Side-chain dynamics of an alpha-helical polypeptide monitored by fluorescence

The "blob" model, developed to analyze the fluorescence decays of polymers randomly labeled with pyrene, has been applied to a series of pyrene-labeled poly(glutamic acid)s (PyPGA) in DMF and carbonated buffer solutions at pH 9. Poly(glutamic acid) (PGA) exists in the ionized form in the buffer solutions as poly(sodium glutamate) (PGNa). PGA adopts an alpha-helical conformation in DMF, whereas in aqueous solution PGNa is a random coil. Fluorescence, UV-vis absorption, and circular dichroism measurements indicate that in our studies pyrene pendants attached themselves along PGA in a clustered manner. Simulations were carried out to establish that the geometry of the PGA alpha-helix induces the high level of pyrene clustering. Since the level of pyrene clustering decreased with lower pyrene content, information about naked PGA was retrieved by extrapolating the trends obtained by fluorescence to zero pyrene content. Analysis of the fluorescence decays demonstrated that during its lifetime an excited pyrene probes a 32 amino acid section of the PGA alpha-helix. This result was supported by molecular mechanics optimizations. This study establishes that the blob model, originally used to monitor the encounters between pyrenes attached randomly onto a polymer adopting a random coil conformation, can also be applied to study the dynamics of the side chains of structured proteins. Since the blob model helps in monitoring the encounters between amino acids in the initial state (i.e., random coil) and in the final state (i.e., structured protein) of the folding pathway of a protein, it could be applicable to the study of protein folding.     

A case for using randomly labeled polymers to study long-range polymer chain dynamics by fluorescence

The process of excimer formation was studied for a series of pyrene end-labeled polystyrenes (PS(X)-Py 2 where X is the polymer molecular weight equal to 3, 4.5, 8, 12.7, and 14.6 K) and two series of polystyrenes randomly labeled with pyrene (CoE-PS and CoA-PS) in seven different solvents. The solvent viscosities ranged from 0.41 to 1.92 mPa x s, while the solvent quality ranged from good to poor solvents for polystyrene, as determined by intrinsic viscosity measurements. Steady-state fluorescence spectra of the pyrene-labeled polymers were acquired, and the excimer to monomer ratios showed that excimer formation increased strongly with a decrease in solvent viscosity. The monomer and excimer time-resolved fluorescence decays were also acquired and fitted globally to either the Birks' scheme or the fluorescence blob model (FBM) for the end- or randomly labeled polymers, respectively. All parameters reporting on the long-range polymer chain dynamics (LRPCD) obtained from the analysis of the fluorescence data acquired with the PS(X)-Py 2, CoE-PS, and CoA-PS series yielded virtually identical trends, demonstrating that these fluorescence experiments yield results that are internally consistent with one another. Considering the substantial advantages associated with the preparation and study of randomly labeled polymers, this report presents an appealing case for the use of randomly labeled polymers in the study of LRPCD.     

Comparison of the association level of a pyrene-labeled associative polymer obtained from an analysis based on two different models

A hydrophobically modified alkali swellable emulsion copolymer (HASE) was labeled with pyrene and its fluorescence behavior was monitored by steady-state and time-resolved fluorescence as increasing amounts of the surfactant sodium dodecyl sulfate (SDS) were added to the solution. In aqueous solution, the pyrene pendants are aggregated. As SDS is added, the surfactant binds to the pyrene aggregates, which leads to their breakup at an onset SDS concentration of 1.25 x 10(-3) mol/L. The breakup of the pyrene aggregates is complete at 4.25 x 10(-3) mol/L, which is slightly larger than the critical micellar concentration of SDS in 0.01 M Na(2)CO(3) aqueous solution at pH 9 found to equal 3.5 x 10(-3) mol/L by surface tension measurements. The pyrene pendants were present as different species in solution, and the fractions representative of all emissive pyrene species were determined from the global analysis of the monomer and excimer fluorescence decays. Two analyses were applied to the decays. In the first analysis, the diffusional encounters between pyrene pendants were described by the blob model. In the second analysis, no assumptions were made on how the pyrene pendants encountered each other. Both analyses yielded identical results which demonstrate that the determination of the fractions of the different emissive pyrene species of a solution of a pyrene-labeled associative polymer does not depend on the model chosen to account for the diffusional encounters taking place between pyrene pendants.     

