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.     

Unusually efficient quenching of the fluoroscence of an energy transfer-based optical sensor for oxygen

A two-fluorophore system consisting of pyrene as donor and perylene as energy acceptor undergoes efficient energy transfer when pyrene is electronically excited. The excitation wavelength was that of pyrene and fluorescence was monitored at the emission wavelength of perylene. The fluorescence of pyrene is strongly quenched by oxygen, but that of perylene is not. The two-fluorophore system, in contrast, is very strongly quenched, with a 4-fold increase in the Stern-Volmer quenching constant as compared to the quenching of pyrene, as a result of the effect of oxygen on the formation of the donor-acceptor exciplex, and quenching by oxygen. The results are used to design a fluorescence-based optical oxygen sensor which offers a sensitivity greatly exceeding that of existing oxygen probes.     

Pyrene Fluorescence in the Presence of Acrylic Acid-Ethyl Methacrylate Copolymers: Effect of the Copolymer Composition in the Formation of Microdomains*

The properties of aqueous solutions of acrylic acid-ethyl methacrylate (EMA) copolymers have been investigated using pyrene and pyrene pyrenebutyltrimethylammonium (PBTA) as probes. Static and dynamic fluorescence have been used to obtain information about the microenviron-ments formed. Micropolarity studies using the I₁/I₃ ratio of the vibronic bands of pyrene show the formation of hydrophobic domains. At low pH the increase of the amount of ethyl methacrylate in the copolymers shows that aqueous microdomains are excluded from the core of the polymer, for the copolymers with high content of EMA low polarity microdomains are still present on the mac-romolecular chain even at higher pH. The pH-induced conformational transition indicates that the more hydro-phobic copolymers adopt a more tightly coiled conformation. Compared to PAA, the decay times for both probes are increased twice for the polymer with 25% molar proportion of EMA. The fluorescence quenching of the probes by nitromethane depends on pH, copolymer composition and probe structure. The efficiency of quenching decreases with increase of the EMA proportion in the copolymers. Pyrene is more efficiently quenched than PBTA as a consequence of the latter being located in more internal (less accessible) sites of the polymer structure.     

Pyrene excimer signaling molecular beacons for probing nucleic acids

Molecular beacon DNA probes, containing 1-4 pyrene monomers on the 5' end and the quencher DABCYL on the 3' end, were engineered and employed for real-time probing of DNA sequences. In the absence of a target sequence, the multiple-pyrene labeled molecular beacons (MBs) assumed a stem-closed conformation resulting in quenching of the pyrene excimer fluorescence. In the presence of target, the beacons switched to a stem-open conformation, which separated the pyrene label from the quencher molecule and generated an excimer emission signal proportional to the target concentration. Steady-state fluorescence assays resulted in a subnanomolar limit of detection in buffer, whereas time-resolved signaling enabled low-nanomolar target detection in cell-growth media. It was found that the excimer emission intensity could be scaled by increasing the number of pyrene monomers conjugated to the 5' terminal. Each additional pyrene monomer resulted in substantial increases in the excimer emission intensities, quantum yields, and excited-state lifetimes of the hybridized MBs. The long fluorescence lifetime ( approximately 40 ns), large Stokes shift (130 nm), and tunable intensity of the excimer make this multiple-pyrene moiety a useful alternative to traditional fluorophore labeling in nucleic acid probes.     

MOLECULAR CONFORMATION OF IONIC SURFACTANTS IN AQUEOUS SOLUTION

The molecular conformation of ionic surfactant in aqueous solution is investigated withfluorescent probes which are intrinsic insurfactant molecules or externally introduced. Quench-lng or pyrene monomer fluorescence by alkyltriphenylphosphonium or N-alkylpyridiniumobeys Stern-Voimer equation, being diffusi6n-controlled dynamic quenching, but the behaviorof quenching with different lengths of alkyl chain is "abnormal", i.e. the longer the chain,the greater the quenching rate constant. The pyrene excimer fluorescence is observed in theaqueous solution of cetyltrimethylammonium bromide (CTMAB), and the inhibition (for cationicquenchers) and promotion (for anionic quenchers) effects of CTMAB on the quenching ofpyrene fluorescence are also observed. The self-coiling conformation of ionic surfactantmolecules in aqueous solution is proposed to be responsible for these observations and theconformation to be dynamic.     

