Probing the lateral organization of membranes: fluorescence repercussions of pyrene probe distribution

Phospholipids pyrene labeled are widely used to investigate dynamics and organizations of membranes. We studied pyrene probe lateral distribution by analyzing the variations of the molar absorption coefficient (epsilon) versus probe concentrations, in small unilamellar vesicles (SUV) made of phospholipids and/or glycolipids, with pyrene labeled phosphatidylcholine (PyPC) or phosphatidylglycerol (PyPG). The results were interpreted according to an infinite associative model. They indicated that an effective self-association process corresponding to K ranging from 30 to 100 M(-1) occurred with those probes incorporated in dimannosyl diacylglycerol (DMDG). In contrast, after SUV labeling of egg yolk phosphatidylcholine (EggPC) or phosphatidylglycerol (EggPG), K values < 1 M(-1) were determined. The corresponding percentages of various stacked forms of pyrene probes were calculated. They indicated that, for a 3% PyPG labeling, the monomer represented 21% of n-mers in DMDG and 94% in EggPC. The analysis of fluorescence experiments carried out on the same samples indicated that: (i) the fluorescence process of pyrene probes was generated by the monomers: and (ii) the excimer forming resulted from a diffusional encounter between one excited and one non-excited monomer. A correction of fluorescence data allowing a more correct interpretation of fluorescence measurements was proposed.     

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.     

Dual pyrene-labeled pyrrolidinyl peptide nucleic acid as an excimer-to-monomer switching probe for DNA sequence detection

The unique ability of pyrene to form excimers with distinct emission characteristic from monomer offers an attractive means to signal the interactions between biomolecules. In this work, dual pyrene-labeled pyrrolidinyl peptide nucleic acid probe with a d-prolyl-2-aminocyclopetanecarboxylic acid α,β-dipeptide backbone (acpcPNA) was designed as an excimer-to-monomer switching probe for DNA sequence detection. In single stranded state, the excimer emission at 470 nm was mainly observed in the fluorescence spectrum. In the presence of DNA target, the hybridization resulted in separation of the two pyrene units, therefore the spectrum displayed increased monomer emission at 380 nm with concomitant decreased excimer emission. Switching ratio, which is defined as the ratio of the monomer to excimer in the double stranded form [F₃₈₀/F₄₇₀(ds)] divided by the same value obtained from the single stranded form [F₃₈₀/F₄₇₀(ss)], was used to describe the performance of the probes. Switching ratios in the range of 5–30 were observed with various dual pyrene-labeled acpcPNA probes bearing pyrenebutyryl label attached five-base apart. Practically no excimer-to-monomer switching behavior was observed with DNA targets carrying a single mismatched base as shown by the small switching ratios of ∼1.     

Detection of point mutations using pyrene-labeled DNA probes

Pyrene-labeled oligodeoxyribonucleotide probes were shown to be suitable for the detection of point mutations. Reagents based on homochiral 2,4-dihydroxybutyramides were used to introduce pyrene residues at the 3"- and 5"- ends of oligonucleotide pairs. The oligonucleotide pair forms a tandem complex with a complementary target, giving rise to an excimer signal (_max 470—490 nm) in the fluorescence spectra when the pyrene residues come into close proximity. The maximum ratio of the intensity of the excimer signal to the monomer signal (_max 380—400 nm) is attained when (S)-N-(1-pyrenylmethyl)-3,3-dimethyl-2,4-dihydroxybutyramide is used to introduce the pyrene residue. The excimer fluorescence completely disappears with an increase in the distance between the pyrene residues (upon the introduction of an additional nucleotide in the target) or in the presence of a mismatch near the contact site of the probes.     

Excited-state energy transfers in single-walled carbon nanotubes functionalized with tethered pyrenes

Single-walled carbon nanotubes were co-functionalized with pyrenemethanol and 3,5-dihexadecanyloxybenzyl alcohol in different ratios with the purpose of altering the content of pyrene moieties tethered to the nanotube surface. The functionalized nanotube samples were characterized by using established instrumental techniques. The absorption and emission results of the samples suggest that there are significant “intramolecular” excited-state energy transfers from both pyrene monomer and excimer to the linked nanotube, though the energy transfer efficiencies may be different between the monomer and excimer. The excimer formation can be limited by reducing the pyrenemethanol fraction to simplify the excited state processes, but contributions from the luminescence of the well-functionalized carbon nanotubes in the same wavelength region becomes an additional complication. Mechanistic implications of the photophysical results are discussed.     