Pyrene excimer signaling molecular beacons for probing nucleic acids

Molecular beacon DNA probes, containing 1-4 pyrene monomers on the 5' end and the quencher DABCYL on the 3' end, were engineered and employed for real-time probing of DNA sequences. In the absence of a target sequence, the multiple-pyrene labeled molecular beacons (MBs) assumed a stem-closed conformation resulting in quenching of the pyrene excimer fluorescence. In the presence of target, the beacons switched to a stem-open conformation, which separated the pyrene label from the quencher molecule and generated an excimer emission signal proportional to the target concentration. Steady-state fluorescence assays resulted in a subnanomolar limit of detection in buffer, whereas time-resolved signaling enabled low-nanomolar target detection in cell-growth media. It was found that the excimer emission intensity could be scaled by increasing the number of pyrene monomers conjugated to the 5' terminal. Each additional pyrene monomer resulted in substantial increases in the excimer emission intensities, quantum yields, and excited-state lifetimes of the hybridized MBs. The long fluorescence lifetime ( approximately 40 ns), large Stokes shift (130 nm), and tunable intensity of the excimer make this multiple-pyrene moiety a useful alternative to traditional fluorophore labeling in nucleic acid probes.     

Pyrene-stacked nanostructures constructed in the recombinant tobacco mosaic virus rod scaffold

The effect of pyrenes introduced into a tobacco mosaic virus (TMV) coat protein monomer on the formation and stability of the TMV assembly was investigated. The possible arrangement of the pyrenes in the inner cavity of the TMV rod was also estimated. The pyrene derivative was introduced to four specific amino acids in the cavity of the TMV rod structure. Rod-structure formation was examined by atomic force microscopy (AFM). Two pyrene-attached mutants (positions 99 and 100) assembled to increase the length of the rod structures by 2.5 microm at pH 5.5. The interaction of the pyrene moieties in the TMV cavity was investigated by steady-state and time-resolved spectroscopic analysis. Strong excimer emission with significantly short wavelength (465 nm) was observed from the two mutants mentioned above. Excitation and UV-visible spectra indicate that the pyrene moieties form pi-stacked structures in the TMV cavity. Details of the pyrene interaction were investigated by analyzing the fluorescence lifetime of the excimer. Results suggest that the pyrenes formed preassociated rigid structures with partially overlapped geometry in the restricted space of the TMV cavity. The pyrenes effectively stabilize the TMV rod through a pi-stacking interaction in a well-ordered way, and the single pyrene moiety introduced into the monomer affects the overall formation of the TMV rod structure.     

Molar absorption coefficient of pyrene aggregates in water

The molar absorption coefficient of pyrene aggregates, epsilon(E0), was determined for a series of pyrene-labeled poly(N,N-dimethylacrylamide)s (Py-PDMA) having different pyrene contents. Aqueous solutions of Py-PDMA having pyrene contents ranging from 263 to 645 mumol of pyrene per gram of polymer were studied by UV-vis absorbance and time-resolved fluorescence spectroscopy. The global analysis of the monomer and excimer fluorescence decays with the fluorescence blob model yielded the fractions of the overall absorption contributed by all the pyrene species present in solution. The combined knowledge of the fractions obtained from the global analysis of the time-resolved fluorescence decays, the total absorption of the Py-PDMA solution obtained from UV-vis spectroscopy, and the total pyrene concentration in the solution obtained from the known pyrene content of each Py-PDMA sample led to the determination of the molar absorption coefficient of pyrene aggregates. Regardless of the pyrene content of the Py-PDMA samples and hence the level of association of the pyrene pendants in solution, all Py-PDMA samples yielded similar epsilon(E0) values over the range of wavelengths studied, namely, from 325 to 350 nm. The averaged epsilon(E0) was found to be red-shifted relative to unassociated pyrenes by 3 nm as well as having a value at the 0-0 peak of 21 000 M(-1).cm(-1) reduced from 34 700 M(-1).cm(-1) for unassociated pyrenes. The determination of epsilon(E0) enabled the first determination of the absolute fraction of associated pyrenes for aqueous solutions of a series of pyrene-labeled water-soluble polymers. The procedure outlined in this study is applicable to any pyrene-labeled water-soluble polymer and provides a new means to study quantitatively the effect of the hydrophilic-to-lipophilic balance on the hydrophobic associations generated by hydrophobically modified water-soluble polymers. As an application, the average number of pyrenes involved in a pyrene aggregate generated by Py-PDMA in water is determined.     

