Perylene attached to 2'-amino-LNA: synthesis, incorporation into oligonucleotides, and remarkable fluorescence properties in vitro and in cell culture

During recent years, fluorescently labeled oligonucleotides have been extensively investigated within diagnostic approaches. Among a large variety of available fluorochromes, the polyaromatic hydrocarbon perylene is an object of increasing interest due to its high fluorescence quantum yield, long-wave emission compared to widely used pyrene, and photostability. These properties make perylene an attractive label for fluorescence-based detection in vitro and in vivo. Herein, the synthesis of 2'- N-(perylen-3-yl)carbonyl-2'-amino-LNA monomer X and its incorporation into oligonucleotides is described. Modification X induces high thermal stability of DNA:DNA and DNA:RNA duplexes, high Watson-Crick mismatch selectivity, red-shifted fluorescence emission compared to pyrene, and high fluorescence quantum yields. The thermal denaturation temperatures of duplexes involving two modified strands are remarkably higher than those for double-stranded DNAs containing modification X in only one strand, suggesting interstrand communication between perylene moieties in the studied 'zipper' motifs. Fluorescence of single-stranded oligonucleotides having three monomers X is quenched compared to modified monomer (quantum yields Phi F = 0.03-0.04 and 0.67, respectively). However, hybridization to DNA/RNA complements leads to Phi F increase of up to 0.20-0.25. We explain it by orientation of the fluorochrome attached to the 2'-position of 2'-amino-LNA in the minor groove of the nucleic acid duplexes, thus protecting perylene fluorescence from quenching with nucleobases or from the environment. At the same time, the presence of a single mismatch in DNA or RNA targets results in up to 8-fold decreased fluorescence intensity of the duplex. Thus, distortion of the duplex geometry caused by even one mismatched nucleotide induces remarkable quenching of fluorescence. Additionally, a perylene-LNA probe is successfully applied for detection of mRNA in vivo providing excitation wavelength, which completely eliminates cell autofluorescence.     

G-quadruplex DNA cleavage preference and identification of a perylene diimide G-quadruplex photocleavage agent using a rapid fluorescent assay

A rapid fluorescence assay for G-quadruplex DNA cleavage was used to investigate the preference of TMPyP4 photochemical and Mn·TMPyP4 oxidative cleavage. Both agents most efficiently cleave the c-Myc promoter G-quadruplex. Direct PAGE analysis of selected assay samples showed that for a given cleavage agent, different cleavage products are formed from different G-quadruplex structures. Cleavage assays carried out in the presence of excess competitor nucleic acid structures revealed the binding selectivity of cleavage agents, while comparisons with duplex cleavage efficiency employing a dual-labeled hairpin oligonucleotide revealed neither agent prefers G-quadruplex over duplex substrates. Finally, this assay was used to identify the perylene diimide Tel11 as a photocleavage agent for the c-Myc G-quadruplex.     

Synthesis of a non-cationic, water-soluble perylenetetracarboxylic diimide and its interactions with G-quadruplex-forming DNA

A number of N,N'-disubstituted perylenetetracarboxylic diimides have been reported to bind effectively to DNA that adopts G-quadruplex motifs. In some cases, this binding may actively drive the transition from single-strand DNA to the quadruplex form. The perylenediimides in the reported cases all have amine-containing side chains, which are thought to interact with the grooves of the quadruplex and help dictate the selectivity of these compounds for quadruplex versus duplex DNA. We synthesized a polyethyleneglycol-swallowtailed (PEG-tailed) perylenediimide that is water-soluble even though it is uncharged. Binding to duplex and quadruplex DNA of this perylenediimide was studied by fluorescence quenching titrations under a variety of salt conditions, and the compound's effect on quadruplex formation was studied by non-denaturing gel electrophoresis. Our results indicate that while the molecule binds to single-stranded DNA quite effectively and with selectivity, it does not drive the transition of the DNA to the tetrameric quadruplex structure, supporting the idea that charge neutralization is a key component of perylene compounds that stabilize tetrameric quadruplexes.     

Fluorescence quenching in lecithin and lecithin/cholesterol liposomes by parmagenetic lipid analogues. Introduction of a new probe approach.