Influence of pyrene-labeling on fluid lipid membranes

We elucidate the influence of pyrene-labeled phospholipids on the structural properties of a fluid dipalmitoylphosphatidylcholine lipid membrane. To this end, we employ extensive atomic-scale molecular dynamics simulations with varying concentrations of pyrene-linked lipids. We find pyrene labeling to perturb the membrane structure significantly in the vicinity of the probe, the correlation length in the bilayer plane being about 1.0-1.5 nm. The local perturbations lead to enhanced ordering and packing of lipid acyl chains located in the vicinity of the probe. Surprisingly, this holds true not only for lipids that reside in the same leaflet as the pyrene-labeled probe but also for lipids in the opposite monolayer. The latter is due to substantial interdigitation of the pyrene moiety into the opposite leaflet, suggesting that occasional excimer formation may take place for probes in different leaflets. As a related issue, we also discuss the location and conformational orientation of the pyrene moieties. In particular, the orientational distribution of pyrene turns out to be more broad and diverse than the distribution of the corresponding acyl tails of nonlabeled lipids.     

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.     

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.     

Influence of intrachain hydrogen bonding on the cyclization of a polystyrene chain

Cyclization of a polystyrene chain (M_n = 10,600; M_w/M_n = 1.09) both ends labeled with 4-(1-pyrenyl)butanoamide groups was studied in cyclohexane between 25 and 95°C. The amide groups (peptide bonds) at both ends can form an intrachain hydrogen bond between the amide hydrogen at one chain end and the carbonyl oxygen at the other. The presence of two sets of conformers, random coils, and chains cyclized through hydrogen bonding, complicates the data analysis. The pyrene excimer kinetics of this polymer is well described by a model composed of two monomers (hydrogen bonded and nonbonded chains) and one excimer, in equilibrium. The cyclization rate constant for hydrogen-bonded chains is larger than the one for nonhydrogen-bonded chains. The pyrene excimer binding energy (ca. 1.6 kcal/mol) is lower than the published value for nonhydrogen-bonded chains (～ 9 kcal/mol), suggesting that intrachain hydrogen bonding hinders the stabilization of the excimer. © 1994 John Wiley & Sons, Inc.     

Label-free detection of polynucleotide single-base mismatch via pyrene probe excimer emission

The pyrene probe and pyrene-labeled oligonucleotides (ODNs) probe are expected to be candidates as fluorescent probe for DNA assay. In particular, label-free detection is a very hot because of its simpleness, speediness and cheapness. Herein, we have investigated the use of a pyrenylakylammonium salt, a novel fluorescent probe for the detection of one single nucleotide polymorphism (SNP) in double stranded DNA. After S1 nuclease digestion, the pyrene probes bind electrostatically to the perfect complement DNA and emit a strong excimer emission. However, treatment of the non-complementary DNA with S1 nuclease caused nucleotide fragments of less than 5 bases, which could not induce excimer emission. By comparing ratio of excimer to monomer fluorescence between normal and mutant DNA after S1 nuclease digestion, One-base mutation in DNA was detected easily. This new method may be applied to the detection of SNP.     

Effect of hydrocarbon chain and pH on structural and topographical characteristics of phospholipid monolayers