A novel design method of ratiometric fluorescent probes based on fluorescence resonance energy transfer switching by spectral overlap integral

A ratiometric measurement, namely, simultaneous recording of the fluorescence intensities at two wavelengths and calculation of their ratio, allows greater precision than measurements at a single wavelength, and is suitable for cellular imaging studies. Here we describe a novel method of designing probes for ratiometric measurement of hydrolytic enzyme activity based on switching of fluorescence resonance energy transfer (FRET). This method employs fluorescent probes with a 3'-O,6'-O-protected fluorescein acceptor linked to a coumarin donor through a linker moiety. As there is no spectral overlap integral between the coumarin emission and fluorescein absorption, the fluorescein moiety cannot accept the excitation energy of the donor moiety and the donor fluorescence can be observed. After cleavage of the protective groups by hydrolytic enzymes, the fluorescein moiety shows a strong absorption in the coumarin emission region, and then acceptor fluorescence due to FRET is observed. Based on this mechanism, we have developed novel ratiometric fluorescent probes (1-3) for protein tyrosine phosphatase (PTP) activity. They exhibit a large shift in their emission wavelength after reaction with PTPs. The fluorescence quenching problem that usually occurs with FRET probes is overcome by using the coumarin-cyclohexane-fluorescein FRET cassette moiety, in which close contact of the two dyes is hindered. After study of their chemical and kinetic properties, we have concluded that compounds 1 and 2 bearing a rigid cyclohexane linker are practically useful for the ratiometric measurement of PTPs activity. The design concept described in this paper, using FRET switching by spectral overlap integral and a rigid link that prevents close contact of the two dyes, should also be applicable to other hydrolytic enzymes by introducing other appropriate enzyme-cleavable groups into the fluorescein acceptor.     

Fusion-fission transport of probes and quenchers in microdomains of an amphiphilic ionene polyelectrolyte

In aqueous solution, amphiphilic ionenes such as the [3,22]-ionene spontaneously adopt globular conformations and form microdomains that are highly micelle-like, i.e. are capable of solubilizing organic molecules, binding and exchanging counterions and accelerating or inhibiting the rates of bimolecular reactions. Time-resolved fluorescence decay of pyrene and pyrene derivatives solubilized in these microdomains at concentrations where excimer formation occurs show that even water-insoluble probes can migrate between the hydrophobic microdomains formed in aqueous solution by a [3,22]-ionene chloride (with the N-terminal groups quaternized with benzyl chloride). Time-resolved studies of the quenching of pyrene fluorescence by alkylpyridine derivatives revealed similar behavior. The observed quenching behavior requires that the migration be between microdomains on the same ionene chain or same group of associated ionene chains and is consistent with migration dominated by fusion/fission transport of the probe and quencher.     

Biotin-, fluorescein- and 'clickable' conjugates of phospha-oseltamivir as probes for the influenza virus which utilize selective binding to the neuraminidase

The synthesis of conjugates of phospha-oseltamivir to the well established reporter groups fluorescein and biotin and an approach to multimeric inhibitors is described. We report powerful inhibition of the influenza neuraminidase by these probes and quantify fluorescence quenching during binding of the fluorescein conjugate through titration with the neuraminidase. Thus, we show that they could be useful tools to efficiently inhibit, detect and quantify the virus and the neuraminidase in biological systems.     

A fluorescence method for quantitative measurements of specific protein at powder surfaces

A new method using fluorescence labelled proteins was developed to determine the quantitative amount of specific protein at the powder surface. The method is based on steady-state fluorescence measurements of pyrene labelled proteins with oxygen gas phase quenching at the powder surface. The surface load of protein was measured for spray-dried dextran powders containing bovine serum albumin (BSA). The results show a patchwise surface load of about 1.3 mg m⁻² at a concentration of 0.33% (dry weight) BSA in the powder. The patchwise surface load stays constant with increased BSA concentration in the powder.     

