Quenching and dequenching of pyrene fluorescence by nucleotide monophosphates in cationic micelles

The fluorescence behavior of pyrene solubilized in the hexadecyltrimethylammonium bromide aqueous micellar solution in the presence of adenosine 5'-monophosphate (AMP) and uridine 5'-monophosphate (UMP) was investigated. AMP and UMP were found to influence oppositely the fluorescence of micellized pyrene. UMP acts as quencher, while AMP acts as dequencher. Both effects saturate at high nucleotide concentration (about 40 mM). Dequenching of micellized pyrene fluorescence is induced also by addition of disodium hydrogen orthophosphate (Na 2HPO 4), while loading with sodium bromide (NaBr) quenches the fluorescence. Furthermore, in absence of micelles, pyrene fluorescence depends on the UMP, according to the Stern-Volmer relation, but is unaffected by AMP. Dynamic light scattering experiments showed that the size and shape of aggregates is not affected by different types of nucleotide loaded into the solution; thus, we conclude that the opposite photophysical effect exploited by AMP and UMP are uncorrelated to any change in micellar microstructure. The whole fluorescence data set was successfully accounted for by assuming that the anionic nucleotides compete with the surfactant counterion (bromide) for the surface of the micelle. Accordingly, substitution of bromide with the more effective quencher UMP results in a strong decrease of the pyrene fluorescence, while the substitution of bromide with the nonquencher AMP results in an increase in the pyrene fluorescence.     

A conformationally constrained nucleotide analogue controls the folding topology of a DNA g-quadruplex

Guanine-rich DNA and RNA sequences can fold into unique structures known as G-quadruplexes. The structures of G-quadruplexes can be divided into several classes, depending on the parallel or antiparallel nature of the strands and the number of G-rich tracts present in an oligonucleotide. Oligonucleotides with single tracts of guanines form intermolecular parallel tetrameric G-quadruplexes. Oligonucleotides with two tracts of guanosines separated by two or more bases can form both intermolecular antiparallel fold-back dimeric and parallel tetrameric G-quadruplexes, and those with four tracts of guanosines can form both intramolecular parallel and antiparallel structures. Intramolecular G-qaudruplexes can fold into several folding topologies including antiparallel crossover basket, antiparallel chair, and parallel propeller. The ability to control the folding of G-quadruplexes would allow the physical, biochemical, and biological properties of these various folding topologies to be studied. Previously, the known methods to control the folding topology of G-quadruplexes included changing the buffer by varying the mono- and divalent cations that are present, and by changing the DNA sequence. Because the glycosidic bonds in the G-quartets of G-quadruplexes with parallel strands are in the anti conformation, we reasoned that incorporation of nucleoside analogues that prefer the anti conformation of the glycosidic bond into G-rich sequences would increase the preference for parallel G-quadruplex formation. As predicted, by positioning the conformationally constrained nucleotide analogue 2'-O-4'-C-methylene-linked ribonucleotide into specific positions of a DNA G-quadruplex we were able to shift the thermodynamically favored structure of a G-quadruplex from an antiparallel to a parallel structure.     

Monitoring DNA structures by dual fluorescence of pyrene derivatives

We have developed a nucleotide modified by a pyrene derivative with dual fluorescence. The dual fluorescence of the fluorophore, which was incorporated into DNA, was effectively controlled at ambient temperature according to DNA structural status. Our nucleoside with dual fluorescence is effective as a conceptually new probe for monitoring DNA hybridization by the color change without multilabeling with fluorescent dyes.     

The synthesis of a conformationally restricted analog of the anti-migraine drug sumatriptan

The synthesis of 5-N-Methylaminosulfonylmethyl-3-(N-methylpyrrolidin-2-ylmethyl)indole (1), a conformationally restricted analog of the anti-migraine drug, sumatriptan, is described. To incorporate our novel stereogenic replacement for the aminoethyl sidechain in sumatriptan, a convergent synthesis of the 3,5-disubstituted indole (1) was employed which utilized an intramolecular Heck reaction as the cornerstone reaction.     

