Ultrafast excited-state dynamics of DNA fluorescent intercalators: new insight into the fluorescence enhancement mechanism

The excited-state dynamics of the DNA bisintercalator YOYO-1 and of two derivatives has been investigated using ultrafast fluorescence up-conversion and time-correlated single photon counting. The free dyes in water exist in two forms: nonaggregated dyes and intramolecular H-type aggregates, the latter form being only very weakly fluorescent because of excitonic interaction. The excited-state dynamics of the nonaggregated dyes is dominated by a nonradiative decay with a time constant of the order of 5 ps associated with large amplitude motion around the monomethine bridge of the cyanine chromophores. The strong fluorescence enhancement observed upon binding of the dyes to DNA is due to both the inhibition of this nonradiative deactivation of the nonaggregated dyes and the dissociation of the aggregates and thus to the disruption of the excitonic interaction. However, the interaction between the two chromophoric moieties in DNA is sufficient to enable ultrafast hopping of the excitation energy as revealed by the decay of the fluorescence anisotropy. Finally, these dyes act as solvation probes since a dynamic fluorescence Stokes shift was observed both in bulk water and in DNA. Very similar time scales were found in bulk water and in DNA.     

Non-covalent interactions of coumarin dyes with cucurbit[7]uril macrocycle: modulation of ICT to TICT state conversion

Non-covalent interaction of coumarin laser dyes, namely coumarin-1 (C1), coumarin-481 (C481) and coumarin-6H (C6H), with a versatile macrocyclic host molecule cucurbit[7]uril (CB7), has been investigated in aqueous solution using photophysical methods. Steady-state and time-resolved fluorescence studies illustrate significant enhancements/modifications in the fluorescence yields, lifetimes and spectral features of C1, C481 and C6H on interaction with CB7, and are assigned to 1 : 1 complex formation between the dyes and the CB7 host. The complex formation is mainly driven by charge-dipole interaction, as evident from the binding constant values (K ~ 10(4)-10(5) M(-1)). The large changes in the excited state behaviour of C1 and C481 as compared to C6H in the presence of CB7 indicate that CB7 binds C1 and C481 through the encapsulation of the 7-N,N'-diethylamino group of the dyes and the structural rigidity imposed by this interaction dramatically alters the excited state properties of the dyes by preventing the conversion of their emissive intramolecular charge transfer (ICT) state to the non-radiative twisted intramolecular charge transfer (TICT) state. The present results direct towards the probable supramolecular approach using water soluble macrocyclic CB7, in the development of aqueous dye laser systems in the blue-green region.     

Comparative studies on biophysical interactions between 4-dicyanomethylene-2,6-dimethyl-4H-pyran (DDP) with bovine serum albumin (BSA) and human serum albumin (HSA) via photophysical approaches and molecular docking techniques

Photophysical studies of 4-Dicyanomethylene-2,6-Dimethyl-4H-Pyran (DDP) dye with globular proteins, Human Serum Albumin (HSA) and Bovine Serum Albumin (BSA) were carried out in aqueous solution. An isosbestic point resulted on the addition of serum albumins, which signifies a complex or an equilibrium state of DDP dye with albumin. Addition of BSA to DDP dye results in a fluorescence enhancement accompanied with a significant hypsochromic shift, whereas with that of HSA, a fluorescence quenching with a considerable blue shift resulted. Excited state studies of DDP dye with serum albumins portray that the role of binding sites of dye with albumins vary considerably and the nature of interaction is presumably attributed to combined hydrogen-bonding and hydrophobic interactions. Molecular docking studies of DDP dye with albumins and two other derivatives 4-(Dicyanomethylene)-2-methyl-6-(4-dimethylaminostyryl)-4H-pyran (DCM) dye and 4-(Dicyanomethylene)-2-methyl-6-(4-t-buyl)-4H-pyran (DCT) dyes with BSA and HSA elucidates that the hydrogen-bonding interaction accompanied with several hydrophobic, pi–pi an pi–alkyl interactions coexist between dye and albumins. The binding energy, intermolecular energy and stability of the DDP, DCM and DCT dyes through docking techniques with albumins authenticate that the dye predominantly acts as hydrogen-bonding acceptor site and the protein molecule as the donor. DDP dye prefers to exist in four different binding sites of HSA, whereas, in the case of BSA, the most preferred site is found to be hydrophobic domain (site I). Interestingly, the most preferred site of DCT dye is III A subdomain of HSA, whereas DCM dye is oriented towards I B subdomain. DDP and DCT are smaller in size and reside in the domain preferred for smaller ligands (II A and IIIA) as resulted in several drugs-HSA interaction whereas DCM dye which is categorized as medium to larger ligand based on the extended structure resides in the most favoured site IB. Fluorescence techniques in combination with molecular docking methods elucidate binding characteristics and the domain in which the dye resides in a micro heterogeneous environment is established in this study.     

