桥环菁染料II:1-(N-烷基-4-吡啶基)-3-(N-烷基-4-吡啶亚基)-4,5-二取代-1,4-环戊二烯菁染料的合成和质子化及荧光性质研究

本文报道带有疏水长链的桥环菁染料的合成。并研究这类菁染料的质子化过程和平衡常数、取代效应, 以及胶束、糖淀粉和环糊精对染料的可见光谱及质子化过程的影响, 本文也考察了桥环菁染料的荧光光谱, 这些研究在理论上和实际应用有一定意义。     

Nonradiative deactivation of the electronic excitation energy in cyanine dyes: influence of binding to DNA

The processes of nonradiative deactivation of electronic excitation energy in cyanine dyes determine their quantum yield. Because of that, the study of the influence of cyanines binding to DNA on these processes can provide information on the causes leading to the cyanines fluorescence intensity enhancement in the presence of DNA. In the presented paper, the activation energies of nonradiative degradation of electronic excitation, quantum yields and rate constants of nonradiative transitions of several cyanines in free state and in the presence of DNA were established and compared. The mechanisms of nonradiative deactivation of dye excitation energy were discussed.     

Studies of 2‐Azaazulenium Derivatives: Unsymmetrical Trimethine Cyanine Dyes Bearing a 2‐Azaazulenium Moiety as One of the Terminal Groups

We report here the synthesis of a series of symmetrical and unsymmetrical trimethine cyanine dyes derived from 2‐azaazulene, combined spectral and quantum‐chemical investigations of their molecular geometry and electron structure, as well as the nature of the lowest electron transitions. Based on the analysis of both calculations and experimental data obtained from absorption and ¹³C NMR spectra, it was concluded that the 2‐azaazulene residue can be treated as a weakly basic terminal group; its donor properties are provided with the participation of the HOMO?1, in contrast to the typical Brooker’s terminal residues with their donor HOMOs. The new classification of the terminal groups of cyanine dyes, and hence the classification of types of unsymmetrical cyanines, is proposed. It is shown that the nature of the higher electron transitions (delocalized or local) in the cyanine dyes depends on their type. In the unsymmetrical trimethine cyanine of the mixed type, negative deviations are observed in their absorption spectra.     

咪碳菁类染料在溶液中的聚集行为

本文通过观察3种咪碳菁类染料在溶液中的聚集行为,从动力学角度分析了影响J 聚集形成的主要因素.     

6,6'-Disubstituted benzothiazole trimethine cyanines--new fluorescent dyes for DNA detection

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.     

水溶液中一种离子菁J-聚集体引起相反电荷离子菁形成J-聚集体的影响因素

水溶液中的聚电解质可引起离子菁生成聚集体,考虑到离子菁J-聚集体与聚电解质的一些相似性,我们研究了其对相反电荷离子菁J-聚集体生成的引发作用。本文分析了离子菁J-聚集体引起相反电荷离子菁生成J-聚集体的影响因素,讨论了引发聚集与被引发聚集的离子菁的电性、它们本身的结构之间的相互关系及外加无机盐对引发聚集效应产生的影响。     

On the nature of excited electronic states in cyanine dyes: implications for visual pigment spectra

CNDO/S CI calculations are carried out on polyenes and on cyanine dyes. In contrast to polyenes, doubly excited configurations have a strong effect on the first optically allowed excited state in cyanines. Protonated Schiff bases of retinal are closely related to cyanine dyes, with important consequences for models of visual pigment spectra and photochemistry.     

Key Structural Elements of Unsymmetrical Cyanine Dyes for Highly Sensitive Fluorescence Turn‐On DNA Probes

Unsymmetrical cyanine dyes, such as thiazole orange, are useful for the detection of nucleic acids with fluorescence because they dramatically enhance the fluorescence upon binding to nucleic acids. Herein, we synthesized a series of unsymmetrical cyanine dyes and evaluated their fluorescence properties. A systematic structure–property relationship study has revealed that the dialkylamino group at the 2‐position of quinoline in a series of unsymmetrical cyanine dyes plays a critical role in the fluorescence enhancement. Four newly designed unsymmetrical cyanine dyes showed negligible intrinsic fluorescence in the free state and strong fluorescence upon binding to double‐stranded DNA (dsDNA) with a quantum yield of 0.53 to 0.90, which is 2 to 3 times higher than previous unsymmetrical cyanine dyes. A detailed analysis of the fluorescence lifetime revealed that the dialkylamino group at the 2‐position of quinoline suppressed nonradiative decay in favor of increased fluorescence quantum yield. Moreover, these newly developed dyes were able to stain the nucleus specifically in fixed HeLa cells examined by using a confocal laser‐scanning microscope.     