Allele specific C-bulge probes with one unique fluorescent molecule discriminate the single nucleotide polymorphism in DNA

A combination of an allele specific C-bulge probe and the fluorescent molecule N,N'-bis(3-aminopropyl)-2,7-diamino-1,8-naphthyridine (DANP) that binds specifically to the C-bulge provides a method for single nucleotide polymorphism (SNP) typing with only one fluorescent molecule without covalent modification of the DNA probe. The allele specific C-bulge probe contains one additional cytosine and produces a C-bulge directly flanking the SNP site upon hybridization to the target DNA. The C-bulge is a scaffold to recruit and retain DANP directly neighboring the SNP site. The DANP fluorescent probe was selectively modulated by the flanking matched and mismatched base pairs. The mutation type could be discriminated by the modulated fluorescent intensity with respect to the allele specific C-bulge probes used for the assay.     

Potential DNA bis-intercalating agents: Synthesis and antitumor activity of novel,conformationally restricted bis(9-aminoacridines)

A series of bis(9-aminoacridines) bridged by conformationally restricted tethers was synthesized and evaluated against L1210 in vitro. Several of these compounds were found to be highly active in this test system, with ID₅₀ values below 10^?7 M. CPK molecular models suggest that this antitumor activity can be correlated to the ability of these bis(9-aminoacridines) to form bis-intercalative complexes with DNA.     

Vibronic activity in the fluorescence and absorption spectrum of pyrene

The vibronic coupling terms responsible for the intensity of the b_3g modes in the absorption and emission spectra of pyrene and pyrene-d₁₀ have been calculated taking into account both the Herzberg-Teller (HT) mechanism and the Born-Op-penheimer (BO) breakdown mechanism. The calculations have been carried out in the orbital-following scheme, implemented by the INDO/S Hamiltonian. The results, reproducing the main spectral features, such as the large difference observed in the intensity patterns of the two spectra, are discussed in terms of interference between HT and BO mechanisms, isotopic redistribution and the Duschinsky effect.     

Application of time-resolved fluorescence in the study of lipid aggregates II. Motions and order of pyrene probes in an aligned lyotropic nematic phase

Time-resolved polarized fluorescence spectroscopy has for the first time, been applied to the study of chromophores in a macroscopically aligned lyotropic nematic phase. The phase is composed of potassium dodecanoate, potassium chloride and water and contains long rod-like aggregates, that are aligned with their long axes parallel to an applied magnetic field. Pyrene, 1-pyrene dodecanoic acid, 1-dodecylpyrene and l-palmitoyl-2-(6-pyrenylhexanoyl)-sn-glycero-3-phosphoryl-choline are solubilized in these aggregates. The photophysics of these probes is a single exponential and typically between 130 and 200 ns in non-degassed samples. For all the probes the plane of the pyrene molecule tends to be oriented perpendicular to the symmetry axis (C_∞ axis) of the aggregate. The order parameters describing the orientation of the electronic transition dipole moment relative to this axis are typically c. -0.05. It is concluded that the translational and the local rotational motions of the probes are fast compared to the fluorescence lifetimes. The correlation times characterizing these motions are shorter than 20 ns. Finally, no slow motions such as fluctuations of the normal to the surface of the rod-like aggregate or a slow wobbling of the C_∞ -axis can be detected during c. 1 μmls.     

Quantum-dot-labeled DNA probes for fluorescence in situ hybridization (FISH) in the microorganism Escherichia coli.

Semiconductor quantum dots (QDs) as a kind of nonisotopic biological labeling material have many unique fluorescent properties relative to conventional organic dyes and fluorescent proteins, such as composition- and size-dependent absorption and emission, a broad absorption spectrum, photostability, and single-dot sensitivity. These properties make them a promising stable and sensitive label, which can be used for long-term fluorescent tracking and subcellular location of genes and proteins. Here, a simple approach for the construction of QD-labeled DNA probes was developed by attaching thiol-ssDNA to QDs via a metal-thiol bond. The as-prepared QD-labeled DNA probes had high dispersivity, bioactivity, and specificity for hybridization. Based on such a kind of probe with a sequence complementary to multiple clone sites in plasmid pUC18, fluorescence in situ hybridization of the tiny bacterium Escherichia coli has been realized for the first time.     

Impact of a conformationally restricted receptor on the BF2 chelated azadipyrromethene fluorosensing platform

Conformational control of the receptor-fluorophore orientation of BF2 chelated azadipyrromethene sensors reveals two photophysically different modes of analyte triggered fluorescence switching both of which exhibit large off-on fluorescence intensity responses to the light input-output of the sensors in the visible red spectral region.     

