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PubMed2001

Cleavage of telomeric G-quadruplex DNA with perylene-EDTA*Fe(II).

Interest in the development of compounds that bind G-quadruplex DNA selectively has been sparked by the discovery that these compounds can inhibit the activity of telomerase. Compounds that bind to this unique structure, as well as compounds that recognize it and cleave it upon binding, have potential uses as anticancer agents and as probes for the presence of G-quadruplex structures in chromatin. Here we report on the G-quadruplex-specific cleavage properties of a perylene derivative, perylene-EDTA*Fe(II). This water-soluble complex cleaves G-quadruplex DNA selectively in the presence of dithiothreitol. We characterize the cleavage reaction with respect to perylene-EDTA*Fe(II) concentration, DNA structural type, cation type (Na+ vs K+), cation concentration, and pH. Visible spectroscopy confirms the selectivity of the perylene-EDTA*metal complex for G-quadruplex DNA. NMR titration of a parallel G-quadruplex with perylene-EDTA (without metal) indicates that the compound binds to G-quadruplex DNA by stacking externally on the 3' G-tetrad.

Binding Sites↗
PubMed2000

Fluorescence resonance energy transfer from pyrene to perylene labels for nucleic acid hybridization assays under homogeneous solution conditions.

We characterized the fluorescence resonance energy transfer (FRET) from pyrene (donor) to perylene (acceptor) for nucleic acid assays under homogeneous solution conditions. We used the hybridization between a target 32 mer and its complementary two sequential 16 mer deoxyribonucleotides whose neighboring terminals were each respectively labeled with a pyrene and a perylene residue. A transfer efficiency of approximately 100% was attained upon the hybridization when observing perylene fluorescence at 459 nm with 347-nm excitation of a pyrene absorption peak. The Förster distance between two dye residues was 22.3 A (the orientation factor of 2/3). We could change the distance between the residues by inserting various numbers of nucleotides into the center of the target, thus creating a gap between the dye residues on a hybrid. Assuming that the number of inserted nucleo-tides is proportional to the distance between the dye residues, the energy transfer efficiency versus number of inserted nucleotides strictly obeyed the Förster theory. The mean inter-nucleotide distance of the single-stranded portion was estimated to be 2.1 A. Comparison between the fluorescent properties of a pyrene-perylene pair with those of a widely used fluorescein-rhodamine pair showed that the pyrene-perylene FRET is suitable for hybridization assays.

DNA, Bacterial↗
PubMed2006

Hydrogen-bonded oligo(p-phenylenevinylene) functionalized with perylene bisimide: self-assembly and energy transfer.

We describe the synthesis, supramolecular ordering on surfaces and in solution, and photophysical characterization of OPV4UT-PERY, an oligo(p-phenylenevinylene) (OPV) with a covalently attached perylene bisimide moiety. In chloroform, the molecule forms dimers through quadruple hydrogen bonding of the ureido-s-triazine array. This is supported by scanning tunneling microscopy (STM) studies, which reveal dimer formation at the liquid (1,2,4-trichlorobenzene)/solid (graphite) interface. Moreover, contrast reversal in bias-dependent STM imaging provides information on the ordering and different electronic properties of the oligo(p-phenylenevinylene) and perylene bisimide moieties. In dodecane, the molecule self-assembles into H-type aggregates that are still soluble as a result of the hydrophobic shell formed by the dodecyloxy wedges. The donor-acceptor molecule is characterized by efficient energy transfer from the photoexcited OPV to the perylene bisimide. Mixed assemblies with analogous OPVs lacking the perylene bisimide unit have been prepared in dodecane solution and energy transfer to the incorporated perylene bisimides has been studied by fluorescence spectroscopy.

Journal Article↗
PubMed2006

Effect of aggregation on the excited-state electronic structure of perylene studied by transient absorption spectroscopy.

The effect of aggregation on the excited-state electronic structure of perylene was studied through transient absorption measurements of isolated molecules, excimers, monomeric crystals (beta-perylene), and dimeric crystals (alpha-perylene). Changes of electronic state were clearly identified from the changes in transient absorption spectra. A detailed investigation was made by combining the obtained results with previous measurements of ground-state absorption and fluorescence spectra. The energy level of the ion-pair state in alpha-perylene crystals was estimated, and the results are compared with previous photoconductivity results. Moreover, the relaxation processes of excited states in alpha-perylene crystals were studied by femtosecond transient absorption measurements.

Journal Article↗
PubMed2004

The growth of perylene on Ru(0001).

