An extraordinary cylinder-to-cylinder transition in the aqueous assemblies of fluorescently labeled rod-coil amphiphiles

We report an unprecedented cylinder-to-cylinder transformation in the self-assemblies of pyrene-labeled rod-coil molecules in water. The extraordinary morphological transformation can be monitored by a fluorescence variation from exciplex to excimer emissions, suggesting the rod-packing transition from antiparallel to interdigitated arrangements as a function of PEO coil length.     

Base-discriminating fluorescent (BDF) nucleoside: distinction of thymine by fluorescence quenching

A novel fluorescence BDF probe containing pyrene-labeled 7-deaza-2[prime or minute]-deoxyadenosine has been developed for the detection of thymine base on a target DNA.     

Conformational changes of pyrene-labeled polyelectrolytes with pH: effect of hydrophobic modifications

Structural changes of pyrene-labeled and unlabeled poly(maleic acid/octyl vinyl ether) (PMAOVE) and poly(maleic acid/methyl vinyl ether) (PMAMVE) with changes in pH have been investigated in this study. The changes in the photophysical properties of pyrene are interpreted to investigate uncoiling or swelling of the polymeric chains with pH. The vibrational fine structure of the pyrene fluorescence (I(3)/I(1)) and the ratio between excimer and monomer fluorescence (I(e)/I(m)) of both pyrene-labeled and unlabeled PMAMVE and PMAOVE suggest that, at pH 4, the polymers are in the coiled form and PMAOVE forms hydrophobic nanodomains. An increase in pH ionizes a number of COOH groups on both PMAMVE and PMAOVE, which leads to the stretching or swelling of the polymers.     

Fluorometric sensing of the salt-induced B-Z DNA transition by combination of two pyrene-labeled nucleobases

We have developed a new fluorescent DNA sensor containing two pyrene-labeled nucleobases, (Pet)G and (Py)C, and the fluorescence color was altered by the salt-induced B-Z DNA transition.     

Molar absorption coefficient of pyrene aggregates in water

The molar absorption coefficient of pyrene aggregates, epsilon(E0), was determined for a series of pyrene-labeled poly(N,N-dimethylacrylamide)s (Py-PDMA) having different pyrene contents. Aqueous solutions of Py-PDMA having pyrene contents ranging from 263 to 645 mumol of pyrene per gram of polymer were studied by UV-vis absorbance and time-resolved fluorescence spectroscopy. The global analysis of the monomer and excimer fluorescence decays with the fluorescence blob model yielded the fractions of the overall absorption contributed by all the pyrene species present in solution. The combined knowledge of the fractions obtained from the global analysis of the time-resolved fluorescence decays, the total absorption of the Py-PDMA solution obtained from UV-vis spectroscopy, and the total pyrene concentration in the solution obtained from the known pyrene content of each Py-PDMA sample led to the determination of the molar absorption coefficient of pyrene aggregates. Regardless of the pyrene content of the Py-PDMA samples and hence the level of association of the pyrene pendants in solution, all Py-PDMA samples yielded similar epsilon(E0) values over the range of wavelengths studied, namely, from 325 to 350 nm. The averaged epsilon(E0) was found to be red-shifted relative to unassociated pyrenes by 3 nm as well as having a value at the 0-0 peak of 21 000 M(-1).cm(-1) reduced from 34 700 M(-1).cm(-1) for unassociated pyrenes. The determination of epsilon(E0) enabled the first determination of the absolute fraction of associated pyrenes for aqueous solutions of a series of pyrene-labeled water-soluble polymers. The procedure outlined in this study is applicable to any pyrene-labeled water-soluble polymer and provides a new means to study quantitatively the effect of the hydrophilic-to-lipophilic balance on the hydrophobic associations generated by hydrophobically modified water-soluble polymers. As an application, the average number of pyrenes involved in a pyrene aggregate generated by Py-PDMA in water is determined.     

Synthesis of ethynylpyrene-modified 3-deaza-2′-deoxyguanosines as environmentally sensitive fluorescent nucleosides: Target DNA-sequence detection via changes in the fluorescence wavelength

Novel pyrene-labeled environmentally sensitive fluorescent (ESF) nucleosides [^1p3zG (1a) and ^2p3zG (1b)] possessing the 3-deazaguanine skeleton were synthesized. Among them, ^1p3zG (1a) exhibited longer fluorescence emission wavelengths compared with the previously reported naphthalene-modified ESF nucleoside ^3nzG (48–71?nm longer in polar solvents) and showed remarkable solvent-polarity-sensitive fluorescence properties. Oligodeoxynucleotide (ODN) probes containing ^1p3zG (1a) clearly discriminated target DNAs by the change in the emission wavelength and intensity through monitoring the microenvironmental change around the DNA minor groove. Thus, these pyrene-labeled ESF nucleosides can be applied in gene detection and molecular diagnostics, as well as in the structural analysis of nucleic acids.     