Synthesis and characterization of novel pyrene-dendronized porphyrins exhibiting efficient fluorescence resonance energy transfer: optical and photophysical properties

A novel series of pyrene dendronized porphyrins bearing two and four pyrenyl groups (Py(2)-TMEG1 and Py(4)-TMEG2) were successfully synthesized. First and second generation Fréchet type dendrons (Py(2)-G1OH and Py(4)-G2OH) were prepared from 1-pyrenylbutanol and 3,5-dihydroxybenzyl alcohol. These compounds were further linked to a trimesitylphenylporphyrin containing a butyric acid spacer via an esterification reaction to obtain the desired products. Dendrons and dendronized porphyrins were fully characterized by FTIR and (1)H NMR spectroscopy and their molecular weights were determined by matrix-assisted laser desorption ionization time of flight mass spectrometry. Their optical and photophysical properties were studied by absorption and fluorescence spectroscopies. The formation of dynamic excimers was detected in the pyrene-labeled dendrons, with more excimer being produced in the higher generation dendron. The fluorescence spectra of the pyrene dendronized porphyrins exhibited a significant decrease in the amount of pyrene monomer and excimer emission, jointly with the appearance of a new emission band at 661 nm characteristic of porphyrin emission, an indication that fluorescence resonance energy transfer (FRET) occurred from one of the excited pyrene species to the porphyrin. The FRET efficiency was found to be almost quantitative ranging between 97% and 99% depending on the construct. Model Free analysis of the fluorescence decays acquired with the pyrene monomer, excimer, and porphyrin core established that only residual pyrene excimer formation in the dendrons could occur before FRET from the excited pyrene monomer to the ground-state porphyrin core.     

Pyrene-terminated phenylenethynylene rigid linkers anchored to metal oxide nanoparticles

Phenylenethynylene (PE) rigid linkers (para and meta) were used to anchor pyrene to the surface of TiO2 (anatase) and ZrO2 nanoparticle thin films through the two COOH groups of an isophthalic acid (Ipa) unit. Four chromophore-linker models were studied in solution and bound. Two are novel meta-pyrene-PE linker systems: dimethyl 5-(3-(1-pyrenylethynyl)phenylethynyl)-isophthalate, carrying one pyrene, and dimethyl 5-(bis-3,5-(1-pyrenylethynyl)phenylethynyl)-isophthalate, carrying two. These were compared with para rigid-rods dimethyl 5-(1-pyrenylethynyl)isophthalate and dimethyl 5-(4-(1-pyrenylethynyl)phenylethynyl)-isophthalate, each carrying one pyrene but varying in length. The length of the PE linkers and the para or meta substitution influence the photophysical properties of the compounds. The extinction coefficient increased, and the long wavelength absorbance of the pyrene chromophore was shifted to the red with increasing conjugation. Compared to unsubstituted pyrene, the pyrene-linker systems were characterized by short fluorescence lifetimes (tau approximately 2 ns in tetrahydrofuran solutions), but quantum yields were close to unity. ZINDO/S CI calculations attribute this effect to a switching in the order of the two lowest-lying singlet states of pyrene. High surface coverages, approximately 10(-8) mol/cm2, and carboxylate binding modes on nanostructured TiO2 films were obtained in all cases. The appearance of a pyrene excimer emission on ZrO2, an insulator, indicates that the pyrene-linker system is closely packed (Py-Py < 4 A) on the surface. The fluorescence emission on TiO2 was completely quenched, consistent with quantitative and rapid electron injection into the semiconductor indicating that the pyrene excimer acts as a sensitizer. Photoelectrochemical studies in regenerative solar cells with I3-/I- as the redox mediator indicated near-quantitative conversion of absorbed photons into an electrical current.     