Highly fluorescent conjugated pyrenes in nucleic acid probes: (phenylethynyl)pyrenecarbonyl-functionalized locked nucleic acids

In recent years, fluorescently labeled oligonucleotides have become a widely used tool in diagnostics, DNA sequencing, and nanotechnology. The recently developed (phenylethynyl)pyrenes are attractive dyes for nucleic acid labeling, with the advantages of long-wave emission relative to the parent pyrene, high fluorescence quantum yields, and the ability to form excimers. Herein, the synthesis of six (phenylethynyl)pyrene-functionalized locked nucleic acid (LNA) monomers M(1)-M(6) and their incorporation into DNA oligomers is described. Multilabeled duplexes display higher thermal stabilities than singly modified analogues. An increase in the number of phenylethynyl substituents attached to the pyrene results in decreased binding affinity towards complementary DNA and RNA and remarkable bathochromic shifts of absorption/emission maxima relative to the parent pyrene fluorochrome. This bathochromic shift leads to the bright fluorescence colors of the probes, which differ drastically from the blue emission of unsubstituted pyrene. The formation of intra- and interstrand excimers was observed for duplexes that have monomers M(1)-M(6) in both complementary strands and in numerous single-stranded probes. If more phenylethynyl groups are inserted, the detected excimer signals become more intense. In addition, (phenylethynyl)pyrenecarbonyl-LNA monomers M(4), M(5), and M(6) proved highly useful for the detection of single mismatches in DNA/RNA targets.     

Separation and detection of a benzo[a]pyrene metabolite with capillary electrophoresis in the presence of DNA using laser-induced fluorescence

A novel approach was developed for the separation and detection of a benzo[a]pyrene B[a]P-DNA metabolite (tetrol I-1) in the presence of DNA using CE and laser induced fluorescence. Tetrol I-1 in the presence of DNA is intercalated and undergoes fluorescence quenching. Thus, an equilibrium is established between the intercalated tetrol I-1 and the uncomplexed tetrol I-1. It is only the uncomplexed tetrol that is fluorescent in the presence of DNA. The tetrol I-1 fluorescence intensities, at two concentrations of tetrol I-1 (0.005 and 0.01mg ml(-1)), were observed while varying the DNA concentration. Stern-Volmer plots were constructed of the fluorescence intensity of the uncomplexed tetrol I-1 versus DNA concentration. From the slopes of the Stern-Volmer plots quenching constants were determined. The quenching constants are essentially the same as an association constant for tetrol I-1 with DNA. The average value obtained for the association constant for the two concentrations of tetrol I-1 was 0.22+/-0.02 mg ml(-1). It was thus demonstrated that uncomplexed tetrol I-1 can be separated from DNA by CE and an association constant for tetrol I-1 bound to DNA can be obtained from the fluorescence quenching data.     

FLUORESCENCE STUDY OF THE PHYSICO-CHEMICAL PROPERTIES OF A BENZO(A)PYRENE7,8-DIHYDRODIOL9,10-OXIDE DERIVATIVE BOUND COVALENTLY TO DNA

Abstract— Covalent complexes between 7 ,8-dihydrodiol 9.10-oxide benzo(a)pyrene (BPDE) and DNA with a modification of one BPDE molecule per 1000 DNA bases were prepared in vitro . The same stereoselective and chemically homogeneous binding of BPDE to native DNA was observed, as reported earlier for human and bovine bronchial explants. The fluorescence of the pyrene-like aromatic moiety of BPDE bound to DNA in vitro was used as a probe of the microenvironment of the BPDE molecule in order to obtain information about the structure of the BPDE-DNA complex dissolved in aqueous solution. Fluorescence techniques, based on the quenching of the singlet excited states by metal ions such as Ag⁺, by iodide ions, and by molecular oxygen are described, which provide a method for differentiating between external and internal (intercalation) binding of polycyclic aromatic molecules to DNA. Silver ions, which bind specifically to DNA bases, exhibit a strong quenching effect on noncovalently bound, intercalated benzo(a)pyrene; on the other hand, there is no quenching effect on the fluorescence of BPDE in the covalent DNA adduct. Quenchers such as O₂ and iodide ions, which do not specifically bind to DNA and are dissolved in the solution external to the DNA molecule, exhibit a quenching effect on the BPDE chromophore. Furthermore, the fluorescence yield of the BPDE-DNA complex decreases with increasing DNA concentration, an effect which is not observed with non-covalently bound intercalated benzo(a)pyrene-DNA complexes, and which is attributed to intermolecular DNA-DNA interactions. The results of these studies indicate that the pyrene-like chromophore in the covalent BPDE-DNA complex is not intercalated between the base pairs, and that it is located in an accessible region external to the DNA helix. Possible structures are discussed.     