A novel fluorescent guanine derivative distinguishable of three structures, single strand, duplex, and quadruplex

We have constructed a pyrene-labeled guanine base, ^8PyG. ^8PyG is a novel fluorescent probe for monitoring the secondary structure of G-rich DNA. The fluorescence emitted from ^8PyG-labeled oligodeoxynucleotide clearly distinguished three structural states, single strand-duplex-quadruplex. Thus, the technique, which monitors the fluorescence of ^8PyG-labeled oligodeoxynucleotide, is a powerful tool for the investigation of DNA structural changes.     

Fluorescence labeling of oligosaccharides useful in the determination of molecular interactions.

A simple method to label oligosaccharides with a multifunctional fluorescent group was developed. Oligosaccharides were quantitatively labeled at their reducing termini with pyrene butanoic acid hydrazide. The pyrene-labeled oligosaccharides were successfully applied to fluorescence polarization measurements and ELISA at picomole quantity, which was not previously reached by other procedures. This labeling method should prove to be useful in a variety of aspects in glycobiology.     

Trapping specific quaternary states of the allosteric enzyme aspartate transcarbamoylase in silica matrix sol-gels

The extreme T and R quaternary structures of the allosteric enzyme aspartate transcarbamoylase have been trapped by encapsulation in a silica sol-gel matrix. Detection of the specific quaternary structure present in the sol-gel was accomplished using a pyrene-labeled version of the enzyme that exhibited monomer fluorescence in the T quaternary structure and excimer fluorescence in the R quaternary structure. Using thin films of the encapsulated enzyme, kinetics of the T and R states could be determined without interconversion of the states. Using a monolith form of the encapsulated enzyme, the transition from the T or the R structure was monitored. Within the sol-gel matrix, the rate of the transition was slowed approximately 105 over that observed in solution.     

Fluorescent Turn-On Probes for the Development of Binding and Hydrolytic Activity Assays for mRNA Cap-Recognizing Proteins

The m⁷G cap is a unique nucleotide structure at the 5′-end of all eukaryotic mRNAs. The cap specifically interacts with numerous cellular proteins and participates in biological processes that are essential for cell growth and function. To provide small molecular probes to study important cap-recognizing proteins, we synthesized m⁷G nucleotides labeled with fluorescent tags via the terminal phosph(on)ate group and studied how their emission properties changed upon protein binding or enzymatic cleavage. Only the pyrene-labeled compounds behaved as sensitive turn-on probes. A pyrene-labeled m⁷GTP analogue showed up to eightfold enhanced fluorescence emission upon binding to eukaryotic translation initiation factor 4E (eIF4E) and over 30-fold enhancement upon cleavage by decapping scavenger (DcpS) enzyme. These observations served as the basis for developing binding- and hydrolytic-activity assays. The assay utility was validated with previously characterized libraries of eIF4E ligands and DcpS inhibitors. The DcpS assay was also applied to study hydrolytic activity and inhibition of endogenous enzyme in cytoplasmic extracts from HeLa and HEK cells.     

Clicked polycyclic aromatic hydrocarbon as a hybridization-responsive fluorescent artificial nucleobase in pyrrolidinyl peptide nucleic acids

Pyrene as well as other aromatic hydrocarbons could be successfully incorporated into pyrrolidinyl peptide nucleic acid bearing a d-prolyl-2-aminocyclopentane carboxylic acid backbone (acpcPNA) as a base surrogate via a triazole linker employing Cu-catalyzed alkyne–azide cycloaddition (click chemistry). The labeling can be performed via a pre-clicked pyrene monomer or by post-synthetic modification of azide-containing acpcPNA on solid support. Thermal denaturation experiments suggested that the pyrene–triazole unit can behave as a universal base in the acpcPNA system. The mode of base-pairing has been proposed based on molecular dynamics simulations. Importantly, the fluorescence spectra of the pyrene-labeled single stranded acpcPNA and its hybrid with DNA are quite different. The ratio of emissions at 380 and 460 nm changed significantly (up to a factor of 7) upon hybrid formation with complementary DNA.     