NUCLEIC ACID HYBRIDIZATION ACCOMPANIED WITH EXCIMER FORMATION FROM TWO PYRENE-LABELED PROBES

Abstract— We developed a novel nucleic acid hybridization method based on excimer formation. We used two different 16-mer oligonucleotide probes that had a combined continuous-sequence run that was complementary to a target 32-mer. Prior to hybridization, the adjacent terminal ends (i.e. the 3'-terminal of one probe and the 5'-terminal of the other probe) were each labeled with one pyrene residue. When these probes simultaneously hybridized to the target, a 495 nm broad fluorescence band was produced. The intensity of this band increased as the intensity of the pyrene monomer bands decreased, indicating that the 495 nm band was attributed to the pyrene excimer. The excimer fluorescence, easily differentiated from the monomer bands for emission wavelength, opens up a new way to perform homogeneous hybridization assays and in vivo imaging of nucleic acids.     

Intramolecular excimer formation and delayed fluorescence in sterically constrained pyrene dimers

The synthesis is described for a series of five molecular dyads comprising pyrene-based terminals covalently linked through a 1,3-disubstituted phenylene spacer. The extent of through-space communication between the pyrene units is modulated by steric interactions imposed by bulky moieties attached at the 6,8-positions of each pyrene unit. For the control compound, only hydrogen atoms occupy the 6,8 positions (DP1), whereas the remaining compounds incorporate ethynylene groups terminated with either triisopropylsilyl (DP2), 1-tert-butylbenzene (DP3), 2,6-di-tert-butylbenzene (DP4) or 1-tert-butyl-3,5-dimethylbenzene (DP5) units. Each compound shows a mixture of monomer and excimer fluorescence in fluid solution at room temperature, but only monomer emission in a glassy matrix at 77 K. The ratio of monomer to excimer fluorescence depends markedly on the molecular structure; DP1 is heavily biased in favour of the excimer and DP4 is enriched with monomer fluorescence. Photophysical properties, including laser induced and delayed fluorescence data, are reported for each compound. Delayed fluorescence occurs by both intramolecular and bimolecular steps, but these events take place on different timescales. The possibility is raised for using intramolecular triplet-triplet annihilation as a means of molecular imaging.     

Study of the semidilute solutions of poly(N,N-dimethylacrylamide) by fluorescence and its implications to the kinetics of coil-to-globule transitions

The large scale motions of poly(N,N-dimethylacrylamide) chains randomly labeled with pyrene (Py-PDMA) were monitored by steady-state and time-resolved fluorescence in semidilute solutions of naked PDMA in acetone and DMF for polymer concentrations ranging from 0 to 550 g/L. Although increasing the polymer concentration of the solution led to a decrease of the mobility of the chromophore attached onto the PDMA backbone, this reduction was rather modest when compared to the large increase of the macroscopic viscosity. This result indicated that locally, the monomer constituting the chains experienced freedom of movement despite the high solution viscosity. The restricted mobility of the chromophore was characterized by the number of monomers occupying the volume probed by the excited chromophore during its lifetime, referred to as a fluorescence "blob". The number of monomers constituting a fluorescence blob, N(F)(-)(blob), and the volume of a fluorescence blob, V(F)(-)(blob), were found to decrease as the polymer concentration of the solution increased, reflecting the decreased mobility experienced by the chromophore. In DMF, the radius of an F-blob was found to scale as N(nu)(F)(-)blob, where nu equaled 0.66 +/- 0.03, very close to the expected value of the Flory exponent of 0.6 for a polymer in a good solvent. The combined knowledge of how N(F)(-)(blob) varies with the fluorescence lifetime of the chromophore and the coil density of the polymer was used to propose a new means of studying coil-to-globule transitions with potential implications for predicting the rate of protein folding.     