Stereoelectronic effects in the reactions of conformationally restricted,substituted cyclohexane-1,2-diones with 1,2-diols

The asymmetric synthesis of a C₂-symmetric cyclic 1,2-diketone is reported along with investigations into its properties as a potential asymmetric protecting group for 1,2-diols as the corresponding 1,2-diacetal.     

Preferred 3D-structure of peptides rich in a severely conformationally restricted cyclopropane analogue of phenylalanine

Terminally blocked, homo-peptide amides of (R,R)-1-amino-2,3-diphenylcyclopropane-1-carboxylic acid (c3diPhe), a chiral member of the family of Calpha-tetrasubstituted alpha-amino acids, from the dimer to the tetramer, and diastereomeric co-oligopeptides of (R,R)- or (S,S)-c3diPhe with (S)-alanine residues to the trimer level were prepared in solution and fully characterized. The synthetic effort was extended to terminally protected co-oligopeptide esters to the hexamer, where c3diPhe residues are combined with achiral alpha-aminoisobutyric acid residues. The preferred conformations of the peptides were assessed in solution by FT-IR absorption, NMR, and CD techniques, and for seven oligomers in the crystal state (by X-ray diffraction) as well. This study clearly indicates that c3diPhe, a sterically demanding cyclopropane analogue of phenylalanine, tends to fold peptides into beta-turn and 3(10)-helix conformations. However, when c3diPhe is in combination with other chiral residues, the conformation preferred by the resulting peptides is also dictated by the chiral sequence of the amino acid building blocks. The (S,S)-enantiomer of this alpha-amino acid, unusually lacking asymmetry in the main chain, strongly favors the left-handedness of the turn/helical peptides formed.     

A conformationally restricted guanosine analog reveals the catalytic relevance of three structures of an RNA enzyme

Recent studies indicate that RNA function can be enhanced by the incorporation of conformationally restricted nucleotides. Herein, we use 8-bromoguanosine, a nucleotide analog with an enforced syn conformation, to elucidate the catalytic relevance of ribozyme structures. We chose to study the lead-dependent ribozyme (leadzyme) because structural models derived from NMR, crystal, and computational (MC-Sym) studies differ in which of the three active site guanosines (G7, G9, or G24) have a syn glycosidic torsion angle. Kinetic assays were carried out on 8BrG variants at these three guanosine positions. These data indicate that an 8BrG24 leadzyme is hyperactive, while 8BrG7 and 8BrG9 leadzymes have reduced activity. These findings support the computational model of the leadzyme, rather than the NMR and crystal structures, as being the most relevant to phosphodiester bond cleavage.     

芘衍生物发光行为的研究

本工作合成了新型的芘衍生物-芘基查尔酮(PD), 研究了其在溶液及胶束中的稳态光物理行为。结果表明: 即使在较低浓度条件下, PD分子间也容易生成基态电荷转移配合物(Inter-CT), 其荧光光谱表现为芘单体荧光、分子内电荷转移态(Intra-CT)荧光以及Inter-CT荧光, 并且具有较好的溶致变色效应、浓度效应以及温度效应, 是一良好的探针分子化合物。     

Highly conformationally constrained halogenated 6-spiroepoxypenicillins as probes for the bioactive side-chain conformation of benzylpenicillin

Summary The halogenated 6-spiroepoxypenicillins are a series of novel semisynthetic-lactam compounds with highly conformationally restricted side chains incorporating an epoxide. Their biological activity profiles depend crucially on the configuration at position C-3 of that epoxide. In derivatives with aromatic-containing side chains, e.g., anilide, the 3R-compounds possess notable Gram-positive antibacterial activity and potent-lactamase inhibitory properties. The comparable 3S-compounds are antibacterially inactive, but retain-lactamase inhibitory activity.Using the molecular simulation programs COSMIC and ASTRAL, we attempted to map a putative, lipophilic accessory binding site on the PBPs that must interact with the side-chain aromatic residue. Comparative computer-assisted modelling of the 3R, and 3S-anilides, along with benzylpenicillin, indicated that the available conformational space at room temperature for the side chains of the 3R and the 3S-anilides was mutually exclusive. The conformational space for the more flexible benzylpenicillin could accommodate the side chains ofboth the constrained penicillin derivatives. By a combination of van der Waals surface calculations and a pharmacophoric distance approach, closely coincident conformers of the 3R-anilide and benzylpenicillin were identified. These conformers must be related to the antibacterial, bioactive conformer for the classical-lactam antibiotics. From these proposed bioactive conformations, a model for the binding of benzylpenicillin to the PBPs relating the three-dimensional arrangement of a putative lipophilic S₂-subsite, specific for the side-chain aromatic moiety, and the 3-carboxylate functionality is presented.This work has been reported in preliminary form at the 4th Royal Society of Chemistry International Symposium on Recent Advances in the Chemistry of-lactam Antibiotics, Churchill College, Cambridge, U.K., 3–6 July 1988.     