含芘荧光化学敏感器化合物同小牛胸腺DNA分子间的相互作用

研究了含芘荧光化学敏感器分子被ctDNA猝灭的荧光光谱.ctDNA分子对该化学敏感器中芘的激发单体,激基缔合物都有猝灭作用.对激发单体的猝灭速度顺序为;化合物(2)>化合物(1)>芘丁酸>化合物(3);对激基缔合物的猝灭速度顺序为;化合物(2)化合物(3).由得到的荧光猝灭数据,可按公式(2)求得荧光化学敏感器分子与ctDNA分子相互作用的稳定常数.发现化合物(2)与ctDNA分子间有着最强的相互作用能力.按ctDNA和含芘荧光化学敏感器的分子结构、构型以及分子内原子-原子的间距等提出了ctDNA分子与该荧光化学敏感器的作用模型,并对上述结果进行了初步解释.     

Pathways for fluorescence quenching in 2-aminopurine π-stacked with pyrimidine nucleobases

Fluorescent analogues of nucleobases are very useful as probes to study DNA dynamics, because natural DNA does not fluoresce significantly. In many of these analogues, such as 2-aminopurine (2AP), the fluorescence is quenched when incorporated into DNA through processes that are not well understood. This work uses theoretical studies to examine fluorescence quenching pathways in 2AP-containing dimers. The singlet excited states of π-stacked dimer systems containing 2AP and a pyrimidine base, thymine or cytosine, have been studied using ab initio computational methods. Computed relaxation pathways along the excited-state surfaces reveal novel mechanisms that can lead to fluorescence quenching in the π-stacked dimers. The placement of 2AP on the 5' or 3' terminus of the dimers has different effects on the excitation energies and the relaxation pathways on the S(1) excited state. Conical intersections between the ground and first excited states exist when 2AP is placed at the 3' side, whereas the placement of 2AP at the 5' side leads to the switching of a bright state to a dark state. Both of these processes can lead to fluorescence quenching and may contribute to the fluorescence quenching observed in 2AP when incorporated in DNA.     

Utilization of heavy-atom effect quenching of pyrene fluorescence to determine the intramembrane distribution of halothane

The interaction of halothane (CF₃CHBrCl) with dipalmitoylphosphatidylcholine (DPPC) membranes containing varying amounts of dipalmitoylphosphatidylglycerol (DPPG) was examined via heavy atom effect quenching of pyrene fluorescence by halothane. The effect of halothane on pyrene fluorescence is consistent with a kinetic model based upon the assumption of the existence of two populations of pyrene in the membrane: one accessible to interactions with halothane; the second inaccessible to halothane on the time scale of the pyrene fluorescence excited state. Both populations of pyrene are affected by the presence of halothane in the membrane. The rate of halothane quenching of pyrene fluorescence is increased significantly for all DPPG/DPPC membranes compared to pure DPPC membranes indicating that any DPPG in the membrane facilitates interaction between halothane and pyrene even though the measured partition coefficients indicate that little change in total halothane concentration in the membrane as a whole occurs as a function of percent DPPG in DPPG/DPPC mixtures.
It is speculated that phase boundaries play an important role in determining the behavior of this model system by determining the location of the pyrene probe. The heavy atom effect quenching of pyrene by halothane provides a useful probe of phase boundaries in membranes.     

