aromatic polyamides with phosphine oxide groups within the parent chain, char yields upon prolonged heating at 650°C were still excellent (26–38%). Also, good solubility in aprotic polar solvents was observed for all polyamides synthesised. The new polyamides clearly represent significant progress in the quest for processible fire retardant materials. © 1997 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 35 : 2865–2870, 1997     

Influence of solvent polarity and medium acidity on the UV-Vis spectral behavior of 1-methyl-4-[4-amino-styryl] pyridinum iodide

Electronic absorption, and excitation spectra of 1-methyl-4-[4-aminostyryl] pyridinum iodide (M-NH2) were measured in solvents of different polarity. The (M-NH2) dye exhibits negative solvatochromism, i.e. a hypsochromic band shift as the solvent polarity increases. The fluorescence quantum yield is also sensitive to the polarity and viscosity of the medium. The ground and excited state protonation constants were calculated and amount to 3.35 and 0.62, respectively. The effect of micellization on the emission spectrum of (M-NH2) are also studied in sodium dodecyl sulphate (SDS). The fluorescence intensity increases as the concentration of SDS increases with an abrupt change at cmc. The quantum yield of the cis trans photoisomerization is also determined in aqueous buffer solution of pH 1.1.     

Synthesis and spectral properties of cyanine dyes based on indeno[2,1-<Emphasis Type="Italic">b</Emphasis>]chromene

Starting from the products of formylation and vinylformylation of indeno[2,1-b]chromene a series of new symmetrical and unsymmetrical polymethine dyes have been synthesized with a residue of indeno[2,1-b]chromene as the terminal group. It was shown that the unsymmetrical dyes obtained have two absorption bands in the visible region, the position, intensity, and shape of which depend on the nature of the second terminal group.__________Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 1, pp. 92–99, January, 2005.     

320 - Interaction of nucleic acids with electrically charged surfaces. VIII. Dependence of changes in DNA double helical structure on pH and on potential of the mercury electrode

Native double-stranded (ds) and thermally denatured DNAs were studied by means of linear sweep voltammetry, (LSV) in connection with h.m.d.e. and a.c. polarography with d.m.e. LSV measurements at various initial potentials (U_i) in dependence of Ph in acid and neutral regions showed that the potential of peak III of denatured and ds DNA was shifted to negative values with increasing pH. It was concluded that the reduction of ds DNA (conditioned by the previous interaction of ds DNA with the mercury electrode charged to potentials more positive than the reduction potential) takes place in the protonated state (similar to the case with thermally denatured DNA).LSV behaviour of thermally denatured and ds DNA was studied in alkaline media in dependence on U_i, pH and ionic strength. It was shown that both DNA forms yielded, over a wide range of pHs and ionic strengths, capacitive LSV peaks which depend on U_i in a way similar to that of reduction peaks in neutral media. Alkaline denaturation of DNA was studied by means of LSV at various U_i and with the aid of a.c. polarography and UV spectrophotometry. It was demonstrated that in accordance with the measurements in neutral media methods working with small voltage excursion during the drop lifetime (represented here by a.c. polarography in connection with d.m.e.) reflected in alkaline media the helix coil transition in the bulk of the solution. Conversely the results of LSV at U_i-1.2 V (i.e. a method working with large voltage excursion during the drop lifetime) did not show the alkaline helix-coil transition. These results agree with our conception of conformational changes in ds DNA at the mercury electrode surface. According to this conception in the narrow potential range around −1.2 V (region u) changes in the in DNA double-helical struture occur which result in the release of bases for the interaction with the electrode (surface denaturation). On the other hand at potentials more negative than the region u (i.e. those corresponding to the potential of the reduction or capacitive peak III) no changes DNA double-helical structure occur. The so-called model A proposed by Berg et al. [1] is in contradiction with the main experimental data presented in this paper or is not suitable for their interpretation.     

Intermolecular interactions in mixtures of dichroic dyes with n-alkyl-4-(4-isothiocyanatophenyl)bicyclo[2,2,2]octanes

On the basis of the polarized absorption spectra, the guest order parameter as a function of temperature for five dichroic azo dyes dissolved in four members (pentyl to octyl) of the homologous series of n-alkyl-4-(4-isothiocyanatophenyl)bicyclo[2,2,2]octanes has been evaluated. Moreover, the influence of the dichroic dye addition on the nematic-isotropic phase transition temperature has been examined. The relation between the molecular geometry of the guest, its orientation efficiency in the nematic host and the clearing temperature of the azo dye-liquid crystal mixtures has been determined. The experimental results have been compared in some detail with calculations performed on the basis of the mean field theory for binary mixtures.     

Synthesis and properties of new pyridine-bridged poly(ether-imide)s based on 4-(4-trifluoromethylphenyl)-2,6-bis[4-(4-aminophenoxy)phenyl]pyridine

