Synthesis and Properties of Oligonucleotides Involving a Perylene Unit Linked to a 2′-Deoxyribose Residue

Abstract

We report here the synthesis and binding properties of oligonucleotides involving a perylene unit linked to the anomeric position of a 2′-deoxyribose residue. Both anomers were separated and incorporated separately at either the 5′-end or the internal position of a pyrimidine sequence. In any case the presence of the perylene unit stabilizes the complexes formed with either the single or the double-stranded target.     

Enantiomeric perylene-glycerolipids as fluorogenic substrates for a dual wavelength assay of lipase activity and stereoselectivity

A new type of fluorogenic alkyldiacyl glycerols was synthesized and used as fluorogenic substrates for the analysis of lipase activities and stereoselectivities. These compounds contain perylene as a fluorophore and the trinitrophenylamino (TNP) residue as a quencher. Both substituents are covalently bound to the ω-ends of the sn-2 and sn-1(3) acyl chains, respectively. Upon glycerolipid hydrolysis, the residues are separated from each other thus allowing determination of lipase activity by the continuous increase in fluorescence intensity which is caused by dequenching. Using enantiomeric pairs of these compounds, we were able to analyze lipase stereoselectivity depending on the reaction medium. Mixtures of enantiomeric fluorogenic alkyldiacyl glycerols, selectively labelled with pyrene or perylene as fluorophores, can be used for a dual-wavelength “stereoassay” of lipases. Since absorption and emission maxima of both labels are clearly separated, hydrolysis of the respective enantiomeric substrates can be determined simultaneously, and the difference in the rates of hydrolysis can be taken as a parameter for the stereopreference of a lipase. Hydrolysis rates measured with perylene-substituted lipids are generally lower than those obtained with the pyrene analogs. Thus, with a mixture of perylene and pyrene-substituted lipids, we observe a higher apparent stereoselectivity of lipases since we measure a combination of stereo- and substrate selectivity. In the presence of albumin, all microbial lipases tested so far exhibit stereopreference for the sn-1 glycerol position. In our assay, the apparent stereoselectivities are highest if in the presence of albumin, the sn-1 position carries pyrene and the sn-3 position is substituted with perylene. The lipase stereoselectivity assay described here requires the simultaneous measurement of the fluorescence intensities at two different wavelengths in a single cuvette and can thus be carried out using existing and cheap instrumentation that was developed for the fluorimetric analysis of Ca⁺⁺ concentrations. © 1996 Wiley-Liss, Inc.     

Perylene-Labeled Oligonucleotide as a Probe in Homogeneous Hybridization Assay

Abstract

An oligodeoxynucleotide bearing a 3′-terminal perylene-containing pseudonucleoside unit was synthesized and used as a probe in homogeneous hybridization. The fluorescence anisotropy of the perylene dye rose upon hybridization of the modified conjugate with the complementary nucleotide sequence. These results provide for designing efficacious hybridization probes.     

N‐Annulated Perylene as a Coplanar π‐Linker Alternative to Benzene as a Low Energy‐Gap,Metal‐Free Dye in Sensitized Solar Cells

Perylenes are well‐known pigments with excellent chemical, thermal, and photochemical stabilities and have been used in various optical and electronic fields. Although for sensitized mesoscopic solar cells there is rapid progress of metal‐free thiophene dyes, which now reach over 11.5% power conversion efficiency (PCE) at air mass 1.5 global (AM1.5G) conditions, the so far reported highest PCE of a perylene dye is only 6.8%. Here, a new metal‐free organic donor‐acceptor (D‐A) dye ( C261 ) featuring a bisarylamino functionalized N‐annulated perylene electron‐releasing segment and a cyanoacrylic acid electron‐withdrawing unit is synthesized. Combining a mesoporous titania film grafted by this structurally simple perylene dye with a non‐corrosive cobalt redox shuttle, an 8.8% PCE is achieved at an irradiance of the AM1.5G sunlight. By selecting the model dye G221 as a reference, theoretical calculations, steady‐state and time‐resolved spectroscopies, and electrical measurements are used to compare the energy‐levels, light absorptions, and mutichannel charge transfer dynamics that contribute to the photovoltaic behavior.     

Interrogating the role of liposome size in mediating the dynamics of a chromophore in the acyl chain region of a phospholipid bilayer

We have examined the temperature-dependent reorientation dynamics of perylene imbedded in bilayers of 1,2-dimyristoyl-sn-phosphatidylcholine (DMPC), where the bilayers exist in the form of unilamellar vesicles. Previous work using 100-nm diameter DMPC vesicles has shown that the phase transition from the gel phase to the fluid phase can be detected using the reorientation dynamics of perylene. In this work we explore the vesicle size dependence of the perylene reorientation dynamics in DMPC vesicles. The size of the vesicles is determined by extrusion and the reorientation dynamics of perylene are measured as a function of vesicle size between 100-nm and 5-microm diameter. We find that, while the phase transition for DMPC is seen in smaller vesicles, perylene becomes insensitive to the phase transition for vesicles larger than ca. 800-nm diameter. We also find a discontinuous change in perylene reorientation dynamics with increasing vesicle size, and we consider this result in the context of the location of perylene within the bilayer.     