The structure of perylene adsorbed on Ru(0001) surface has been studied by ultraviolet photoemission spectroscopy (UPS) and low-energy electron diffraction. An ordered p(4x4) structure is observed from a monolayer (about 4 A thickness) of the perylene on Ru(0001) surface. UPS measurements show the molecular features, from the perylene multiplayer, between 2 and 10 eV below the Fermi level. Angle-resolved ultraviolet photoemission spectroscopy measurements suggest that the perylene molecular plane is parallel to the substrate. Temperature dependent UPS measurements show that the perylene multilayer is stable on Ru(0001) surface up to 125 degrees C. The desorption of the multilayer and the decomposition of the monolayer are observed above 125 degrees C.

Journal Article↗
PubMed2006

Fluorescent 5-alkynyl-2'-deoxyuridines: high emission efficiency of a conjugated perylene nucleoside in a DNA duplex.

Four fluorescent 5-alkynyl-2'-deoxyuridines were studied in DNA oligonucleotides and their duplexes. The fluorescence response to hybridization differs dramatically for nucleosides containing a perylene fluorochrome either conjugated or not conjugated to the nucleobase. The conjugated nucleoside, 5-(perylen-3-ylethynyl)-2'-deoxyuridine, shows enhanced long-wavelength emission in the DNA duplex, in contrast to the blue fluorescence of perylene on a flexible linker (in 5-[(perylen-3-yl)methoxyprop-1-ynyl]-2'-deoxyuridine), which is quenched upon duplex formation.

DNA↗
PubMed1985

The effects of pressure and cholesterol on rotational motions of perylene in lipid bilayers.

Using steady-state fluorescence polarization measurements, an isothermal pressure-induced phase transition was observed in dimyristoyl-L-alpha-phosphatidylcholine multilamellar vesicles containing perylene. The temperature-to-pressure equivalence, dT/dP, estimated from the phase transition pressure, P1/2, is about 22 K X kbar-1, which is comparable to values determined from diphenylhexatriene polarization (Chong, P.L.-G. and Weber, G. (1983) Biochemistry 22, 5544-5550). In addition, we have employed a new method, introduced in this paper, to calculate the rate of in-plane rotation (Rip) and the rate of out-of-plane rotation (Rop) of perylene in lipid bilayers. The effects of pressure and cholesterol on the rotational rates of perylene in two lipid bilayer systems have been examined. They are 1-palmitoyl-2-oleoyl-L-alpha-phosphatidylcholine (POPC) multilamellar vesicles (MLV) and 50 mol% cholesterol in POPC (MLV). Rop is smaller than Rip due to the fact that the out-of-plane rotation requires a larger volume change than the in-plane rotation. Cholesterol seems not to affect Rop significantly, but pressure causes a decrease in Rop by about a factor of three. In contrast, the effects of pressure and cholesterol on Rip are less straightforward. At 1 atm cholesterol increases Rip by a factor of about two. Similarly, in the absence of cholesterol 1.5 kbar pressure essentially triples Rip. However, if both cholesterol is added and pressure is applied, Rip decreases sharply. The possible interactions between cholesterol and perylene are discussed.

Benz(a)Anthracenes↗
PubMed1992

Labelling of liposomes with intercalating perylene fluorescent dyes.

The high fluorescent potential and the exceptional photostability of lipophilic derivatives of perylene-3,4:9,10-bis(dicarboximides) are utilized for the fluorescence-labelling of liposomes. The preparation of the liposomes is effected by supersonic starting from a lipid mixture consisting of the matrix lipids soy lecithin, cholesterol, alpha-tocopherol and the perylene dyes. From a multitude of perylene derivatives investigated only those are optimally incorporated into the bilayer membrane of unilamellar liposomes which are substituted at both nitrogen atoms by one or two linear hydrocarbon groups. In order to attain an optimal fluorescent quantum yield, about 200 to 300 dye molecules can be incorporated per liposome. The liposomes thus obtained have a diameter of about 70 to 80 nm, are homogeneous and may be stored for more than seven months. Neither the fluorescent properties nor the stability of these liposomes are influenced by the additional incorporation of various ara C-derivatives and lipophilic anchor groups which subsequently enable the coupling of antibodies to the liposomes. As the water-insoluble perylene dyes are incorporated into the bilayer membrane, the aqueous inner volume of the liposomes remains available for a further utilization.

Cholesterol↗
PubMed2006

Theoretical solar-to-electrical energy-conversion efficiencies of perylene-porphyrin light-harvesting arrays.