1. Perylene, whether incorporated into lecithin or lecithin/cholesterol (1:1) liposomes, exhibits identical fluorescence spectra, but fluorescence in the presence of cholesterol is enhanced by 30-50%. 2. The fluorescence of perylene in pure dipalmitoyllecithin vesicles increases sharply at the transition temperature (Tt equals 41 degrees C). No such fluorescence jump is observed in lecithin/cholesterol (1:1) micelles. 3. In lecithin liposomes maximal quenching of perylene fluorescence at 25 degrees C is effected by cholestane spin label (80%) followed by androstane spin label (70%), 5-nitroxide stearate (60%) and 16-nitroxide stearate (50%). 4. In liposomes containing 5 mol % cholesterol these differences are reduced; however, the sequence of quenching efficiencies is the same except for the nitroxide stearates, which interchange their positions. 5. 5. Paramagnetic quenching of perylene fluorescence is stable below 35 degrees C and above 45 degrees C, but decreases sharply about the phase-transition temperature of dipalmitoyllecithin. 6. In lecithin/cholesterol (1:1, molar ratio) lipsomes fluorescence quenching diminishes linearly, but only slightly, with increasing temperature. 7. Cholestane spin label and androstane spin label at concentrations of greater than 20 mol % themselves suppress the quenching discontinuity at Tt, indicating a cholesterol-like structural effect. 8. The quenching phenomena observed are attributed to a non-random accommodation of fluorophore and quencher molecules (co-clustering) below the phase transition and a statistical distribution of both impurities above Tt. 9. In the presence of cholesterol the clustering tendencies are reduced or even eliminated; this is compatible with the concept that cholesterol fluidizes the phosphatide acyl chains below the transtion temperature.     

A real‐time fluorescence assay for protease activity and inhibitor screening based on the aggregation‐caused quenching of a perylene probe

We have established a real‐time and label‐free fluorescence turn‐on strategy for protease activity detection and inhibitor screening via peptide‐induced aggregation‐caused quenching of a perylene probe. Because of electrostatic interactions and high hydrophilicity, poly‐l ‐glutamic acid sodium salt (PGA; a negatively charged peptide) could induce aggregation of a positively charged perylene probe (probe 1) and the monomer fluorescence of probe 1 was effectively quenched. After a protease was added, PGA was enzymatically hydrolyzed into small fragments and probe 1 disaggregated. The fluorescence recovery of probe 1 was found to be proportional to the concentration of protease in the range from 0 to 1 mU/ml. The detection limit was down to 0.1 mU/ml. In the presence of a protease inhibitor, protease activity was inhibited and fluorescence recovery reduced. Moreover, we demonstrated the potential application of our method in a complex mixture sample including 1% human serum. Our method is simple, fast and cost effective.     

Perylene diimide G-quadruplex DNA binding selectivity is mediated by ligand aggregation

Two N,N'-disubstituted perylene diimide G-quadruplex DNA ligands, PIPER [N,N'-bis-(2-(1-piperidino)ethyl)-3,4,9,10-perylene tetracarboxylic acid diimide] and Tel01 [N,N'-bis-(3-(4-morpholino)-propyl)-3,4,9,10-perylene tetracarboxylic acid diimide] were studied. Visible absorbance, resonance light scattering, and fluorescence spectroscopy were used to characterize the pH-dependent aggregation of these ligands. The G-quadruplex DNA binding selectivity of these ligands as monitored by absorption spectroscopy is also pH-dependent. The ligands bind to both duplex and G-quadruplex DNA under low pH conditions, where the ligands are not aggregated. At higher pH, where the ligands are extensively aggregated, the apparent G-quadruplex DNA binding selectivity is high.     

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.     

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 32mer and its complementary two sequential 16mer deoxyribonucleotides whose neighboring terminals were each respectively labeled with a pyrene and a perylene residue. A transfer efficiency of ~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 Å (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 nucleotides 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 Å. 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.     

Mammalian 3-oxosteroid delta4-delta5-isomerase: a membrane-bound enzyme. I. Fluorescence study of the relationship between the enzymatic binding site, phospholipids, water and ions.

The microsomal membranes and the proteolipidic particles obtained by disruption of the microsomes by alkaline-earth ions at molar concentration have been compared by measuring the fluorescence properties of 1-anilino-naphthalene-3-sulfonate and naphthyl-1-phenylamine. The protein lipid arrangement of these two systems appears to be not essentially different. The study of fluorescence polarization of an hydrophobic probe (perylene) in function of Mg2+ concentration suggests a possible mechanism of disruption of the membrane by Mg2+ involving the strong structure-making effect of the ion. The comparison of the fluorescence polarization changes of perylene and equilenine (a competitive inhibitor of the isomerase) with the ionic concentration indicates that there is no direct relation between the bulk lipidic phase and the enzymatic binding site properties. Moreover, the emission of equilenine is completely quenched by I-, in contrast with the napththyl-1-phenylamine and perylene probes, which clearly demonstrates the accessibility of the catalytic site to water molecules and ions.     