Biosynthesis of the dimethylbenzene moiety of riboflavin and dimethylbenzimidazole: evidence for the involvement of C-1 of a pentose as a precursor.

The relative incorporations of specially labeled pyruvate, lactate, erythritol, D-erythrose, D-ribose, and D-glucose precursors into the dimethylbenzene carbon atoms of the 5,6-dimethylbenzimidazole unit of vitamin B12 by Propionibacterium shermanii have been determined. The incorporation data provide information regarding the putative four-carbon biosynthetic unit which is involved in the formation of 6,7-dimethyl-8-ribityllumazine and which is the source of the eight dimethylbenzene carbon atoms of both 5,6-dimethylbenzimidazole and riboflavin. The relative incorporations of the labeled lactate and pyruvate precursors are not consistent with either acetoin or 2,3-butanedione functioning as the four-carbon biosynthetic unit. The relative incorporations of the labeled hexose, pentose, and tetrose precursors indicate that the observed incorporation of C-1 of the pentose into the dimethylbenzene carbon atoms does not involve metabolism to a tetrose intermediate, but occurs more directly. It is concluded that the C-1 position of a pentose precursor is involved in the formation of the putative four-carbon biosynthetic unit.     

Variation in Mesophyll Cell Number and Size in Wheat Leaves

The numbers of mesophyll cells in wheat leaves were determinedin a variety of wheat species differing in ploidy level andin leaves from different positions on the wheat plant. Leafsize and mesophyll cell number are linearly related in bothcases but differences were observed in mesophyll cell numberper unit leaf area with changing leaf size. Where changes incell size are caused either by nuclear ploidy or leaf position,differences in mesophyll cell number per unit leaf are negativelycorrelated with mesophyll cell plan area. The decrease in cellsize with increasing leaf position also results in a greaternumber of chloroplasts per unit leaf area. These results arediscussed in relation to anatomical variation of the wheat leaf. Mesophyll cell, cell numbers, leaf size, Triticum     

Water‐soluble 3,4:9,10‐perylene tetracarboxylic ammonium as a high‐performance fluorochrome for living cells staining

Highly water‐soluble 3,4:9,10‐perylene tetracarboxylic ammonium with quantitative fluorescence quantum yield was designed. Owing to the high negative electrostatic potential of the perylene plane, the perylene dye remained stable over a broad pH range and was successfully applied as a high‐performance fluorochrome for living hippocampal neurons staining. Copyright © 2009 John Wiley & Sons, Ltd.     

Formation of radical cations in a model for the metabolism of aromatic hydrocarbons

To test the hypothesis that electrophilic radical cations are the major ultimate electrophilic and carcinogenic forms of benz[a]anthracene (BA), dibenz[a,h]anthracene (DBA), and benzo[a]pyrene (BP), we have focused on a chemical model of metabolism which parallels and duplicates known or potential metabolites of some polycyclic hydrocarbons formed in cells. Studies of this model system show that radical cations are hardly formed, if at all, in the case of BA or DBA but are definitely formed in the cases of the carcinogen BP as well as the non-carcinogenic hydrocarbons, pyrene and perylene. We conclude that the carcinogenicities of BA, DBA, BP, pyrene, and perylene are independent of one-electron oxidation to radical cation intermediates.     

New analogues of bradykinin containing a conformationally restricted dipeptide fragment in their molecules.

The present paper describes the synthesis and some pharmacological properties of two new bradykinin analogues containing the ethylene-bridged dipeptide Phe-Phe in their molecules. In a further two peptides this modification was combined with acylation of the N-terminus with 1-adamantaneacetic acid. Finally, we synthesized four analogues by removing the Ser6 residue from the four peptides mentioned above. The activity of the new analogues was assayed on isolated rat uterus (RUT) and in rat blood pressure tests (BPT). The results clearly indicate that the proposed modification, alone or in combination with other changes, resulted in either a drop in antiuterotonic activity or even in conversion to an agonism. Although this tendency is not so distinct in blood pressure assays, the antagonistic potency of the new analogues is also diminished. Nevertheless, it was demonstrated that the D-amino acid in position 7 which, until recently, was considered necessary for antagonism, may be replaced, together with the amino acid occupying position 8, by a suitable, sterically restricted L,L-dipeptide unit.     