The efficiencies of organic solar cells that incorporate light-harvesting arrays of organic pigments were calculated under 1 sun of air mass 1.5 solar irradiation. In one set of calculations, photocurrent efficiencies were evaluated for porphyrin, phthalocyanine, chlorin, bacteriochlorin, and porphyrin-bis(perylene) pigment arrays of different length and packing densities under the assumption that each solar photon absorbed quantitatively yielded one electron in the external circuit. In another more realistic set of calculations, solar conversion efficiencies were evaluated for arrays comprising porphyrins or porphyrin-(perylene)2 units taking into account competitive excited-state relaxation pathways. A system of coupled differential equations for all reactions in the arrays was solved on the basis of previously published rate constants for (1) energy transfer between the perylene and porphyrin pigments, (2) excited-state relaxation of the perylene and porphyrin pigments, and (3) excited-state electron injection into the semiconductor. This formal analysis enables determination of the optimal number of pigments in an array for solar-to-electrical energy conversion. The optimal number of pigments depends on the molar absorption coefficient and the density at which the arrays can be packed on an electrode surface. Taken together, the ability to employ fundamental photophysical, kinetic, and structural parameters of modular molecular architectures in assessments of the efficiency of solar-to-electrical energy conversion should facilitate the design of molecular-based solar cells.

Electrons↗
PubMed1997

Mechanisms of nitroso compound-induced inhibition of superoxide generation in neutrophils: fluorescence quenching of perylene by nitroso-compounds in the membrane fractions of neutrophils.

To investigate the mechanism of nitroso compound-induced inhibition of the respiratory burst in neutrophils, we studied fluorescence quenching of perylene by nitroso-compounds in the membrane fractions of neutrophils at 17, 27, and 37 degrees C and the reagent-induced inhibition of superoxide generation at 28 and 37 degrees C. With increasing temperature, the quenching of perylene fluorescence and inhibition of superoxide generation by nitrosobenzene (NB) were both diminished, while those by 2-nitrosotoluene (NT) were both enhanced. The temperature dependence of the inhibition constants and the quenching constants indicates that the binding of NB is exothermic (deltaH= -27 kJ/mol for inhibition and deltaH= -29 kJ/mol for quenching) and essentially enthalpy-driven. On the other hand, that of NT is endothermic (deltaH= +16 kJ/mol for inhibition and quenching) and essentially entropy-driven. Quenching studies of perylene fluorescence in synthetic vesicles made of endogenous polar lipids of neutrophils showed that the enthalpy changes of NB- and NT-binding with perylene in lipids were similar to each other. Moreover, their values were in good agreement with that of NT, but not of NB, in the membrane fractions, an assembly of proteins and lipids, of neutrophils. These results suggest that NB inhibits the activity by binding to proteins in the membrane, whereas inhibition by NT occurs through hydrophobic interaction with lipids and/or proteins.

Animals↗
PubMed2001

[The comparisons of fluorescence quenching between perylene and pyrene].

The fluorescence quenching of perylene and pyrene by dimethyl terephthalate (DMTP) and N,N-dimethylaniline (DMA) have been investigated. The results show that pyrene can form exciplex with DMTP or DMA at room temperature and perylene can only form exciplex with DMA. The fluorescence quenching date is in conformity with the Stern-Volmer equation: F0/F = 1 + KSV[Q] = 1 + Kq.tau 0[Q], the F0/F-[Q] straight lines are drawn. The Stren-Volmer constants and fluorescence quenching rate constants (KSV and Kq) are obtained. The Stern-Volmer quenching constants of pyrene is larger than that of perylene. The differences is due to the molecular structure of perylene which is not a typical large conjugated system and less coplanar configuration than pyrene.

Aniline Compounds↗
PubMed2005

Synthesis and characterization of 3,5-bis(2-hydroxyphenyl)-1,2,4-triazole functionalized tetraaryloxy perylene bisimide and metal-directed self-assembly.

[structure: see text] New perylene bisimide dyes bearing 3,5-bis(2-hydroxyphenyl)-1,2,4-triazole receptor units with different spacers have been synthesized and characterized. The fluorescence and electronic properties of these compounds have been studied. MALDI-TOF, UV-vis, and fluorescence titration experiments proved that monotopic perylene bisimide ligands could be assembled into dimmers by Fe(III) coordination. The coordination properties of the ditopic perylene bisimide ligands have also been studied preliminarily. Furthermore, the SEM images indicated that well-defined nanoscale structures could be fabricated by self-assembly due to metal ion coordination and pi-pi stacking interactions of perylene rings with the help of a proper spacer.

Journal Article↗
PubMed2006

Investigation of the two-photon absorption cross-section in perylene tetracarboxylic derivatives: nonlinear spectra and molecular structure.

We investigated the 2PA absorption spectrum of a family of perylene tetracarboxylic derivatives (PTCDs): bis(benzimidazo)perylene (AzoPTCD), bis(benzimidazo)thioperylene (Monothio BZP), n-pentylimidobenzimidazoperylene (PazoPTCD), and bis(n-butylimido)perylene (BuPTCD). These compounds present extremely high two-photon absorption, which makes them attractive for applications in photonics devices. The two-photon absorption cross-section spectra of perylene derivatives obtained via Z-scan technique were fitted by means of a sum-over-states (SOS) model, which described with accuracy the different regions of the 2PA cross-section spectra. Frontier molecular orbital calculations show that all molecules present similar features, indicating that nonlinear optical properties in PTCDs are mainly determined by the central portion of the molecule, with minimal effect from the lateral side groups. In general, our results pointed out that the differences in the 2PA cross-sections among the compounds are mainly due to the nonlinearity resonance enhancement.

