A new pyrene-based fluorescent probe for the determination of critical micelle concentrations

A new pyrene-based fluorescent probe for the determination of critical micelle concentrations (CMC) is described. The title compound 1 is obtained in five steps, starting from pyrene. Fluorescence spectroscopic properties of 1 are studied in homogeneous organic solvents and aqueous micellar solutions. In a wide range of organic solvents, probe 1 exhibits a characteristic monomer emission of the pyrene fluorophore, with three distinct peak maxima at 382, 404, and 425 nm. The spectra change dramatically in aqueous solution, where no monomer emission of the pyrene fluorophore is detected. Instead, only strong excimer fluorescence with a broad, red-shifted emission band at lambda(max) = 465 nm is observed. In micellar aqueous solution, a superposition of the monomer and excimer emission is found. The appearance of the monomer emission in micellar solution can be explained on the basis of solubilization of 1 by the surfactant micelles. The ratio of the monomer to excimer fluorescence intensities of 1 is highly sensitive to changes in surfactant concentration. This renders 1 a versatile and sensitive probe molecule for studying the micellization of ionic and nonionic surfactants. For a representative selection of common surfactants, the critical micelle concentrations in aqueous solution are determined, showing excellent agreement with established literature data.     

Electroactive chitosan nanoparticles for the detection of single-nucleotide polymorphisms using peptide nucleic acids

Here we report an electrochemical biosensor that would allow for simple and rapid analysis of nucleic acids in combination with nuclease activity on nucleic acids and electroactive bionanoparticles. The detection of single-nucleotide polymorphisms (SNPs) using PNA probes takes advantage of the significant structural and physicochemical differences between the full hybrids and SNPs in PNA/DNA and DNA/DNA duplexes. Ferrocene-conjugated chitosan nanoparticles (Chi-Fc) were used as the electroactive indicator of hybridization. Chi-Fc had no affinity towards the neutral PNA probe immobilized on a gold electrode (AuE) surface. When the PNA probe on the electrode surface hybridized with a full-complementary target DNA, Chi-Fc electrostatically attached to the negatively-charged phosphate backbone of DNA on the surface and gave rise to a high electrochemical oxidation signal from ferrocene at ∼0.30 V. Exposing the surface to a single-stranded DNA specific nuclease, Nuclease S1, was found to be very effective for removing the nonspecifically adsorbed SNP DNA. An SNP in the target DNA to PNA made it susceptible to the enzymatic digestion. After the enzymatic digestion and subsequent exposure to Chi-Fc, the presence of SNPs was determined by monitoring the changes in the electrical current response of Chi-Fc. The method provided a detection limit of 1 fM (S/N = 3) for the target DNA oligonucleotide. Additionally, asymmetric PCR was employed to detect the presence of genetically modified organism (GMO) in standard Roundup Ready soybean samples. PNA-mediated PCR amplification of real DNA samples was performed to detect SNPs related to alcolohol dehydrogenase (ALDH). Chitosan nanoparticles are promising biometarials for various analytical and pharmaceutical applications. Figure The electrochemical method for SNP detection using PNA probes and chitosan nanoparticles takes advantage of the significant structural and physicochemical differences between PNA/DNA and DNA/DNA duplexes. Single-stranded DNA specific enzymes selectively choose these SNP sites and hydrolyze the DNA molecules on gold electrode (AuE) surface. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

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.     

Detection of single nucleotide polymorphisms by a gold nanowire-on-film SERS sensor coupled with S1 nuclease treatment

Single nucleotide polymorphisms (SNPs) can serve as important biomarkers for genetic diseases, for which accurate detection of SNPs is essential for early diagnosis. We have developed a novel SNP sensor by combining a Au nanowire-on-film surface-enhanced Raman scattering (SERS) platform with S1 nuclease reaction. The combined sensor system provides reproducible SERS signals only in the presence of perfectly matched target DNAs, to probe DNAs as a result of single-stranded DNA-specific degradation by S1 nuclease. Furthermore, point mutations in DNA causing Wilson disease and Avellino corneal dystrophy were successfully identified by this sensor, thereby indicating its practical ability to diagnose genetic diseases.     