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.     

光谱法研究噻菁染料与血清蛋白的相互作用

本文通过吸收和荧光光谱法研究了一种噻菁染料与人血清蛋白及牛血清蛋白的相互作用。吸收光谱数据表明,与血清蛋白结合后,噻菁染料单体的吸收峰发生红移,同时强度也有很大变化;还通过吸收光谱计算确定了噻菁染料与血清蛋白的结合位点数（ n ）。与人血清蛋白或牛血清蛋白结合后,噻菁染料的荧光量子产率增加。分析噻菁染料的荧光强度随溶液中血清蛋白浓度的变化得到了二者反应的表观结合常数（ K _a）和自由能变化（ ΔG ）。根据表观结合常数（ K _a）可以判断,人血清蛋白比牛血清蛋白与噻菁染料的结合更强。     

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.     

Spectrometric Study on the Interaction of Indocyanine Green with Human Serum Albumin

The interaction of indocyanine green(ICG) with human serum albumin(HSA) was investigated via various spectrometric(UV-visible, fluorescence and circular dichroism) techniques. The experimental results indicate that the interaction of ICG with HSA depends on the values of R(R is defined as the molar ratio of HSA to ICG). The interaction of ICG with HSA can form two complexes with intrinsic binding constants(K_a) of 2.97×10⁵(R≤2) and 2.63×10⁴(R>2), respectively. The fluorescence and induced CD(ICD) spectra of ICG demonstrate that binding the first mole of HSA to ICG can form a chiral ICG-HSA complex with strong fluorescence emission, and the chirality and fluorescence of ICG-HSA complex can be significantly reduced by adding another mole of HSA to ICG. Furthermore, although both ICG and ICG-HSA complexes followed an energy-dependent endocytosis process to enter living cells, the cellular uptaken dynamic mechanism of ICG was significantly affected by the HSA conjugation.     

Studies on the binding of nevadensin to human serum albumin by molecular spectroscopy and modeling

The binding of nevadensin to human serum albumin (HSA) in aqueous solution was investigated for the first time by molecular spectroscopy and modeling at pH 7.4. Spectrophotometric observations are rationalized in terms of a static quenching process and binding constant (K_a, K_b) and the number of binding sites (n ≈ 1) were evaluated by fluorescence quenching methods. Thermodynamic data showed that nevadensin was included in the hydrophobic cavity of HSA mainly via hydrophobic interactions. The value of 3.09 nm for the distance r between the donor (HSA) and acceptor (nevadensin) was derived from the fluorescence resonance energy transfer. Spectrophotometric techniques were also applied to investigate the structural information of HSA molecules on the binding of nevadensin and the results showed that the binding of nevadensin to HSA did not change significantly molecular conformation of HSA in our experimental conditions. Furthermore, the study of molecular modeling also indicated that nevadensin could strongly bind to the site I (subdomain IIA) of HSA mainly by a hydrophobic interaction and there are hydrogen bond interactions between nevadensin and the residues Arg-218, Arg-222, Lys-195, and Asp-451. As compared to the other flavonoids, the flavonoids containing methoxy groups which are in aromatic rings can bind to HSA with higher affinity.     

The auxiliary determination of the binding site of berberine binding to human serum albumin by surface-enhanced Raman scattering

We report on the joint application of fluorescence, ultraviolet-visible (UV-Vis) and Raman spectroscopy to the study of berberine with human serum albumin (HSA). We propose the surface-enhanced Raman scattering (SERS) technique to improve the understanding of the quenching interaction caused by berberine which could be applied in recognition process of fluorescent drugs with large biomolecules. The fluorescence and UV-Vis spectroscopic results show that the fluorescence intensity of HSA is significantly decreased in the presence of berberine, and the quenching mechanism is static. The SERS technique demonstrates clear advantages over direct measurements in physiological conditions. By means of this method, we are able to deduce important information concerning the binding property of berberine when interacting with HSA. We show the nitrogen atom is free but the dioxolane is involved in the spontaneously electrostatic inducement and subsequently hydrophobic binding.     