A highly discriminating quencher-free molecular beacon for probing DNA

We inserted a fluorene-labeled deoxyuridine derivative, synthesized using Sonogashira coupling, efficiently into the loop region of a DNA hairpin using phosphoramidite chemistry. This molecular beacon, which features no additional fluorescence quencher, discriminates between perfect and one-base-mismatched base pairing by changes in its fluorescence intensity. The discrimination factor is 14.7 for the recognition of a single (A/C) base mismatch.     

Multilabeled pyrene-functionalized 2'-amino-LNA probes for nucleic acid detection in homogeneous fluorescence assays

Homogeneous fluorescence assays for detection of nucleic acids are widely used in biological sciences. Typically, probes such as molecular beacons that rely on distance-dependent fluorescence quenching are used for such assays. Less attention has been devoted to tethering a single kind of fluorophores to oligonucleotides and exploiting hybridization-induced modulation of fluorescence intensity for nucleic acid detection. Herein, thermal denaturation experiments and fluorescence properties of oligodeoxyribonucleotides containing one or more 2'-N-(pyren-1-yl)carbonyl-2'-amino-LNA monomer(s) X are described. These pyrene-functionalized 2'-amino-LNAs display large increases in thermal stability against DNA/RNA complements with excellent Watson-Crick mismatch discrimination. Upon duplex formation of appropriately designed 2'-N-(pyren-1-yl)carbonyl-2'-amino-LNA probes and complementary DNA/RNA, intensive fluorescence emission with quantum yields between 0.28 and 0.99 are observed. Quantum yields of such magnitudes are unprecedented among pyrene-labeled oligonucleotides. Molecular modeling studies suggest that the dioxabicyclo[2.2.1]heptane skeleton and amide linkage of monomer X fix the orientation of the pyrene moiety in the minor groove of a nucleic acid duplex. Interactions between pyrene and nucleobases, which typically lead to quenching of fluorescence, are thereby reduced. Duplexes between multiple modified probes and DNA/RNA complements exhibit additive increases in fluorescence intensity, while the fluorescence of single stranded probes becomes increasingly quenched. Up to 69-fold increase in fluorescence intensity (measured at lambda(em) = 383 nm) is observed upon hybridization to DNA/RNA. The emission from duplexes of multiple modified probes and DNA/RNA at concentrations down to less than 500 nM can easily be seen by the naked eye using standard illumination intensities.     

Efficient Discrimination of Single Nucleotide Polymorphisms (SNPs) Using Oligonucleotides Modified with C5‐Pyrene‐Functionalized DNA and Flanking Locked Nucleic Acid (LNA) Monomers

Oligodeoxyribonucleotides modified with 5‐[3‐(1‐pyrenecarboxamido)propynyl]‐2′‐deoxyuridine monomer X and proximal LNA monomers display higher affinity for complementary DNA, more pronounced increases in fluorescence emission upon DNA binding, and improved discrimination of SNPs at non‐stringent conditions, relative to the corresponding LNA‐free probes across a range of sequence contexts. The results reported herein suggest that the introduction of LNA monomers influences the position of nearby fluorophores via indirect conformational restriction, a characteristic that can be utilized to develop optimized fluorophore‐labeled probes for SNP‐discrimination studies.     

A case for using randomly labeled polymers to study long-range polymer chain dynamics by fluorescence

The process of excimer formation was studied for a series of pyrene end-labeled polystyrenes (PS(X)-Py 2 where X is the polymer molecular weight equal to 3, 4.5, 8, 12.7, and 14.6 K) and two series of polystyrenes randomly labeled with pyrene (CoE-PS and CoA-PS) in seven different solvents. The solvent viscosities ranged from 0.41 to 1.92 mPa x s, while the solvent quality ranged from good to poor solvents for polystyrene, as determined by intrinsic viscosity measurements. Steady-state fluorescence spectra of the pyrene-labeled polymers were acquired, and the excimer to monomer ratios showed that excimer formation increased strongly with a decrease in solvent viscosity. The monomer and excimer time-resolved fluorescence decays were also acquired and fitted globally to either the Birks' scheme or the fluorescence blob model (FBM) for the end- or randomly labeled polymers, respectively. All parameters reporting on the long-range polymer chain dynamics (LRPCD) obtained from the analysis of the fluorescence data acquired with the PS(X)-Py 2, CoE-PS, and CoA-PS series yielded virtually identical trends, demonstrating that these fluorescence experiments yield results that are internally consistent with one another. Considering the substantial advantages associated with the preparation and study of randomly labeled polymers, this report presents an appealing case for the use of randomly labeled polymers in the study of LRPCD.     

