Pyrene is highly emissive when attached to the RNA duplex but not to the DNA duplex: the structural basis of this difference

Through binding and fluorescence studies of oligonucleotides covalently attached to a pyrene group via one carbon linker at the sugar residue, we previously found that pyrene-modified RNA oligonucleotides do not emit well in the single-stranded form, yet the attached pyrene emits with a significantly high quantum yield upon binding to a complementary RNA strand. In sharp contrast, similarly modified pyrene–DNA probes exhibit very weak fluorescence both in the double-stranded and single-stranded forms. The pyrene-modified RNA oligonucleotides therefore provide a useful tool for monitoring RNA hybridization. The purpose of this paper is to present the structural basis for the different fluorescence properties of pyrene-modified RNA/RNA and pyrene-modified DNA/DNA duplexes. The results of absorption, fluorescence anisotropy and circular dichroism studies all consistently indicated that the pyrene attached to the RNA duplex is located outside of the duplex, whereas the pyrene incorporated into the DNA duplex intercalates into the double helix. (1)H NMR measurements unambiguously confirmed that the pyrene attached to the DNA duplex indeed intercalates between the base pairs of the duplex. Molecular dynamics simulations support these differences in the local structural elements around the pyrene between the pyrene–RNA/RNA and the pyrene–DNA/DNA duplexes

Fluorescence of covalently attached pyrene as a general RNA folding probe

Fluorescence techniques are commonly and powerfully applied to monitor biomolecular folding. In a limited fashion, the fluorescence emission intensity of covalently attached pyrene has been used as a reporter of RNA conformational changes. Here, we pursue two goals: we examine the relationship between tether identity and fluorescence response, and we determine the general utility of pyrene fluorescence to monitor RNA folding. The P4–P6 domain of the Tetrahymena group I intron RNA was systematically modified at multiple nucleotide positions with pyrene derivatives that provide a range of tether lengths and compositions between the RNA and chromophore. Certain tethers typically lead to a superior fluorescence signal upon RNA folding, as demonstrated by equilibrium titrations with Mg(2+). In addition, useful fluorescence responses were obtained with pyrene placed at several nucleotide positions dispersed throughout P4–P6. This suggests that monitoring of tertiary folding by fluorescence of covalently attached pyrene will be generally applicable to structured RNA molecules

Positive allosteric binding behavior of pyrene-appended triazole-modified thiacalix[4]arene-based fluorescent receptors

The novel heteroditopic receptors 5a∼c have been synthesized, which bear a thiacalix[4]arene in the 1,3-alternate conformation. Two urea moieties possessing various aryl groups with either electron-donating or -withdrawing groups at their p-positions function as anion-binding sites. At the opposite side of the cavity are two pyrene-appended triazole rings, which act as cation-binding sites. The binding property of receptor 5c was investigated by means of 1H NMR and UV–vis spectroscopy and by fluorescence titration experiments in the presence of various transition metal cations and anions in CH2Cl2–DMSO (10:1, v/v) solution. Interestingly, it was found that receptor 5c possessing two p-nitrophenyl ureido moieties, most efficiently complexes in the urea cavity or bistriazoles; the plausible allosteric effect of receptor 5c was also investigated

Self-assembly of triblock copolymers in aqueous solution

Indexación: ScieloThe aggregation of PE4VP-b-PS-b-PE4VP block copolymers was studied in aqueous solution. Triblock copolymers P4VP-b-PS-b-P4VP were synthesized by sequential anionic polymerization of poly(styrene) and poly(4-vinylpirydine) using sodium naphthalene as a bifunctional initiator. Subsequently, the 4-vinylpyridine units were quaternized with ethyl bromide to obtain cationic PE4VP-b-PS-b-PE4VP block copolymers. Both star and crew-cut micelles were formed. The concentrations at which micelles are formed cmc were determined, by steady-state and time-resolved fluorescence probing methods, as a function of quatemization degree. The results indicate that cmc of crew-cut micelles increases with increasing charge density of the PE4VP blocks. For star micelles there is not a clear dependency of cmc with the percentage of quatemization. The lifetime of pyrene fluorescence and the ratio I1/I3 were determined at concentrations of copolymers well above the cmc, and the results show that the location of pyrene into the micelle changes with the charge density of the micelle corona. The micropolarity sensed by pyrene decreases with increasing quatemization degree. The presence of aggregates was confirmed by transmission electronic microscopy.http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-97072008000200013&lng=es&nrm=is

Synthesis of a ditopic homooxacalix[3]arene for fluorescence enhanced detection of heavy and transition metal ions

A pyrene-appended ratiometric fluorescent chemosensor L based on a synthetic approach of insulating the fluorophore from the ionophore by a specific molecular spacer has been synthesised and characterised. The fluorescence spectra changes of L suggested that the chemosensor can detect heavy and transition metal (HTM) ions ratiometrically and with variable sensitivity according to the substituents present. ¹H NMR titration experiments indicated that the three triazole ligands prefer binding with Hg²⁺, Pb²⁺ and Zn²⁺, resulting in a conformational change that produces monomer emission of the pyrene accompanied by the excimer quenching. However, the addition of Fe³⁺, which may be accommodated by the cavity of L, makes the pyrene units move closer to each other, and a discernible increase in the emission intensity of the static excimer is observed. Therefore, it is believed that the ditopic scaffold of the calix[3]arene as a specific molecular spacer here plays an important role in the blocking of the heavy atom effect of HTM ions by insulating the fluorophore from the ionophore given the long distance between the metal cation and the pyrene moiety