Photophysics of Hypericin and Hypocrellin A in Complex with Subcellular Components: Interactions with Human Serum Albumin

Time-resolved fluorescence and absorption measurements are performed on hypericin complexed with human serum albumin, HSA (1:4, 1:1 and approximately 5:1 hypericin: HSA complexes). Detailed comparisons with hypocrellin A/HSA complexes (1:4 and 1:1) are made. Our results are consistent with the conclusions of previous studies indicating that hypericin binds to HSA by means of a specific hydrogen-bonded interaction between its carbonyl oxygen and the N1-H of the tryptophan residue in the IIA subdomain of HSA. (They also indicate that some hypericin binds nonspecifically to the surface of the protein.) A single-exponential rotational diffusion time of 31 ns is measured for hypericin bound to HSA, indicating that it is very rigidly held. Energy transfer from the tryptophan residue of HSA to hypericin is very efficient and is characterized by a critical distance of 94 A, from which we estimate a time constant for energy transfer of approximately 3 x 10(-15) s. Although it is tightly bound to HSA, hypericin is still capable of executing excited-state intramolecular proton (or hydrogen atom) transfer in the approximately 5:1 complex, albeit to a lesser extent than when it is free in solution. It appears that the proton transfer process is completely impeded in the 1:1 complex. The implications of these results for hypericin (and hypocrellin A) are discussed in terms of the mechanism of intramolecular excited-state proton transfer, the mode of binding to HSA and the light-induced antiviral and antitumor activity.     

一种新型芳香二胺桥联β-环糊精对染料的分子识别

以单-(6-对甲苯磺酰基)-β-环糊精和3,3′-亚甲基联苯胺为原料, 合成了一种新型刚性结构的芳香二胺桥联环糊精, 3,3′-亚甲基联苯胺桥联(6-氨基-6-脱氧-β-环糊精)2. 并用荧光光谱和紫外光谱技术分别测定了在25 ℃时, pH为7.20的磷酸缓冲溶液中β-环糊精(1)和新型桥联环糊精(2)与几种染料分子, 如吖定红(AR)、中性红(NR)、2-对甲苯胺基-6-萘磺酸钠(TNS)、1-苯胺基-8-萘磺酸铵(ANS)、罗丹明B(RhB)和亮绿(BG)形成超分子配合物的稳定常数KS. 化学计量比表明, 桥联环糊精2与客体形成了1∶1的超分子配合物, 其对客体的键合能力和分子选择性远远强于母体?茁-环糊精, 如桥联环糊精2对BG的键合能力可以达到母体环糊精的22.2倍. 从主-客体间的尺寸匹配关系和多重识别机理等方面探讨了桥联环糊精对客体分子的协同键合作用.     

Studies on interaction between gatifloxacin and human serum albumin as well as effect of copper(II) on the reaction

The binding characteristics of gatifloxacin (GTFX) and human serum albumin (HSA) have been studied by fluorescence spectroscopy in aqueous solution, and the interaction influenced by copper(II) was also explored in the paper. The results show that the two-reaction equilibrium constant and the number of binding sites were K = 1.16 x 10(5) l mol(-1), n = 1.27 for GTFX and K = 1.62 x 10(5) l mol(-1), n = 1.74 for GTFX-Cu2+, respectively. The quenching mechanism of fluorescence of HSA by GTFX is a static quenching procedure. The binding distance between GTFX and HSA and the energy transfer efficiency are obtained based on the theory of Fōrster spectroscopy energy transfer. The effect of GTFX on the conformation of HSA was also been analyzed by using synchronous fluorescence spectroscopy. The interaction of GTFX and HSA has been studied by flow-mixed microcalorimetry in the absence and presence of copper(II) and their thermodynamic parameters were obtained. The enthalpy changes and the entropy changes were calculated to be DeltaH approximately 0, DeltaS > 0 in the absence of copper(II),which indicated that static forces played major role in the interaction of GTFX and HSA, and to be DeltaH approximately 0, DeltaS > 0 in the presence of copper(II),which indicated that the static forces also played major role on the reaction. The molar free energy changes of the two reactions are identical with each other because the entropy-enthalpy compensation happened between the two reactions.     