Journal Article↗
PubMed2006

Solvent mediated intramolecular photoinduced electron transfer in a fluorene-perylene bisimide derivative.

Photoinduced electron transfer from fluorene to perylene bisimide has been studied for 2,7-bis(N-(1-hexylheptyl)-3,4:9,10-perylene-bisimide-N'-yl))-9,9-didodecylfluorene (PFP) in 11 different organic solvents. The intramolecular charge-separated state in PFP is almost isoenergetic with the locally excited state of the perylene bisimide. As a consequence of the small change in free energy for charge separation, the electron transfer rate strongly depends on subtle changes in the medium. The rate constant k(CS) for the electron transfer from fluorene to perylene bisimide moiety in the excited state varies over more than 2 orders of magnitude ( approximately 10(8)-10(10) s(-1)) with the solvent but does not show the familiar increase with polarity. The widely differing rate constants can be successfully explained by considering (1) the contribution of the polarization energy of the dipole moment in the transition state and by (2) the classical Marcus-Jortner model and assuming a spherical cavity for the charge-separated state. Using the first model, we show that lnk(CS) should vary linearly with Deltaf [Deltaf = (epsilon(r) - 1)/(2epsilon(r) + 1) - (n(2) - 1)/(2n(2) + 1), where epsilon(r) and n represent the static dielectric constant and the refractive index of the solvent, respectively], in accordance with experimental results. The second model, where the reorganization energy scales linearly with Deltaf, provides quantitative agreement with experimental rate constants within a factor of 2.

Journal Article↗
PubMed2006

Molecular layer-by-layer self-assembly of water-soluble perylene diimides through pi-pi and electrostatic interactions.

A layer-by-layer deposition process has been carried out for two oppositely charged water-soluble perylene diimide dyes without the use of intervening polyelectrolyte layers. The strong pi-pi interactions between the perylene moieties help stabilize the layers and simultaneously diminish the fluorescence quantum yield of the array without strongly affecting the absorption or fluorescence spectra. There is an alternation of fluorescence intensity according to which perylene species is on the outer layer, which is interpreted as the effect of facile energy transfer between the perylenes.

Journal Article↗
PubMed2006

Synthesis and optical and electrochemical properties of core-fluorinated perylene bisimides.

[reaction: see text] A series of bay position difluoro- or tetrafluoro-substituted perylene bisimides have been synthesized by nucleophilic halogen exchange reaction of the corresponding dibromo- and tetrachloro-substituted perylene bisimides, respectively, with potassium fluoride. Compared to the parent unsubstituted perylene bisimides, these compounds display hypsochromically shifted absorption and fluorescence spectra with fluorescence quantum yields up to unity enabling bright yellow emission. Their electrochemical properties and crystal structures of two perylene bisimides are also reported.

Journal Article↗
PubMed2004

The role of intermolecular polarization for the stability of lithium intercalation compounds of alpha- and beta-perylene.

Lithium intercalation compounds of alpha- and beta-perylene are investigated by photoelectron spectroscopy. Spectroscopic data together with a Born-Haber cycle provide information on the formation enthalpy of those materials. This approach allows understanding the amount of charge transferred from the alkali metal atoms to the pi system, and illuminates the role of molecular versus solid-state properties in the formation of the intercalation compounds. In the bulk of alpha-perylene material, molecular dimerization survives upon intercalation which reduces the Madelung energy of the intercalation compound but increases the electron-accepting capability of the organic system and facilitates the ionization of lithium atoms in the molecular solid environment. The lower ionization potential results in a larger charge transfer (about two electrons per molecule) in alpha-perylene compared to the monomeric system, beta-perylene.

Journal Article↗
PubMed2006

Energy transfer and photodegradation of a Perylene Orange:LDS821 system in poly(methyl methacrylate).

The luminescence of Perylene Orange and LDS821 in poly(methyl methacrylate) (PMMA) following a 532 nm irradiation yielded information on photodegradation and energy transfer. The irradiation of the Perylene Orange/LDS821/PMMA films resulted in (i) a maximum in the Perylene Orange fluorescence photodegradation profile and (ii) an enhancement of the LDS821 fluorescence relative to the LDS821/PMMA films. These results are attributed to an energy transfer from the Perylene Orange to the LDS821 with an energy transfer rate constant of 5.1+/- 0.75 (2sigma) x 10(11) M(-1) s(-1) and a Förster critical radius of 65.7 A. Fluorescence half-quenching and time-resolved fluorescence measurements attributed energy transfer to the Förster energy transfer with minor contributions of radiative energy transfer.

Journal Article↗