Structural characteristics (structure, elasticity, topography, and film thickness) of dipalmitoyl phosphatidylcholine (DPPC) and dioleoyl phosphatidylcholine (DOPC) monolayers were determined at the air-water interface at 20 degrees C and pH values of 5, 7, and 9 by means of surface pressure (pi)-area (A) isotherms combined with Brewster angle microscopy (BAM) and atomic force microscopy (AFM). From the pi-A isotherms and the monolayer elasticity, we deduced that, during compression, DPPC monolayers present a structural polymorphism at the air-water interface, with the homogeneous liquid-expanded (LE) structure; the liquid-condensed structure (LC) showing film anisotropy and DPPC domains with heterogeneous structures; and, finally, a homogeneous structure when the close-packed film molecules were in the solid (S) structure at higher surface pressures. However, DOPC monolayers had a liquid-expanded (LE) structure under all experimental conditions, a consequence of weak molecular interactions because of the double bond of the hydrocarbon chain. DPPC and DOPC monolayer structures are practically the same at pH values of 5 and 7, but a more expanded structure in the monolayer with a lower elasticity was observed at pH 9. BAM and AFM images corroborate, at the microscopic and nanoscopic levels, respectively, the same structural polymorphism deduced from the pi-A isotherm for DPPC and the homogeneous structure for DOPC monolayers as a function of surface pressure and the aqueous-phase pH. The results also corroborate that the structural characteristics and topography of phospholipids (DPPC and DOPC) are highly dependent on the presence of a double bond in the hydrocarbon chain.     

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.     

Color-tunable fluorescent organogels: columnar self-assembly of pyrene-containing oligo(glutamic acid)s

New fluorescent gelators containing pyrene moieties and dendritic oligopeptides have been developed. These molecules self-assemble into 1D helical columnar structures that lead to the formation of 3D fibrous random networks. The resulting gel materials show monomer emission of pyrenes because the hydrogen-bonded array of the oligopeptide moieties greatly suppresses the formation of pyrene excimers. In contrast, in the sol states green excimer emission of the pyrenes is observed because of the dissociation of intermolecular hydrogen bonds. This is the first example of the reverse-mode color switching of fluorescence for supramolecular pyrene assemblies.     

7-Deazapurine and 8-aza-7-deazapurine nucleoside and oligonucleotide pyrene "click" conjugates: synthesis, nucleobase controlled fluorescence quenching, and duplex stability

7-Deazapurine and 8-aza-7-deazapurine nucleosides related to dA and dG bearing 7-octadiynyl or 7-tripropargylamine side chains as well as corresponding oligonucleotides were synthesized. "Click" conjugation with 1-azidomethyl pyrene (10) resulted in fluorescent derivatives. Octadiynyl conjugates show only monomer fluorescence, while the proximal alignment of pyrene residues in the tripropargylamine derivatives causes excimer emission. 8-Aza-7-deazapurine pyrene "click" conjugates exhibit fluorescence emission much higher than that of 7-deazapurine derivatives. They are quenched by intramolecular charge transfer between the nucleobase and the dye. Oligonucleotide single strands decorated with two "double clicked" pyrenes show weak or no excimer fluorescence. However, when duplexes carry proximal pyrenes in complementary strands, strong excimer fluorescence is observed. A single replacement of a canonical nucleoside by a pyrene conjugate stabilizes the duplex substantially, most likely by stacking interactions: 6-12 °C for duplexes with a modified "adenine" base and 2-6 °C for a modified "guanine" base. The favorable photophysical properties of 8-aza-7-deazapurine pyrene conjugates improve the utility of pyrene fluorescence reporters in oligonucleotide sensing as these nucleoside conjugates are not affected by nucleobase induced quenching.     

Synthesis of ionic polyurethanes with pyrene rings: Spectral properties and fluorescence quenching study

Hydrophilic ionic polyurethanes with 4‐chloromethylphenylcarbamoyl‐1‐oxymethylpyrene located on the quaternary ammonium structure from a polymer based on poly(ethylene glycol), isophorone diisocyanate, and N‐methyldiethanolamine were prepared by a quaternization reaction, in which the amount of pyrene covalently attached to the polymeric backbone ranged from 1.14 to 19.82 mmol of fluorophore/100 g of polymer. It was interesting to compare the photoluminescence of the pyrene polyurethane carrying a few mole percent of pyrene moieties with that of a third polymer resulting from its subsequent quaternization with benzyl chloride up to a concentration of ionic groups as in the latter (quaternization degree = 14.15%). The process of excimer formation between the pyrene molecules attached to the ionic polyurethane was investigated in tetrahydrofuran (THF), dimethylformamide, film, and THF/H₂O to illustrate the expected differences in the polymer behavior compared with that of the starting pyrene derivative. The formation of aggregates or core–shell micelles was sustained by the fluorescence data, which indicated the existence of pyrene units in the ground state of the molecule, giving rise thus to an explanation for the high excimer‐to‐monomer intensity ratio. The fluorescence decay of pyrene polyurethanes in the presence of various concentrations of nitrobenzene used as a quencher was analyzed too when the fluorescence quenching in the polymer solution normally followed Stern–Volmer kinetics. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 3945–3956, 2005     