Molecular Recognition Studies on Supramolecular Systems 34. Synthesis of Aromatic Diamino-bridged Bis(β-cyclodextrin)s and their Inclusion Complexation with Dye Molecules

A series of 6,6'-bis( g -cyclodextrin)s with rigid aromatic diamino tethers, i.e. p -phenylenediamino-bridged-bis(6-amino-6-deoxy- g -cyclodextrin) ( 3 ), 4,4'-bianilino-bridged-bis(6-amino-6-deoxy- g -cyclodextrin) ( 4 ) and 3,3'-bianilino-bridged-bis(6-amino-6-deoxy- g -cyclodextrin) ( 5 ), have been synthesized by the reaction of mono[6- O -( p -toluenesulfonyl)]-( g -cyclodextrin) with corresponding materials. The inclusion complexation behavior of native g -cyclodextrin ( 1 ), mono-(6-anilino-6-deoxy)- g -cyclodextrin ( 2 ), and novel bis( g -cyclodextrin) 3 - 5 with some representative dyes, i.e. ammonium 8-anilino-1-naphthalenesulfonate (ANS), Brilliant Green, Methyl Orange, Acridine Red and Rhodamine B, was investigated at 25C in aqueous phosphate buffer solution (pH 7.20) by means of fluorescence, ultraviolet, circular dichroism spectrometry as well as fluorescence lifetime measurement. The spectrophotometric titrations gave the complex stability constants ( K S ) and Gibbs free energy changes ( j G 0 ) for the stoichiometric 1:1 inclusion complexation of hosts examined with dye molecules. As compared with 1 or 2 , bridged bis( g -cyclodextrin)s displayed significantly enhanced binding abilities towards these dyes. Typically, dimer 3 showed the highest binding ability upon inclusion complexation with acridine red affording 17 times higher K S for 3 than for 1 . The molecular binding abilities and selectivities of dyes by bridged bis( g -cyclodextrin)s have been discussed from the viewpoint of induced-fit interaction and multipoint recognition mechanism.     

Investigation on the Binding Behavior of Ellagic Acid to Human Serum Albumin in Aqueous Solution

Ellagic acid (EA), one of the polyphenols in fruits and nuts, has pharmacological activity. To explore binding behavior of EA to protein, human serum albumin (HSA) was chosen and investigated by fluorescence spectroscopy, Fourier transform infrared (FT-IR) spectroscopy and molecular modeling in aqueous solution. Fluorescence titration results indicated that EA effectively quenched the intrinsic fluorescence of HSA by static quenching and the binding process was spontaneous. According to the Scatchard equation, there was only one class of binding sites can bind to HSA, the binding constants at three different temperatures (298, 310 and 318 K) were 8.47 × 10⁴, 7.39 × 10⁴ and 6.00 × 10⁴, respectively. It was found by FT-IR spectra that EA altered HSA secondary structure. Thermodynamic analysis showed that hydrophobic interaction and hydrogen bonds played an important role in stabilizing EA–HSA complex. A molecular docking study suggested that the HSA residues for EA binding located in sub-domain IIA.     

A comparative study of assembly and disassembly process of dimeric and monomeric cyanine dyes with DNA templates

H-aggregates of dimeric cyanine dyes (TC-P4) formed in PBS could be disassembled by G-quadruplex into dimer and/or monomer, resulting in higher fluorescent selectivity than its corresponding monomer (TC).     

Studies on the interaction of gallic acid with human serum albumin in membrane mimetic environments

In this study the interaction between gallic acid and human serum albumin (HSA) in AOT/isooctane/water microemulsions was characterized for the first time using fluorescence quenching technique in combination with UV absorption spectroscopy, Fourier transform infrared (FT-IR) spectroscopy, circular dichroism (CD) spectroscopy and dynamic light scattering (DLS) technique. In water-surfactant molar ratio (omega(o))=20 microemulsions fluorescence data revealed the presence of one binding site of gallic acid on HSA and its binding constants (K) were (1.18+/-0.02)x10(4), (1.13+/-0.02)x10(4), (1.03+/-0.02)x10(4), (0.95+/-0.02)x10(4), (0.87+/-0.02)x10(4) and (0.82+/-0.03)x10(4)M(-1) at 282, 289, 296, 303, 310 and 317 K, respectively. The affinities in microemulsions were much higher than that in buffer solution. FT-IR and CD data suggested that the protein conformations were altered with the reductions of alpha-helices from 54-56% for free HSA in buffer to 40-41% for free HSA in microemulsion. After binding with gallic acid, the alpha-helices of HSA in microemulsion increased 2-7% for different drug-protein molar ratio. The thermodynamic functions standard enthalpy (Delta H(0)) and standard entropy (DeltaS(0)) for the reaction were calculated to be -8.10 kJ mol(-1) and 49.42 J mol(-1)K(-1). These results indicated that gallic acid bound to HSA mainly by hydrophobic interaction and electrostatic interaction in microemulsions. In addition, the displacement experiments confirmed that gallic acid could bind to the site I of HSA, which was approved by the molecular modeling study. Furthermore, the DLS data suggested that HSA may locate at the interface of the microemulsion and gallic acid could interact with them.     