Effect of salt and surfactant on aqueous solution properties of pyrene-labeled poly(3-dimethyl (methylmethacryloyl ethyl) ammonium propane sulfonate)

Photophysical and solution properties of pyrene-labeled poly(3-dimethyl(methylmethacryloyl ethyl) ammonium propane sulfonate), poly(DMAPS/Py), were studied in terms of fluorescence emission measurement. The I_E/I_M was shown as a function of polymer concentration in deionized water. I_E/I_M value decreases with an increase in the salt concentration. The addition of surfactants to the aqueous solution of poly(DMAPS/Py) can either induce the mixed micelle of intra-polymer and its surrounding surfactants and/or mixed micelle of inter-polymers and their surrounding surfactants. Models of interactions between poly(DMAPS/Py) and surfactant or divalent salt in aqueous solution are proposed.     

Side-chain dynamics of an alpha-helical polypeptide monitored by fluorescence

The "blob" model, developed to analyze the fluorescence decays of polymers randomly labeled with pyrene, has been applied to a series of pyrene-labeled poly(glutamic acid)s (PyPGA) in DMF and carbonated buffer solutions at pH 9. Poly(glutamic acid) (PGA) exists in the ionized form in the buffer solutions as poly(sodium glutamate) (PGNa). PGA adopts an alpha-helical conformation in DMF, whereas in aqueous solution PGNa is a random coil. Fluorescence, UV-vis absorption, and circular dichroism measurements indicate that in our studies pyrene pendants attached themselves along PGA in a clustered manner. Simulations were carried out to establish that the geometry of the PGA alpha-helix induces the high level of pyrene clustering. Since the level of pyrene clustering decreased with lower pyrene content, information about naked PGA was retrieved by extrapolating the trends obtained by fluorescence to zero pyrene content. Analysis of the fluorescence decays demonstrated that during its lifetime an excited pyrene probes a 32 amino acid section of the PGA alpha-helix. This result was supported by molecular mechanics optimizations. This study establishes that the blob model, originally used to monitor the encounters between pyrenes attached randomly onto a polymer adopting a random coil conformation, can also be applied to study the dynamics of the side chains of structured proteins. Since the blob model helps in monitoring the encounters between amino acids in the initial state (i.e., random coil) and in the final state (i.e., structured protein) of the folding pathway of a protein, it could be applicable to the study of protein folding.     

Quencher-free, end-stacking oligonucleotides for probing single-base mismatches in DNA

[reaction: see text] Fluorescence can be quenched through PET from the fluorophore to neighboring C, T, and G bases, but not to the A moiety. The hairpin stem stability arising from pi-stacking and the PET between the pyrene-labeled 2'-deoxynucleotide units and their neighboring bases are the two main factors that affect the operation of these novel fluorescent oligonucleotides.     

Effect of side-chain length on the side-chain dynamics of alpha-helical poly(L-glutamic acid) as probed by a fluorescence blob model

Two series of pyrene-labeled poly(glutamic acid) (Py-PGA) were synthesized utilizing two different linkers for pyrene attachment, namely 1-pyrenemethylamine (PMA) and 1-pyrenebutylamine (PBA). Several Py-PGAs were synthesized for each series with pyrene contents ranging from 4 to 15 mol %. Py-PGA forms a rigid alpha-helix in DMF that effectively locks the backbone in place, thus enabling only side-chain or linker motions to be monitored by time-resolved fluorescence. Time-resolved fluorescence decays were acquired for the pyrene monomer of the Py-PGA constructs and the fluorescence blob model (FBM) was used to quantify the dynamics of the different linkers connecting pyrene to the backbone. Nitromethane was used to shorten the lifetime of the pyrene monomer, in effect controlling the probing time of the pyrene group, from 50 to 155 ns for PGA-PBA and from 50 to 215 ns for PGA-PMA. The FBM analysis of the fluorescence decays led to the conclusion that excimer formation around the rigid alpha-helix backbone takes place in a compact environment. The number of glutamic acid units within a blob, N blob, decreased only slightly with decreasing probing time for both Py-PGA constructs as a result of the compact distribution of the chromophores around the alpha-helix. The PGA alpha-helix was modeled using Hyperchem software and the ability of two pyrene groups to encounter was evaluated as they were separated by increasing numbers of amino acids along the alpha-helix. The number of amino acids required for two pyrenes to lose their ability to overlap and form excimer matched closely the N blob values retrieved using the FBM.