Doubly Strapped Zwitterionic NIR-I and NIR-II Heptamethine Cyanine Dyes for Bioconjugation and Fluorescence Imaging

Heptamethine cyanine dyes enable deep tissue fluorescence imaging in the near infrared (NIR) window. Small molecule conjugates of the benchmark dye ZW800-1 have been tested in humans. However, long-term imaging protocols using ZW800-1 conjugates are limited by their instability, primarily because the chemically labile C4′-O-aryl linker is susceptible to cleavage by biological nucleophiles. Here, we report a modular synthetic method that produces novel doubly strapped zwitterionic heptamethine cyanine dyes, including a structural analogue of ZW800-1 , with greatly enhanced dye stability. NIR-I and NIR-II versions of these doubly strapped dyes can be conjugated to proteins, including monoclonal antibodies, without causing undesired fluorophore degradation or dye stacking on the protein surface. The fluorescent antibody conjugates show excellent tumor-targeting specificity in a xenograft mouse tumor model. The enhanced stability provided by doubly strapped molecular design will enable new classes of in vivo NIR fluorescence imaging experiments with possible translation to humans.     

A simple and effective “capping” approach to readily tune the fluorescence of near-infrared cyanines

Heptamethine cyanines are favorable for fluorescence imaging applications in biological systems owing to their near-infrared (NIR) absorption and emission. However, it is very difficult to quench the fluorescence of NIR dyes by the classic photoinduced electron transfer mechanism due to their relatively high-lying occupied molecular orbital energy levels. Herein, we present a simple and effective “capping” approach to readily tune the fluorescence of NIR cyanines. The resulting new functional NIR CyBX (X = O, N, or S) dyes not only retain the intact tricarbocyanine scaffold, but also have a built-in switch to regulate the fluorescence by spiro-cyclization. When compared to traditional cyanines, novel CyBX dyes have a superior character in that their NIR optical properties can be readily tuned by the intrinsic spiro-cyclization mechanism. We expect that this “capping” strategy can be extended across not only the visual spectrum but also to structurally distinct fluorophores.     

Structure and fluorescence properties of indole cyanine and merocyanine dyes with partially locked polymethine chain

The fluorescent properties of a series of symmetric cationic cyanine dyes and merocyanines with trimethylene bridge connecting N-atom of the indole residue with α-position of the polymethine chain have been explored in detail. It is shown that the constraining group influences their fluorescent properties both by steric and electronic effects. It revealed an essential decrease of the fluorescence quantum yields of the constrained symmetric cyanine dyes in comparison with those of their analogues without bridge group in their chromophore. This effect diminishes essentially at polymethine chain lengthening. In the case of merocyanines the bridge group can cause a decrease as well a substantial increase of their fluorescence quantum yields depending on their type of solvatochromism and solvent polarity. The conclusions made on the basis of the experimental data are in good agreement with the results of semiempirical quantum-chemical calculations.     

Efficient reverse click labeling of azide oligonucleotides with multiple alkynyl Cy-Dyes applied to the synthesis of HyBeacon probes for genetic analysis

A convenient method of oligonucleotide labeling using click chemistry has been developed. A 2′-mesyloxyethyl ribothymidine phosphoramidite monomer was incorporated into DNA at several loci during solid phase oligonucleotide synthesis and converted to 2′-azidoethyl ribothymidine in high yield on the synthesis resin. The resultant azide oligonucleotides were doubly and triply labeled with alkyne-modified cyanine dyes and their biophysical properties were studied. The influence of the dye structures and method of labeling on the fluorescence properties of the DNA probes is discussed and compared with a standard labeling method using active esters of Cy-Dyes.     

Photophysical properties of fluorescent DNA-dyes bound to single- and double-stranded DNA in aqueous buffered solution.