6-氨基-5-氰基-3-甲基-4-(3-硝基苯)-1-苯基吡唑[3,4-b]并吡啶与人血清白蛋白结合作用的光谱特征

采用紫外光谱法和荧光光谱法研究了6-氨基-5-氰基-3-甲基-4-(3-硝基苯)-1-苯基吡唑[3,4-b]并吡啶(6A)与人血清白蛋白(HSA)的结合作用,利用同步荧光法和三维荧光法研究了6A与HSA作用前后人血清白蛋白的构象变化。观测到生理pH7.4条件下6A使HSA的紫外吸收峰增强,特征荧光峰猝灭。Stern-Volmer曲线显示,6A对HSA的荧光猝灭可能是一个单一的静态猝灭过程,并且得出18℃和37℃时的结合位点数和结合常数。根据F rster非辐射转移理论可求出6A与HSA作用距离r=3.73 nm;根据基本热力学参数ΔH、ΔS和ΔG判断6A和HSA主要通过氢键和范德华力发生相互作用。     

Intriguing H-aggregate and H-dimer formation of coumarin-481 dye in aqueous solution as evidenced from photophysical studies

Photophysical properties of coumarin-481 (C481) dye in aqueous solution show intriguing presence of multiple emitting species. Concentration and wavelength dependent fluorescence decays and time-resolved emission spectra and area-normalized emission spectra suggest the coexistence of dye monomers, dimers, and higher aggregates (mostly trimers) in the solution. Because of the efficient intramolecular charge transfer (ICT) state to twisted intramolecular charge transfer (TICT) state conversion, the dye monomers show very short fluorescence lifetime of ~0.2 ns. Fluorescence lifetimes of dimers (~4.1 ns) and higher aggregates (~1.4 ns) are relatively longer due to steric constrain toward ICT to TICT conversion. Observed results indicate that the emission spectra of the aggregates are substantially blue-shifted compared to monomers, suggesting H-aggregation of the dye in the solution. Temperature-dependent fluorescence decays in water and time-resolved fluorescence results in water-acetonitrile solvent mixtures are also in support of the dye aggregation in the solution. Though dynamic light scattering studies could not recognize the dye aggregates in the solution due to their small size and low concentration, fluorescence up-conversion measurements show a relatively higher decay tail in water than in water-acetonitrile solvent mixture, in agreement with higher dye aggregation in aqueous solution. Time-resolved fluorescence results with structurally related non-TICT dyes, especially those of coumarin-153 dye, are also in accordance with the aggregation behavior of these dyes in aqueous solution. To the best of our knowledge, this is the first report on the aggregation of coumarin dyes in aqueous solution. Present results are important because coumarin dyes are widely used as fluorescent probes in various microheterogeneous systems where water is always a solvent component, and the dye aggregation in these systems, if overlooked, can easily lead to a misinterpretation of the observed results.     

Photobleaching of asymmetric cyanines used for fluorescence imaging of single DNA molecules

The photobleaching of the cyanine dyes YO and YOYO has been investigated for both free and DNA-bound dyes, using absorption and fluorescence spectroscopy coupled with fluorescence microscopy. For the free dyes, the nature of the reactive species involved in the photodegradation process is different for the monomer and the dimer, as shown by scavenger studies. For DNA-bound dyes, photoinduced fading of the visible absorption band occurs by different pathways depending on the drug binding mode and can be attenuated by appropriate scavengers. However, none of these scavengers were found to have any significant effect on the photobleaching of dye fluorescence. It appears that the reduction of fluorescence intensity comes from a quenching of the dye fluorescence by modified DNA bases, possibly 8-oxo-7,8-dihydro-2'-deoxyguanosine.     

Influence of the interaction of chromophores of bis-cyanine dyes on the photogeneration of charge carriers in poly-N-epoxypropylcarbazole films

An increase in photoconductivity and in the extinguishing effect of an external electric field has been observed in the photoluminescence of doped poly-N-epoxypropylcarbazole films on changing from cyanine dyes with normal chromophores to the corresponding bis-cyanines. It was concluded that an increase in photogeneration of triplet electron-hole pairs arose with such replacement of the dye and that dissociation of the pairs was responsible for the photoconductivity. Translated from Teoreticheskaya i éksperimental'naya Khimiya, Vol. 34, No. 6, pp. 371–375, November–December, 1998.