Fluorescence quenching of pyrene monomer and excimer by CH3I

The fluorescence quenching rate constants of pyrene monomer and excimer by CH₃I were obtained at several temperatures in methylcyclohexane. Both quenching processes are kinetically controlled, allowing insight on the mechanism of quenching. The rate constants have both temperature-independent and temperature-dependent components. The temperature-independent component for both monomer and excimer fluorescence is consistent with quenching due to enhanced intersystem crossing to a lower energy triplet state. The monomer temperature-dependent component comes from the enhancement of the intersystem crossing to a higher energy triplet state. The thermally activated excimer quenching is associated with the excimer dissociation step to give a pyrene in a second triplet state plus a ground state pyrene molecule.     

Electric field effects on absorption and fluorescence spectra of trimethylsilyl- and trimethylsilylethynyl-substituted compounds of pyrene in a PMMA film

External electric field effects on absorption and fluorescence spectra of 1,3,6,8-tetrakis(trimethylsilyl)pyrene and 1,3,6,8-tetrakis(trimethylsilylethynyl)pyrene (TMSPy and TMS(E)Py, respectively) have been examined in a poly(methyl methacrylate) (PMMA) film at various concentrations at various temperatures. TMS(E)Py preferentially forms an aggregate in a PMMA film, as the concentration increases, indicating that the acetylenic groups enhance the pi-pi interactions between pyrene molecules. The change in molecular polarizability following excitation has been determined both for the monomer and for the aggregate, based on the electroabsorption spectra. The change in molecular polarizability following emission has also been determined in both compounds, based on the electrofluorescence spectra. TMSPy exhibits two excimer fluorescence emissions at high concentrations which are ascribed to the partially overlapping excimer and the sandwich-type excimer, respectively, besides the monomer fluorescence emitted from the locally excited state. The sandwich-type excimer fluorescence as well as monomer fluorescence is quenched by an electric field, whereas the fluorescence of the partially overlapping excimer is enhanced by an electric field. Excimer fluorescence of TMS(E)Py, which arises from the sandwich-type excimer, is quenched by an electric field at any temperature. Only one species of the partially overlapping excimer is confirmed in TMSPy, while no partially overlapping excimer is confirmed in TMS(E)Py.     

A Selective Cucurbit[8]uril-Peptide Beacon Ensemble for the Ratiometric Fluorescence Detection of Peptides

A convenient supramolecular strategy for constructing a ratiometric fluorescent chemosensing ensemble, consisting of a macrocyclic host (cucurbit[8]uril CB[8]), and a pyrene-tagged amphiphilic peptide beacon (AP 1), is reported. AP 1 unfolds upon encapsulation of the pyrene termini into the hydrophobic CB[8] cavity. This changes pyrene excimer to monomer emission. Substrates with higher affinity for the CB[8] cavity can displace AP 1 from the ensemble. The released AP 1 folds again to form a pyrene excimer, which allows for the ratiometric fluorescence monitoring of the substrate. In this report, the ensemble capacity for ratiometric fluorescence monitoring of biological substrates, such as amino acid derivatives, specific peptides, and proteins, in aqueous media is demonstrated.     

Solvent-dependent conformational and fluorescence change of an N-phenylbenzohydroxamic acid derivative bearing two pyrene moieties

The conformation of N-phenylbenzohydroxamic acid has been reported to change depending on the solvent properties. Here, we newly synthesized N-phenylbenzohydroxamic acid derivative, which contains two pyrene moieties separated from the phenyl rings by ethylene linkers. It showed solvent-dependent conformational change, and its fluorescence was also solvent-dependent, that is, only monomer fluorescence of pyrene was observed in DMSO or DMF, whereas the excimer fluorescence was observed in CH₂Cl₂ or CHCl₃. Thus, the structural characteristics could be converted to fluorescence change as output, which would be a good candidate as a fluorescent sensor.     