The absorption and fluorescence spectra, fluorescence quantum yields, lifetimes and time-resolved fluorescence spectra are reported for nine different fluorescent DNA-dyes. The work was initiated in search of a quantitative method to detect the ratio of single-to-double stranded DNA (ssDNA/dsDNA) in solution based on the photophysics of dye-DNA complexes; the result is a comprehensive study providing a vast amount of information for users of DNA strains. The dyes examined were the bisbenzimide or indole-derived stains (Hoechst 33342, Hoechst 33258 and 4',6-diamidino-2-phenylindole), phenanthridinium stains (ethidium bromide and propidium iodide) and cyanine dyes (PicoGreen, YOYO-1 iodide, SYBR Green I and SYBR Gold). All were evaluated under the same experimental conditions in terms of ionic strength, pH and dye-DNA ratio. Among the photophysical properties evaluated only fluorescence lifetimes for the cyanine stilbene dyes allowed a convenient differentiation between ssDNA and dsDNA. The bisbenzimide dyes showed multiexponential decays when bound to either form of DNA, making lifetime-based analysis cumbersome with inherent errors. These dyes also presented biexponential decay when free in aqueous buffered solutions at different pH. A mechanism for their deactivation is proposed based on two different conformers decaying with different kinetics. The phenanthridinium dyes showed monoexponential decays with ssDNA and dsDNA, but there was no discrimination between them. High dye-DNA ratios (e.g. 1:1) resulted in multiexponential decays for cyanine dyes, resulting from energy transfer or self-quenching deactivation. Shifts in both absorption and fluorescence maxima for both ssDNA and dsDNA DNA-cyanine dye complexes were small. Broadening of dye-ssDNA absorption and fluorescence bands for the cyanine dyes relative to dye-dsDNA bands was detected and attributed to higher degrees of rotational freedom in the former.     

New asymmetric monomethine cyanine dyes for nucleic-acid labelling: absorption and fluorescence spectral characteristics

Absorption spectra and fluorescence properties of a series of newly synthesized asymmetric monomethine cyanine dyes are studied. The dyes carry one or two positive charges. They are devoid of their own fluorescence in solution and become fluorescent upon binding to nucleic acids only. The fluorescence maxima of the new dyes are localized between 530 and 650 nm. The wavelength and intensity of fluorescence are dependent on molecular structure of the dye, type of nucleic acid and the concentration of both nucleic acid and salts. Some of the dyes are capable of distinguishing between single-stranded and double-stranded (ds) polynucleotides giving fluorescence maxima localized at different wavelengths. Detection threshold for dsDNA for most of the dyes is comparable to that of ethidium bromide. The sensitivity of the dye-dsDNA complexes to NaCl concentrations show that the new dyes interact with dsDNA by both intercalation and electrostatically.     

The length of the polymethine chain and the spectral-luminescent properties of symmetrical cyanine dyes

The general characteristics that relate the length of the polymethine chain of symmetrical cyanine dyes to their spectral-luminescent properties depending on the electron-donor character of the heterocycles and the nature of the solvent are formulated. For various types of symmetrical cyanines, the Stokes shifts decrease with the elongation of the polymethine chain due to weakening of the vibronic interactions. The vinylene shifts of the band maxima are essentially constant and fall within the range 100 to 130 nm depending on the nature of the heterocycles and the solvent. When the polymethine chain elongates the fluorescence quantum yields first increase and then decrease. The greater the effective length of the heterocycle the stronger the decrease. The fluorescence decay occurring when the polymethine chain gets longer is associated with intensification of the internal conversion. For symmetrical cyanines, the changes in the shapes of the electronic bands (their width, asymmetry, excess, and fine structure) as the chain elongates are governed by the competing effects of the vibronic and intermolecular interactions. The former decrease as the chain lengthens, causing the narrowing of the absorption bands for the lower vinylogs. On the other hand, the latter increase as chain lengthens, which leads to broadening of the bands for the higher vinylogs. The higher the solvent nucleophilicity and the greater the deviation of the electron-donor ability of the heterocycle from the average value the greater the broadening. Any elongation of the polymethine chain of symmetrical cyanines causes only narrowing of the bands and an increase in the asymmetry, excess, and structuring in the fluorescence spectra, which, unlike the absorption spectra, is independent of the electron-donor character of the heterocycles and the nature of the solvent. These effects are caused by the fact that, in contrast to absorption, changes in the shape of emission bands with increasing chain length are governed predominantly by vibronic rather than by intermolecular interactions.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 7, pp. 1227–1239, July, 1994.     