Optimization of high-molecular-weight polycyclic aromatic hydrocarbons' degradation in a two-liquid-phase bioreactor

A microbial consortium degrading the high-molecular-weight polycyclic aromatic hydrocarbons (HMW PAHs) pyrene, chrysene, benzo[a]pyrene and perylene in a two-liquid-phase reactor was studied. The highest PAH-degrading activity was observed with silicone oil as the water-immiscible phase; 2,2,4,4,6,8, 8-heptamethylnonane, paraffin oil, hexadecane and corn oil were much less, or not efficient in improving PAH degradation by the consortium. Addition of surfactants (Triton X-100, Witconol SN70, Brij 35 and rhamnolipids) or Inipol EAP22 did not promote PAH biodegradation. Rhamnolipids had an inhibitory effect. Addition of salicylate, benzoate, 1-hydroxy-2-naphtoic acid or catechol did not increase the PAH-degrading activity of the consortium, but the addition of low-molecular-weight (LMW) PAHs such as naphthalene and phenanthrene did. In these conditions, the degradation rates were 27 mg l-1 d-1 for pyrene, 8.9 mg l-1 d-1 for chrysene, 1.8 mg l-1 d-1 for benzo[a]pyrene and 0.37 mg l-1 d-1 for perylene. Micro-organisms from the interface were slightly more effective in degrading PAHs than those from the aqueous phase.     

Synthesis of a dibromoperylene phosphoramidite building block and its incorporation at the 5' end of a G-quadruplex forming oligonucleotide: spectroscopic properties and structural studies of the resulting dibromoperylene conjugate

Previous studies indicate that some perylene bisimide derivatives can drive the assembly of DNA G-quadruplexes, thus suggesting the possible advantage in the adoption of perylene-conjugated G-rich oligonucleotides in biological and biotechnological applications. Nevertheless, the typical poor solubility of perylene bisimides strongly limits the number of suitable chemical strategies to prepare perylene-conjugated oligonucleotides. In order to overcome these difficulties, we employed the earlier described core twisted perylene derivatives possessing unique optical and electronic properties, besides good solubility in common solvents. As a first result, the large-scale synthesis of a new dibromoperylene derivative (PEOEBr) phosphoramidite building block is herein reported. Furthermore, the structural behavior of the conjugated PEOEBr-GGGTTAGGG (HTRp2) human telomeric repeat was investigated by using CD, UV, fluorescence, and gel electrophoresis techniques in desalted water and in K(+)- and Na(+)-containing buffers. We observed that the peculiar property of PEOEBr moieties to form dimers instead of extended aggregates drives the HTRp2 strands toward dimerization and mainly promotes the formation of quadruplex species having both the 5'-ends located at the same side of the structures. However, the counterions present in solutions (K(+) or Na(+)) as well as the strand concentration, also contribute to influence the topology and the stoichiometry of formed structures. Furthermore, unlike the unmodified sequence GGGTTAGGG (HTR2), HTRp2 strands quickly associate into G-quadruplexes even in desalted water, as assessed by CD experiments.     

Partition of a fluorescent molecule between liquid-crystalline and crystalline regions of membranes

Summary We have determined the partition coefficient of the fluorescent molecule perylene between liquid crystalline and crystalline regions of vesicle membranes formed from binary mixtures of several lipids. We measured the fluorescence intensity of perylene in these vesicles as a function of temperature and used the intensity profiles, together with a theory developed in a previous paper, to determine the partition coefficient defined as the ratio of the concentration of perylene in the liquid-crystalline (fluid) regions of the membrane to the concentration in the crystalline (solid) phase. In vesicles composed of dipalmitoyl phosphatidylcholine/distearoyl phosphatidylcholine (dppc/dspc) mixtures and of dipalmitoyl phosphatidylcholine/dipalmitoyl phosphatidylethanolamine (dppc/dppe) mixtures, the partition coefficient is close to unity. Its value is 1.04±0.18 for dppc/dsp mixtures and 1.10±0.26 for dppc/dppe mixtures. In vesicles composed of dimyristoyl phosphatidylcholine/distearoyl phosphatidylcholine mixtures, the partition coefficient was more difficult to determine and its value ranged from 0.3 to 7.     

The number and distances of positive charges of polyamine side chains in a series of perylene diimides significantly influence their ability to induce G-quadruplex structures and inhibit human telomerase

We have synthesized eight polyamine perylene diimides to conjugate the efficiency of perylene derivatives in stabilizing G-quadruplex structures and the polyamines' biological activity, due to specific interactions with different DNA domains. Our study was carried out by investigating the ability of these derivatives to induce inter- and intramolecular G-quadruplex structures by polyacrylamide gel electrophoresis (PAGE) and to inhibit telomerase in a modified TRAP assay. The two properties appear to be satisfactorily correlated and they show that the number and distances of positive charges in the side chains dramatically influence both these features. Although our previous studies on perylene derivatives with mono-positively charged side chains indicated that self assembly in aqueous solution leads to a major efficiency, the result observed with the spermine derivative suggests that a too strong aggregation is unfavourable, because it determines a lower solubility of the compounds.     