Immobilization of pyrene on quartz plate surface via a flexible long spacer and its sensing properties to dicarboxylic acids

It is known that polycyclic aromatic hydrocar-bons (PAHs) form excimer easily, and show both monomer and excimer emission in polar medium[1]. This character comes from their hydrophobic nature and plane structures. The ratio of the intensity of ex-cimer emission to that of monomer emission is a func-tion of distance between neighbouring PAHs in a sys-tem. It is not difficult to understand that many factors, such as the concentration of PAHs, temperature, pres-ence and concentration of othe…     

The effect of γ‐cyclodextrin addition in the self‐assembly behavior of pyrene labeled poly(acrylic) acid with different chain sizes

The interaction between poly(acrylic acid) polymers (PAA) of low‐ (2000 g/mol) and high‐ (450,000 g/mol) molecular weight (M_w) hydrophobically modified with pyrene (PAAMePy) and β‐ and γ‐cyclodextrins (β‐CD, γ‐CD) was investigated with fluorescent techniques. The interaction with β‐CD promotes little variation in the spectral and photophysical behavior of the polymer, whereas significant changes are observed upon addition of γ‐CD. The degree of inclusion (between the pyrene groups of the polymer and the cyclodextrins) is followed through the observation of the changes in the absorption, excitation (collected in the monomer and excimer emission regions) and emission (I_E/I_M ratio) spectra and from time‐resolved data. Within the studied range of γ‐CD concentration, the fluorescence decays of the long chain (high M_w) PAAMePy polymers were found tri‐exponential in the monomer and excimer emission regions in agreement with previous studies. In the case of the low M_w PAAMePy polymers, tri‐exponential decays were observed at the monomer and excimer emission wavelengths. However, when a γ‐CD concentration of 0.01 and 0.03 M is reached for, respectively, the low‐ and high‐labeled pyrene short chain (low M_w) polymers, the fluorescence decays in the excimer region become biexponential (two excimers) with no rising component, thus showing that all pyrene groups are encapsulated (and preassociated) into the γ‐CD cavity. In the case of the high M_w polymers, the addition of γ‐CD has been found to change the level of polymer interaction from pure intramolecular (water in the absence of cyclodextrin) to a coexistence of intra‐ with intermolecular interactions. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 1402–1415, 2008     

含芘荧光化学敏感器化合物同小牛胸腺DNA分子间的相互作用

研究了含芘荧光化学敏感器分子被ctDNA猝灭的荧光光谱.ctDNA分子对该化学敏感器中芘的激发单体,激基缔合物都有猝灭作用.对激发单体的猝灭速度顺序为;化合物(2)>化合物(1)>芘丁酸>化合物(3);对激基缔合物的猝灭速度顺序为;化合物(2)化合物(3).由得到的荧光猝灭数据,可按公式(2)求得荧光化学敏感器分子与ctDNA分子相互作用的稳定常数.发现化合物(2)与ctDNA分子间有着最强的相互作用能力.按ctDNA和含芘荧光化学敏感器的分子结构、构型以及分子内原子-原子的间距等提出了ctDNA分子与该荧光化学敏感器的作用模型,并对上述结果进行了初步解释.     

Sensing isothermal changes in the lateral pressure in model membranes using di-pyrenyl phosphatidylcholine

In this work we present data from a homologous series of di-pyrenyl phosphatidylcholine (dipyPC) probes which can sense lateral pressure variations in the chain region of the amphiphilic membrane (lateral pressures are tangential to the interface). The dipyPC has pyrene moieties attached to the ends of equal length acyl chains on a phosphatidylcholine molecule. Ultraviolet stimulation produces both monomer and excimer fluorescence from pyrene. At low dilutions of dipyPC in model membranes the excimer signal is entirely intra-molecular and since it depends on the frequency with which the pyrene moieties are brought into close proximity, the relative intensity of the excimer to monomer signal, eta, is a measure of the pressure. We synthesised or purchased dipyPC probes with the pyrene moieties attached to acyl chains having 4, 6, 8 and 10 carbon atoms and then measured eta in fully hydrated bilayers composed of dioleoylphosphatidylcholine and dioleoylphosphatidylethanolamine (DOPC and DOPE respectively). Although the resolution of our measurements of lateral pressure as a function of distance into the monolayer was limited, we did observe a dip in the excimer signal in the region of the DOPC/DOPE cis double bond. As we isothermally increased the DOPE composition, and hence the desire for interfacial curvature, we observed, as expected, that the net excimer signal increased. However this net increase was apparently brought about by a transfer of pressure from the region around the glycerol backbone to the region near the chain ends, with the lateral pressure dropping above the cis double bond but increasing at a greater rate beyond the double bond.