Optical antisense imaging of tumor with fluorescent DNA duplexes

Antisense targeting of tumor with fluorescent conjugated DNA oligomers has the potential of improving tumor/normal tissue ratios over that achievable by nuclear antisense imaging. When administered as a linear duplex of two fluorophore-conjugated oligomers arranged in a manner that inhibits fluorescence as the duplex and designed to dissociate only in the presence of the target mRNA, the fluorescence signal should in principle be inhibited everywhere except in the target cell. Optical imaging by fluorescence quenching using linear fluorophore-conjugated oligomers has not been extensively investigated and may not have been previously considered for antisense targeting. We evaluated in cell culture and in KB-G2 tumor bearing nude mice a 25-mer phosphorothioate (PS) anti- mdr1 antisense DNA conjugated with the Cy5.5 emitter on its 3' equivalent end and hybridized as a linear duplex with a shorter 18-mer phosphodiester (PO) complementary DNA (cDNA) with the Black Hole inhibitor BHQ3 on its 5' end. In serum environments, 90% of the DNA25-Cy5.5 fluorescence was inhibited immediately following addition of the cDNA18-BHQ3 and showed only slight loss of inhibition over 24 h at 37 degrees C. As evidence of antisense specific binding, when incubated with the DNA25-Cy5.5/cDNA18-BHQ3 duplex, the fluorescence was lower in KB-31 (Pgp +/-) cells compared to KB-G2 (Pgp++) cells, but when incubated with the control cDNA18-Cy5.5/DNA25-BHQ3 duplex in which the fluorophores were reversed, the fluorescence of both cell types was low. As further evidence of specific binding, the fluorescent intensity of total RNA from KB-G2 cells incubated with the study duplex showed evidence of dissociation and hybridization with the target mRNA. Furthermore, the fluorescence microscopy images of KB-G2 cells incubated with DNA25-Cy5.5 as the singlet or study duplex show that migration in both cases is to the nucleus. The animal studies were performed in mice bearing KB-G2 tumor in one thigh and receiving iv the study or control duplexes. The tumor/normal thigh fluorescence ratio was clearly positive as early as 30 min postinjection in the study mice and reached a maximum at 5 h. By contrast, much lower fluorescence was observed in mice receiving the control duplex at the same dosage. Fluorescence microscope imaging showed that the Cy5.5 fluorescence was much higher in tumor sections from the animal that had received the study rather than control duplex. Thus combining a fluorophore-conjugated antisense DNA with an inhibitor-conjugated shorter complementary cDNA inhibited fluorescence both in cell culture and in tumored animals except in the presence of the target mRNA. This proof of concept investigation of optical antisense targeting therefore suggests that further studies including optimization of this approach are appropriate.     

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.     

Selective G-quadruplex ligands: The significant role of side chain charge density in a series of perylene derivatives

The human telomeric G-quadruplex structure is a promising target for the design of cancer drugs. The selectivity of G-quadruplex ligands with respect to duplex genomic DNA is of especial importance. The high selectivity of polyamine conjugated perylene derivatives appears to be regulated by side-chain charge density, as indicated by data from a FRET melting assay and induced CD spectroscopy.     

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. ¹H 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.     

TaqMan探针双重荧光定量PCR同时检测解脲支原体和巨细胞病毒

目的探讨双重荧光定量PCR技术的优化条件,建立基于TaqMan探针技术荧光定量法检测同时检测解脲支原体和巨细胞病毒的新方法。方法分别采用普通定性PCR扩增母婴垂直传播常见的病原体（解脲支原体和巨细胞病毒）测序鉴定,然后分别采用TaqMan探针的单重和双重定量PCR技术对解脲支原体和巨细胞病毒同时定性定量检测。结果解脲支原体和巨细胞病毒单种定性PCR检测均为阳性,TaqMan探针单重和双重定量PCR检测解脲支原体和巨细胞病毒阳性率和特异性均为100％,相同样品TaqMan探针单重、双重定量PCR分别检测的结果符合率100％。结论TaqMan探针双重荧光定量PCR技术可同时检测两种靶分子,结果可靠,应用前景广阔。     