Use of recombinant DNA techniques in cloning DNA repair genes and in the study of metagenesis in mammalian cells

18 polycyclic aromatic hydrocarbons (PAHs) and 7 quinones were tested for mutagenicity using Salmonella typhimurium TA97, TA98 and TA100 with or without metabolic activation. In the presence of metabolic activation, TA97 was more susceptible to mutation than either TA98 or TA100 by many of PAHs tested. PAHs such as 1-methylphenanthrene, fluoranthene, pyrene, benzo[a]pyrene, benzo[e]pyrene and perylene had high mutagenic effects on TA97 in the presence of metabolic activation. 1,6- and 1,8-pyrenequinones were also highly mutagenic on TA97 in the presence or absence of metabolic activation. It appears that pyrene is mutagenic through its metabolic conversion to pyrenequinones.     

Mutational analysis of a blood coagulation factor VIII-binding peptide.

A peptide screened from a combinatorial peptide library with the sequence EYKSWEYC performed best as a ligand for affinity chromatography of human blood coagulation factor VIII (FVIII). With this peptide immobilized on monolithic CIM columns via epoxy groups we were able to capture FVIII from diluted plasma. Rational substitution of amino acids by spot synthesis revealed that lysine and cysteine can be exchanged for almost all other proteinogenic amino acids without loss of affinity to FVIII. This offers the possibility of site-specific attachment via either one of these residues or the N- or C-terminus. The aliphatic positions O5 (tryptophan) and O7 (tyrosine), together with the charged position O6 (glutamic acid), seem to form the core of the binding unit. In the positions with aliphatic amino acids, substitution by tyrosine or phenylalanine, and in the positions with charged amino acids, substitution by aspartic acid or lysine, preserved the affinity to FVIII. The functionality of the selected peptides was confirmed by affinity chromatography. Selective binding and elution could be achieved.     

Identification of a novel inner-core oligosaccharide structure in Neisseria meningitidis lipopolysaccharide.

The structure of the lipopolysaccharide (LPS) from three Neisseria meningitidis strains was elucidated. These strains were nonreactive with mAbs that recognize common inner-core epitopes from meningococcal LPS. It is well established that the inner core of meningococcal LPS consists of a diheptosyl-N-acetylglucosamine unit, in which the distal heptose unit (Hep II) can carry PEtn at the 3 or 6 position or not at all, and the proximal heptose residue (Hep I) is substituted at the 4 position by a glucose residue. Additional substitution at the 3 position of Hep II with a glucose residue is also a common structural feature in some strains. The structures of the O-deacylated LPSs and core oligosaccharides of the three chosen strains were deduced by a combination of monosaccharide analysis, NMR spectroscopy and MS. These analyses revealed the presence of a structure not previously identified in meningococcal LPS, in which an additional beta-configured glucose residue was found to substitute Hep I at the 2 position. This provided the structural basis for the nonreactivity of LPS with these mAbs. The determination of this novel structural feature identified a further degree of variability within the inner-core oligosaccharide of meningococcal LPS which may contribute to the interaction of meningococcal strains with their host.     

Accelerated assembly of G-quadruplex structures by a small molecule.

In the presence of alkali cations, notably potassium and sodium, DNA oligomers that possess two G-rich repeats associate into either a tetrameric parallel G-quadruplex or a variety of dimeric antiparallel G-quadruplexes. The formation of such structures is normally a very slow process. Some proteins, such as the beta-subunit of the Oxytricha telomere-binding protein, promote the formation of G-quadruplex structures in a chaperone-like manner. In this report, we present data concerning the role of a perylene derivative, PIPER, in the assembly of G-quadruplex structures as the first example of a small ligand behaving as a driver in the assembly of polynucleotide secondary structures. Gel-shift experiments demonstrate that PIPER can dramatically accelerate the association of a DNA oligomer containing two tandem repeats of the human telomeric sequence (TTAGGG) into di- and tetrameric G-quadruplexes. In so doing, PIPER alters the oligomer dimerization kinetics from second to first order. The presence of 10 microM PIPER accelerates the assembly of varied dimeric G-quadruplexes an estimated 100-fold from 2 microM oligomer. These results imply that some biological effects elicited by G-quadruplex-interactive agents, such as the induction of anaphase bridges, may stem from the propensity such compounds have for assembling G-quadruplexes.