Recent Development of DNA-modified AIEgen Probes for Biomedical Application

A variety of DNA-based probes are utilized for the detections of multiple analytes and DNA nanotechnology has been thriving for recent decades and achieving numerous nanostructures,mainly focusing on DNA morphology modulation and multifunctional systems engineered into to the complicated works.Among the numerous detections,fluorescence method is a non-invasive,highly selective and sensitive means for varieties of applications,but their emissions are often compromised by the aggregation-caused quenching(ACQ)effect,which weakens their applications.The aggregation induced emission luminogens(AIEgens)are created with non emissive or weakly emissive in a low concentration but emit strong fluorescence in a high concentration with aggregated states.Herein,numerous functionalized AIEgens have been emerged and used for detection and imaging and DNA-modified AIEgen probes are introduced.In this vein,here we report the progress on DNA-modified AIEgen probes in recent years and highlight their conjugation strategies including covalent bonding,electrostatic interaction and their applications of biosensing.Moreover,multiple DNA strands are needed to introduce into the DNA-modified AIEgen probes for more purposes.At the end,some challenges are mentioned to discuss the new trend of DNA-modified AIEgen probes.     

Pyrene solubilization capacity in octaethylene glycol monododecyl ether (C12E8) micelles

We used fluorescence quenching, vibronic band ratios and excimer fluorescence techniques to quantify the statistics of pyrene solubilization in nonionic octaethylene glycol monododecyl ether (C₁₂E₈) micelles. Using a two-phase model (aqueous and micellar pseudophases) to interpret fluorescence results, we found that all three of these experimental methods provide consistent information about pyrene partitioning between aqueous and micellar pseudophases. From dynamic quenching experiments we determined the pyrene partition coefficient and the average number of pyrene molecules solubilized per micelle over a range of surfactant concentrations. The pyrene partition coefficient increases with increasing surfactant concentration. We confirmed the partitioning results by excimer fluorescence measurements. Quenching results indicate that pyrene is accessible to Cu²⁺ quenchers even in the limit of high surfactant concentration where solubilized pyrene is in the infinite dilution limit in the micellar pseudophase. This suggests that solubilized pyrene resides in the micellar palisade layer. We determined the maximum number of pyrene solubilizates allowed per micelle (micellar solubilization capacity) by applying a three-phase model to fluorescence experiments conducted in the presence of solid phase pyrene. The estimated maximum capacity is 6 pyrene molecules per micelle. The three phase partitioning model successfully predicted the excimer fluorescence in the presence of solid pyrene.     

Two-dye and one- or two-quencher DNA probes for real-time PCR assay: synthesis and comparison with a TaqMan? probe

A typical TaqMan? real-time PCR probe contains a 5'-fluorescent dye and a 3'-quencher. In the course of the amplification, the probe is degraded starting from the 5'-end, thus releasing fluorescent dye. Some fluorophores (including fluorescein) are known to be prone to self-quenching when located near each other. This work is aimed at studying dye-dye and dye-quencher interactions in multiply modified DNA probes. Twenty-one fluorogenic probes containing one and two fluoresceins (FAM), or a FAM-JOE pair, and one or two BHQ1 quenchers were synthesized using non-nucleoside reagents and "click chemistry" post-modification on solid phase and in solution. The probes were tested in real-time PCR using an ~300-bp-long natural DNA fragment as a template. The structural prerequisites for lowering the probe background fluorescence and increasing the end-plateau fluorescence intensity were evaluated and discussed.     

基于T-T碱基错配的荧光传感器特异性检测汞离子

在本文中,我们研制了一种基于T-T碱基错配特异性键合汞离子的荧光传感器用于汞离子的检测。该传感器由两条分别标记了荧光基团（F）和淬灭基团（Q）的DNA探针组成,并且含有两对用于结合汞离子的T-T错配碱基。当汞离子存在时,两条探针之间形成T-Hg2+-T结构,作用力增强,从而拉近了荧光基团与淬灭基团之间的距离,发生能量转移,使荧光信号在一定程度上被淬灭。在优化的条件下,我们使用该传感器对汞离子进行检测,动力学响应范围为50nM到1000nM,线性相关方程为y= 5281.13 - 1650.56 lg[Hg2+] ( R2 = 0.985),检测下限为79nM。此外,我们还考察了该传感器的选择性,当用其它干扰离子（浓度都为1.0µM）代替待测离子进行实验时,没有发生明显的荧光淬灭,说明该传感器具有较高的选择性。该传感器的构建为汞离子的检测提供了一条快速、简便的新途径。     

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 .