Simian virus 40 large T-antigen G-quadruplex DNA helicase inhibition by G-quadruplex DNA-interactive agents

On the basis of growing evidence for G-quadruplex DNA structures in genomic DNA and the presumed need to resolve these structures for DNA replication, the G-quadruplex DNA unwinding ability of a prototypical replicative helicase, SV40 large T-antigen (T-ag), was investigated. Here, we demonstrate that this G-quadruplex helicase activity is robust and comparable to the duplex helicase activity of T-ag. Analysis of the SV40 genome demonstrates the presence of sequences that may form intramolecular G-quadruplexes, which are the presumed natural substrates for the G-quadruplex helicase activity of T-ag. A number of G-quadruplex-interactive agents as well as new perylene diimide (PDI) derivatives have been investigated as inhibitors of both the G-quadruplex and the duplex DNA helicase activities of T-ag. A unique subset of these G-quadruplex-interactive agents inhibits the G-quadruplex DNA unwinding activity of T-ag, relative to those reported to inhibit G-quadruplex DNA unwinding by RecQ-family helicases. We also find that certain PDIs are both potent and selective inhibitors of the G-quadruplex DNA helicase activity of T-ag. Surface plasmon resonance and fluorescence spectroscopic G-quadruplex DNA binding studies of these T-ag G-quadruplex helicase inhibitors have been carried out, demonstrating the importance of attributes in addition to binding affinity for G-quadruplex DNA that may be important for inhibition. The identification of potent and selective inhibitors of the G-quadruplex helicase activity of T-ag provides tools for probing the specific role of this activity in SV40 replication.     

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.     

A dual role for substrate S-adenosyl-L-methionine in the methylation reaction with bacteriophage T4 Dam DNA-[N6-adenine]-methyltransferase

The fluorescence of 2-aminopurine ((2)A)-substituted duplexes (contained in the GATC target site) was investigated by titration with T4 Dam DNA-(N6-adenine)-methyltransferase. With an unmethylated target ((2)A/A duplex) or its methylated derivative ((2)A/(m)A duplex), T4 Dam produced up to a 50-fold increase in fluorescence, consistent with (2)A being flipped out of the DNA helix. Though neither S-adenosyl-L-homocysteine nor sinefungin had any significant effect, addition of substrate S-adenosyl-L-methionine (AdoMet) sharply reduced the Dam-induced fluorescence with these complexes. In contrast, AdoMet had no effect on the fluorescence increase produced with an (2)A/(2)A double-substituted duplex. Since the (2)A/(m)A duplex cannot be methylated, the AdoMet-induced decrease in fluorescence cannot be due to methylation per se. We propose that T4 Dam alone randomly binds to the asymmetric (2)A/A and (2)A/(m)A duplexes, and that AdoMet induces an allosteric T4 Dam conformational change that promotes reorientation of the enzyme to the strand containing the native base. Thus, AdoMet increases enzyme binding-specificity, in addition to serving as the methyl donor. The results of pre-steady-state methylation kinetics are consistent with this model.     

Microviscosity of mucosal cellular membranes in toad urinary bladder: Relation to antidiuretic hormone action on water permeability

Summary The microviscosity of cellular membranes (or membrane fluidity) was measured in suspensions of single mucosal cells isolated from the urinary bladder of the toad,Bufo marinus, by the technique of polarized fluorescence emission spectroscopy utilizing the hydrophobic fluorescent probe, perylene. At 23°C, 5mm dibutyryl cyclic 3,5-AMP decreased the apparent microviscosity of the cell membranes from 3.31 to 3.07 P, a minimum decrease of 7.3% (P<0.001) with a physiological time course. Direct visualization of the cell suspension indicated that 98% of the cells were viable, as indicated by Trypan Blue dye exclusion. The fluorescent perylene could be seen only in plasma membranes, suggesting that the measured viscosity was that of plasma membrane with little contribution from the membranes of cellular organelles. Addition of antidiuretic hormone to intact hemibladders stained with perylene produced changes in fluorescence consistent with a similar 7% decrease in apparent microviscosity with a physiological time course. However, finite interpretation of the findings in intact tissue cannot be made because the location and the fluorescent lifetime of the probe could only be conducted on the isolated cells. Comparison with previously determined relationships between water permeability and microviscosity in artificial bilayers suggests that the 7% (a lower limit) decrease in microviscosity would produce only a 6.5% increase in water permeability.