A novel pyridine-containing aromatic diamine monomer, 4-(4-trifluoromethylphenyl)-2,6-bis[4-(4-aminophenoxy)phenyl]pyridine (FAPP), was synthesized via the modified Chichibabin pyridine synthesis of 4-(4-nitrophenoxy)-acetophenone with 4-trifluoromethyl-benzaldehyde, followed by a catalytic reduction. A series of fluorinated pyridine-bridged aromatic poly(ether-imide)s were prepared from the resulting diamine monomer with various aromatic dianhydrides via a conventional two-step process. The resulting polyimides exhibited good solubility in aprotic amide solvents and m-cresol, such as N,N-dimethylacetamide, N-methyl-2-pyrrolidone, and m-cresol, etc., which possessed the inherent viscosities of 0.76-0.91 dL/g. Strong and flexible poly(ether-imide) films were obtained, which showed excellent thermal properties with the glass transition temperatures of 268-353 °C, the temperature at 5% weight loss of 547-595 °C, and the residue at 700 °C of 65-74% in nitrogen, good mechanical properties with the tensile strengths of 87.6-104.2 MPa and elongations at breakage of 8.9-12.6%, and good optical transparency with the cut-off wavelengths of 357-380 nm, as well as low dielectric constants in the range of 2.49-3.04 at 1 MHz and low water uptake 0.43-0.69%. Furthermore, the resulted polyimides derived from FAPP were compared with non-fluorinated analogous polyimides and fluorinated analogous polyimides with trifluoromethyl groups in different positions, and the effects of substituents were also investigated and discussed.     

Synthesis and binding properties of calix[4]arenes with [2 + 2'] mixed ligating functional groups

A series of mixed [2 + 2'] p-tert-butylcalix[4]arene have been synthesised by selective 1,3-dialkylation of phenolic groups using various alkylating agents such as benzyl bromide, methyl iodide, ethyl bromoacetate, and 2-methoxyethyl tosylate. The extraction and complexation properties of the synthesized calixarenes towards alkali and alkaline earth metal cations have been investigated in acetonitrile by means of UV spectrophotometry and 1H NMR spectroscopy. The results show the formation of ML and/or ML2 species depending on the ligand and the cation. The enthalpies and entropies of complexation of alkali metal cations by a tetraglycol, diglycol-dibenzyl and diglycol-diester derivatives have been obtained from calorimetric measurements. The results revealed that the formation of ML species is controlled by enthalpy while the formation of ML2 from ML is entropy driven.     

对磺酸基杯[4]芳烃与血红蛋白相互作用的光谱研究

用荧光光谱法和紫外可见分光光度法研究了表面活性剂存在下对磺酸基杯[4]芳烃与牛血红蛋白的相互作用机理。由Stern-Volmer方程及紫外可见吸收光谱图确定对磺酸基杯[4]芳烃对血红蛋白的荧光猝灭过程为动态猝灭,求出了猝灭常数。由热力学参数判断二者之间的作用力主要是疏水作用。依据能量转移理论得出荧光给体-受体间的距离r。在同步荧光光谱中,对磺酸基杯[4]芳烃的加入对血红蛋白构象的改变不大。     

Influence of the [2.1.1]-(2,6)-pyridinophane macrocycle ring size constraint on the structure and reactivity of copper complexes

The macrocycle [2.1.1]-(2,6)-pyridinophane (L) binds to CuCl to give a monomeric molecule with tridentate binding of the ligand but in a distorted tetrahedral "3 + 1" geometry, where one nitrogen forms a longer (by 0.12 A) bond to Cu. In dichloromethane solvent this pyridine donor undergoes facile site exchange with a second pyridine in the macrocycle, to give time-averaged mirror symmetry. Both experimental and density functional theory studies of the product of chloride abstraction, using NaBAr(F)(4) in CH(2)Cl(2), show that the Cu(+) binds in a trigonal pyramidal, not planar, arrangement in LCu(+). This illustrates the ability of macrocyclic ligand constraint to impose an electronically unfavorable geometry on 3-coordinate Cu(I). LCuBAr(F)(4) and a triflate analogue LCu(I)(OTf) readily react with oxygen in dichloromethane to produce, in the latter case, a hydroxo-bridged dimer [LCu(II)(micro-OH)](2)(OTf)(2), of the intact (unoxidized) ligand L. Since the analogous LCuCl does not react as fast with O(2) in CH(2)Cl(2), outer-sphere electron transfer is concluded to be ineffective for oxidation of cuprous ion here.     

Syntheses based on dimethylpyrazoles. 9. Synthesis and spectral peculiarities of isomeric pyrazolo[3′,4′-5,6]- and-[5′,4′-5,6]-pyrimido[1,2-b]benzo[d,e]isoquinoline-4,12-diones

2-Methyl-2,4,12,13H-pyrazolo[3,4-5,6]pyrimido[1,2-b]benzo[d,e]isoquinoline-4,12-dione and its 8-nitro- and 8-amino-substituted derivatives were obtained starting from 4-amino-3-carbamoyl-1-methylpyrazole and naphthalic and 4-nitronaphthalic anhydrides. The spectral properties of the synthesized compounds were studied.See [1] for Communication 8.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 2, pp. 237–241, February, 1990.     

Influence of the cation on the properties of binuclear iron nitrosyl complexes. Synthesis and crystal structure of [Pr4 nN]2[Fe2S2(NO)4]

The binuclear nitrosyl complexes Q₂[Fe₂S₂(NO)₄], where Q=Me, Et, Prⁿ, and Buⁿ, were synthesized. The crystals of [Pr₄ ⁿN]₂Fe₂S₂(NO)₄ were studied by X-ray analysis. The influence of the cation size on the electronic structure and symmetry of its local environment in the synthesized complexes was examined. The decrease in the isomeric shifts in the⁵⁷Fe Mössbauer spectra is related to the increase in the length of the alkyl substituent chain of the quaternary tetraammonium cation and is consistent with changing the structural parameters: a decrease in the bond angle of the Fe?NO bond and stretching vibrations of the NO groups due to changes in intermolecular contacts.