Unique hydrophobic interactions of pyrene in aqueous solution as effected by polyelectrolytes and surfactants

Pyrene substituents covalently bounded to polyelectrolytes show not only excited-state interactions but also unique ground-state interactions in aqueous solution. The pyrene moieties in pyrenesubstituted ionic molecules also show these interactions when aqueous solutions of these molecules are treated with polyelectrolytes or surfactants well below their critical micelle concentrations. These hydrophobic interactions are revealed by changes in absorption, fluorescence, and excitation spectra. The well-resolved vibrational bands in the absorption and excitation spectra of pyrene become somewhat diffuse, whereas monomer fluorescence is reduced and replaced by excimer fluorescence. The rationale for these results is that the pyrene moieties in these ionic solutions seek out hydrophobic locations on the polyelectrolytes or surfactants, where pyrene aggregation is responsible for these interactions and the corresponding changes in spectra.     

Unambiguous detection of target DNAs by excimer-monomer switching molecular beacons

A new class of molecular beacons were developed in which pyrene fluorophores were connected both at 3' and 5' ends of a single-stranded oligonucleotide. The two pyrene-based fluorophores were synthesized from the same starting material, so that the preparation of the beacons was simplified. The detection strategy of the beacons for target DNAs is based on "excimer-monomer emission switching" of the pyrene fluorophores: excimer emission of the pyrene moieties changed to monomer one when the beacons hybridized with the targets. This type of two-state mode of fluorescence allows unambiguous detection of the target DNAs because strict 1:1 correlation between the nonhybridized and the hybridized beacons can be monitored by the presence of isoemissive points of the fluorescence changes. The beacons can detect target 19-mer DNAs and can discriminate the targets from their single-nucleotide mismatches at 1 nM concentration. Advantages of the excimer-monomer switching molecular beacons were discussed in comparison with conventional ones.     

New cyclen-cored dendrimers functionalized with pyrene: Synthesis characterization,optical and photophysical properties

New cyclen (1,4,7,10-teraazacyclododecane) cored dendrimers up to the second generation, functionalized with 4, 8 and 16 pyrene units, respectively, were synthesized following a convergent procedure. All new compounds were characterized by NMR spectroscopies and ESI or MALDI TOF mass spectrometry. The optical and photophysical properties of the new dendrimers were studied in THF solution. Absorption spectra showed the typical absorption bands of pyrene moieties. In the fluorescence spectra, monomer as well as excimer emission were observed for all compounds. An increased proportion of excimer emission was observed in the dendrimer of the highest generation.     

Cu2+-induced blue shift of the pyrene excimer emission: a new signal transduction mode of pyrene probes

A pentiptycene-bispyrenyl system (1) has been synthesized and investigated as a fluorescent chemosensor for metal ions. A novel blue shift along with an intensity enhancement of the pyrene excimer emission is observed for 1 in the presence of Cu(2+). Such a new signal transduction mode of pyrene probes results from the formation of a static pyrene excimer that has very different characteristics from its dynamic counterpart.     

Exploring the organization and dynamics of hippocampal membranes utilizing pyrene fluorescence

The organization and dynamics of cellular membranes in the nervous system are crucial for the function of neuronal membrane receptors and signal transduction. Previous work from our laboratory has established hippocampal membranes as a convenient natural source for studying neuronal receptors. In this paper, we have monitored the organization and dynamics of hippocampal membranes and their modulation by cholesterol using pyrene fluorescence. The apparent dielectric constant experienced by pyrene in hippocampal membranes turns out to be approximately 20+/-3, depending on the experimental condition. Our results show that the polarity of the hippocampal membrane is increased upon cholesterol depletion, as monitored by changes in the ratio of pyrene vibronic peak intensities (I1/I3). This is accompanied by an increase in lateral diffusion, measured as an increase in the pyrene excimer/monomer ratio. These results are relevant in understanding the complex organization and dynamics of hippocampal membranes and could have implications in neuronal diseases characterized by defective cholesterol metabolism.