Direct evidence of a blocking heavy atom effect on the water-assisted fluorescence enhancement detection of Hg²⁺ based on a ratiometric chemosensor

At the current stage of chemosensor chemistry, the critical question now is whether the heavy atom effect caused by HTM ions can be blocked or avoided. In the present work, we provide unequivocal evidence to confirm that the heavy atom effect of Hg²⁺ is inhibited by water and other solvent molecules based on results using the chemosensor L. Most importantly, the heavy atom effect and blocking thereof were monitored within the same system by the use of ratiometric fluorescence signal changes of the pyrene motif. These observations not only serve as the foundation for the design of new ‘turn-on’ chemosensors for HTM ions, but also open up new opportunities for the monitoring of organic reactions

Fluorescent turn-on sensors based on pyrene-containing Schiff base derivatives for Cu2+ recognition: spectroscopic and DFT computational studies

A new fluorescent chemosensor L1, pyrene containing long chain Schiff base derivative in 1-position has been synthesized. Similarly, the receptors L2 and L3 are also designed in order to compare the binding ability for detection of Cu2+. The receptors exhibit very weak fluorescence (Φ = 0.01) due to the photoinduced electron transfer (PET). Upon addition of 10 equiv. of Cu2+, the emission intensity of ligands L1 and L2 are increased 65-fold (Φ = 0.31) and 25-fold (Φ = 0.08) in CH3CN/CH2Cl2 solvents system respectively. NMR titration experiments, spectroscopic and DFT computational studies confirmed the binding phenomena and sensitivity of Cu2+

Synthesis and characterisation of pyrene-labelled polydimethylsiloxane networks: towards the in situ detection of strain in silicone elastomers

Pyrene-substituted polyhydromethylsiloxanes (PHMS-Py-x) were synthesised by the hydrosilylation reaction of prop-3-enyloxymethylpyrene with polyhydromethylsiloxane (M-n = 3700). The ratio of pyrene substituent to Si-H unit was varied to afford a range of pyrene-functionalised polysiloxanes. These copolymers were subsequently incorporated into polydimethylsiloxane (PDMS) elastomers by curing via either Pt(0) catalysed hydrosilylation with divinyl-terminated PDMS (M-n = 186) and tetrakis(dimethylsiloxy) silane, or Sn(II) catalysed condensation with alpha,omega-dihydroxyPDMS (M-n = 26 000) and tetraethoxysilane. An alternative method involving the synthesis and integration of [3-(pyren-1-ylmethoxy)propyl]triethoxysilane (Py-TEOS) into PDMS elastomers was also investigated: a mixture of alpha,omega-dihydroxyPDMS (M-n = 26 000), tetraethoxysilane, and Py-TEOS was cured using an Sn( II) catalyst. Certain of the resulting fluorescent pyrene-labelled elastomers were studied by differential scanning calorimetry and dynamic mechanical analysis. No significant changes were observed in the thermal or mechanical properties of the elastomers containing pyrene when compared to otherwise identical samples not containing pyrene. All of the pyrene-containing elastomers were demonstrated to be fluorescent under suitable excitation in a photoluminescent spectrometer. Two of the elastomers were placed in a photoluminescence spectrometer and subjected to cycles of extension and relaxation (strain = 0-16.7%) while changes in the emission spectra were monitored. The resulting spectra of the elastomer containing the PHMS-Py-50 copolymers were variable and inconsistent. However, the emission peaks of elastomers containing Py-TEOS displayed clear and reproducible changes in fluorescence intensity upon stretching and relaxation. The intensity of the monomer and excimer emission peaks was observed to increase with elongation of the sample and decrease upon relaxation. Furthermore, the ratio of the intensities of the excimer : monomer peak decreased with elongation and increased with relaxation. In neither case was there appreciable hysteresis, suggesting that fluorescent labelling of elastomers is a valid approach for the non-invasive in situ monitoring of stress and strain in such materials

Synthesis, structure and photophysical properties of pyrene–based [5]helicenes : an experimental and theoretical study

Pyrene-cored [5]helicenes were prepared by a facile, efficient Wittig reaction and an intramolecular photocyclization reaction utilising 2,7-di-tert-butylpyrene-4-carbaldehyde and naphthalene/pyrene-based phosphorus ylides. Optical properties based on UV−vis absorption and fluorescence spectra were investigated. X-ray crystallography revealed that the pyrene-based [5]helicenes exhibited strong face-to-face π−π interactions and edge-to-face π−π interactions. HOMO and LUMO energies and molecular orbitals were also studied by density functional theory (DFT) calculations. This study has revealed that the torsion angle of the helical structure plays a role in determining the π−π interactions and the frontier molecular orbital energy levels. Thus, pyrene-based helicenes need to be considered when one designs new highly efficient organic light-emitting diodes and organic semiconductor materials

A study of allosteric binding behaviour of a 1,3-alternate thiacalix[4]arene-based receptor using fluorescence signal

A novel heteroditopic thiacalix[4]arene receptor L possessing 1,3-alternate conformation, which contains two pyrene moieties attached to the lower rim via urea linkages together with a crown ether moiety appended at the opposite side of the thiacalix[4]arene cavity, has been synthesized. The complexation behaviour of receptor L was studied by means of fluorescence spectra and ¹H NMR titration experiments in the presence of K⁺ ions and a variety of other anions. The results suggested that receptor L can complex efficiently via the urea cavity or the crown ether moiety, and a positive/negative allosteric effect operating in receptor L was observed