Features of the state and the fluorescence of pyrene in a perfluorosulfonic membrane

Controlled accumulation of pyrene in the pore space of perfluorosulfonic membranes is accompanied by the changes in absorption, fluorescence, and excitation spectra of the latter indicating the dominating and inhomogeneous distribution of the guest matter in the nanoscale channels of the substrate with a gradual increase in the number of the closely located molecules capable of photodimerization.     

Magnetic field dependence of delayed fluorescence of pyrene in solution

The magnetic field effect on the intensities of monomer (I_M) and excimer (I_D) delayed fluorescence of pyrene has been found to be identical. This result suggests a common spin-selective step in the processes giving rise to I_M and I_D, and is discussed in the light of previously proposed mechanisms. An unusual solvent effect is found on the I_M (I_D) versus field strength curves. This is attributed to photochemical doublet-radical formation. Doublet-radical formation affects the field dependence of I_M and I_D through spin selectivity in the triplet quenching reaction.     

Polyelectrolyte effects on the quenching of pyrene fluorescence in solutions of a pyrene substituted poly(acrylic acid)

The quenching of pyrene fluorescence by nitromethane, Tl⁺, Cu²⁺, I^?, and 4-dimethylaminopyridine (DMAP) in aqueous solutions of a pyrene substituted poly(acrylic acid) ( 1 ) was influenced by the “polyelectrolyte effect” of 1 . The efficiency of quenching in solutions of 1 was measured in terms of the Stern–Volmer constants for dynamic and static quenching which were obtained from comparison of the intensity and lifetime of pyrene fluorescence in solutions of 1 and a monomer model compound. The efficiency of quenching in solutions of 1 was always greater at high pH ( 9 ) in comparison to that at low pH ( 4 ). The ionization of carboxylic groups in 1 caused an expansion of the polymer mainchain and concomitant exposure of the pyrene molecules to the aqueous phase and quencher. The polyanion domain of 1 favored the condensation of cationic quenchers and could account for very efficient quenching in case of Cu²⁺ and Tl⁺. A very efficient quenching of pyrene fluorescence in solutions of 1 by DMAP at high pH was attributed to the hydrophobic interactions of DMAP and pyrene moiety. The iodide ions were less efficient quenchers of pyrene fluorescence due to electrostatic repulsion from the polyanion. The efficiency of quenching by nitromethane was not significantly affected by ionization of the carboxylic groups in 1 .     

Electron exchange in conformationally restricted donor-spacer-acceptor dyads: angle dependence and involvement of upper-lying excited States

The rate constant for triplet energy transfer (k(TET)) has been measured in fluid solution for a series of mixed-metal Ru-Os bis(2,2':6',2'-terpyridine) complexes built around a tethered biphenyl-based spacer group. The length of the tether controls the central torsion angle for the spacer, which can be varied systematically from 37 to 130 degrees . At low temperature, but still in fluid solution, the spacer adopts the lowest-energy conformation and k(TET) shows a clear correlation with the torsion angle. A similar relationship holds for the inverse quantum yield for emission from the Ru-terpy donor. Triplet energy transfer is more strongly activated at higher temperature and the kinetic data require analysis in terms of two separate processes. The more weakly activated step involves electron exchange from the first-excited triplet state on the Ru-terpy donor and the size of the activation barrier matches well with that calculated from spectroscopic properties. The pre-exponential factor derived for this process correlates remarkably well with the torsion angle and there is a large disparity in electronic coupling through pi and sigma orbitals on the spacer. The more strongly activated step is attributed to electron exchange from an upper-lying triplet state localized on the Ru-terpy donor. Here, the pre-exponential factor is larger but shows the same dependence on the geometry of the spacer. Strangely, the difference in coupling through pi and sigma orbitals is much less pronounced. Despite internal flexibility around the spacer, k(TET) shows a marked dependence on the torsion angle computed for the lowest-energy conformation.