Cyanine dyes containing N-substituted azaaromatic moieties

Syntheses and properties of cyanine dyes bearing N-substituted pyridine and quinoline rings including cationic cyanines and merocyanines are reviewed.Institute of Chemistry, Pedagogical University al. Armii Krajowej 13/15 42-201 Czestochowa, Poland. Published in Khimiya Geterotsiklicheskikh Soedinenii, No. 7, pp. 882–898, July, 1995. Original article submitted March 6, 1995     

Cyanine‐Like Dyes with Large Bond‐Length Alternation

Herein, the synthesis and properties of alkyne‐bridged carbocations, which are analogous in structure to cyanine dyes, are reported. An alkene‐bridged dye, linked at the third position of the indole, was also synthesized as a reference compound. These new carbocations are stable under ambient conditions, allowing characterization by UV/Vis and NMR (¹H and ¹³C) spectroscopies. These techniques revealed a large degree of delocalization of the positive charge, similar to a previously reported porphyrin carbocation. The linear and nonlinear optical properties are compared with cyanine dyes and triarylmethyl cations, to investigate the effects of the bond‐length alternation and the overall molecular geometry. The value of Re(γ), the real part of the third‐order microscopic polarizability, of ?1.3×10^?33 esu for the alkyne‐linked cation is comparable to that of a cyanine dye of similar length. Nondegenerate two‐photon absorption spectra showed that the alkene‐bridged dye exhibited characteristics of cyanines, whereas the alkyne‐bridged dye is reminiscent of octupolar chromophores, such as the triarylmethyl carbocation brilliant green. Such attributes were confirmed and rationalized by quantum chemical calculations.     

Multifunctional nanostructures based on inorganic nanoparticles and oligothiophenes and their exploitation for cellular studies

The combination of materials that possess different properties (such as, for instance, fluorescence and magnetism) into one single object of nanoscale size represents an attractive challenge for biotechnology, especially for their potential relevance in biomedical applications. We report here the preparation of novel bifunctional conjugates based on the linkage of inorganic nanoparticles to organic oligothiophene fluorophores (OTFs). In comparison to the organic dyes commonly used in bioimaging and more similarly to colloidal quantum dots, OTFs have broad optical absorption spectra, and therefore OTF fluorophores emitting at different colors can be excited with a single excitation source, allowing for easier multiplexing analysis. In this work we show the preparation of OTF-nanoparticle conjugates based on gold and iron oxide nanoparticles and their characterization using different techniques such as gel electrophoresis, photoluminescence spectroscopy, dynamic light scattering, and so on. In addition, by performing an in vitro study on human tumor cells we show that OTF-nanoparticle conjugates emitting at different colors can be used for multiplexing detection. Also, in the case of iron oxide-OTF conjugates, once uptaken by the cells, we show that they preserve both their fluorescent and their magnetic properties.     

Combining aminocyanine dyes with polyamide dendrons: a promising strategy for imaging in the near-infrared region

Cyanine dyes are known for their fluorescence in the near-IR (NIR) region, which is desirable for biological applications. We report the synthesis of a series of aminocyanine dyes containing terminal functional groups such as acid, azide, and cyclooctyne groups for further functionalization through, for example, click chemistry. These aminocyanine dyes can be attached to polyfunctional dendrons by copper-catalyzed azide alkyne cycloaddition (CuAAC), strain-promoted azide alkyne cycloaddition (SPAAC), peptide coupling, or direct S(NR)1 reactions. The resulting dendron-dye conjugates were obtained in high yields and displayed high chemical stability and photostability. The optical properties of the new compounds were studied by UV/Vis and fluorescence spectroscopy. All compounds show large Stokes shifts and strong fluorescence in the NIR region with high quantum yields, which are optimal properties for in vivo optical imaging.     

Homodimeric monomethine cyanine dyes as fluorescent probes of biopolymers

The fluorescence properties of newly synthesized homodimeric monomethine cyanine dyes in the presence of biopolymers are investigated. They do not fluoresce in TE buffer and bidistilled water but become strongly fluorescent (Q(F)=0.3-0.9) in the region 530-650 nm when bound to dsDNA and ssDNA. The detection limit of dsDNA is about 1.7 ng/ml. Some of dyes studied are able to distinguish between dsDNA and ssDNA, RNA, BSA in solution and gel electrophoresis. The influence of different factors (temperature, pH and viscosity of the medium, presence of histone) on the formation of the dye-biopolymer complexes is investigated. The results of steady-state and dynamic fluorescence measurements concerning the different types of binding between dyes and biopolymers show that the new dyes are applicable in molecular biology as highly sensitive fluorescence labels.