Fluorescent detection of single nucleotide polymorphism utilizing a hairpin DNA containing a nucleotide base analog pyrrolo-deoxycytidine as a fluorescent probe

A novel fluorescent method for the detection of single nucleotide polymorphism (SNP) was developed using a hairpin DNA containing nucleotide base analog pyrrolo-deoxycytidine (P-dC) as a fluorescent probe. This fluorescent probe was designed by incorporating a fluorescent P-dC into a stem of the hairpin DNA, whose sequence of the loop moiety complemented the target single strand DNA (ss-DNA). In the absence of the target ss-DNA, the fluorescent probe stays a closed configuration in which the P-dC is located in the double strand stem of the fluorescent probe, such that there is weak fluorescence, attributed to a more efficient stacking and collisional quenching of neighboring bases. In the presence of target ss-DNA, upon hybridizing the ss-DNA to the loop moiety, a stem-loop of the fluorescent probe is opened and the P-dC is located in the ss-DNA, thus resulting in strong fluorescence. The effective discrimination of the SNP, including single base mismatch ss-DNA (A, T, G) and double mismatch DNA (C, C), against perfect complementary ss-DNA was achieved by increased fluorescence intensity, and verified by thermal denaturation and circular dichroism spectroscopy. Relative fluorescence intensity had a linear relationship with the concentration of perfect complementary ss-DNA and ranged from 50 nM to 3.0 μM. The linear regression equation was F/F₀ = 2.73 C (μM) + 1.14 (R = 0.9961) and the detection limit of perfect complementary ss-DNA was 16 nM (S/N = 3). This study demonstrates that a hairpin DNA containing nucleotide base analog P-dC is a promising fluorescent probe for the effective discrimination of SNP and for highly sensitive detection of perfect complementary DNA.     

A calixarene based fluorescent Sr2+ and Ca2+ probe

A fluorescent probe, PyCalix, which has two pyrene moieties at the lower rim of a calix[4]arene fixed in the cone conformation was synthesized and its complexation behavior with alkali and alkaline earth cations was studied by fluorescence spectrometry. The compound showed intramolecular excimer emission at approximately 480 nm in the fluorescence spectra. Upon complexation with alkaline earth metal cations, a decrease of excimer emission was observed. The decrease of excimer emission was accompanied by an increase of monomer emission of pyrenes at 397 nm. The order of complexation constants of PyCalix with metal ions was Sr(+ approximately Ca2+ > Ba2+ > Mg2+ > K+ > Na+ > Cs+ for all reagents. PyCalix doped polyvinyl chloride (PVC) membrane was fabricated and our results showed that this membrane can be used for selective detection of Sr2+.     

Electrochemical biosensor for microRNA detection based on hybridization protection against nuclease S1 digestion

Nuclease S1 can catalyze the nonspecific endo- and exonucleolytic cleavage of single-stranded DNA and RNA to yield nucleoside 5′-phosphates and 5′-phosphooligonucleotides. However, it cannot hydrolyze double-stranded DNA, double-stranded RNA, or DNA-RNA hybrid. Inspired by this specific property, a simple electrochemical method was developed for microRNA detection based on hybridization protection against nuclease S1 digestion. In the absence of hybridization process, the assembled probe DNA on the electrode surface can be easily digested by nuclease S1 and a strong electrochemical signal can be generated due to the decreased repulsive force towards the redox probe. However, after hybridization with target microRNA, the digestion activity of nuclease S1 is inhibited, which can lead to a weak electrochemical signal. Based on the change of the electrochemical signal, the detection of target microRNA-319a can be achieved. Under optimal experiment conditions, the electrochemical signal was proportional to microRNA-319a concentration from 1000 to 5 pM and the detection limit was 1.8 pM (S/N = 3). The developed method also showed high detection selectivity and reproducibility. Furthermore, the proposed method was successfully applied to assay the expression level of microRNA-319a in the leaves of rice seedlings after being incubated with different concentrations of 6-benzylaminopurine.     

Protease Probes that Enable Excimer Signaling upon Scission

Peptide‐based probes that fluoresce upon proteolytic cleavage are invaluable tools for monitoring protease activity. The read‐out of protease activity through pyrene excimer signaling would be a valuable asset because the large Stokes shift and the long lifetime of the excimer emission facilitate measurements in autofluorescent media such as blood serum. However, proteolytic cleavage abolishes rather than installs the proximity relationships required for excimer signaling. Herein, we introduce a new probe architecture to enable the switching on of pyrene excimer emission upon proteolytic scission. The method relies on hairpin‐structured peptide nucleic acid (PNA)/peptide hybrids with pyrene units and anthraquinone‐based quencher residues positioned in a zipper‐like arrangement within the PNA stem. The excimer hairpin peptide beacons afforded up to a 50‐fold enhancement of the pyrene excimer emission. Time‐resolved measurements allowed the detection of matrix metalloprotease 7 in human blood serum.     

Highly sensitive determination of ssDNA and real-time sensing of nuclease activity and inhibition based on the controlled self-assembly of a 9,10-distyrylanthracene probe

We report here a fluorescent biosensor for highly sensitive determination of single-stranded DNA (ssDNA) with remarkable fluorescence enhancement and label-free sensing of S1 nuclease activity and inhibition in real time based on ssDNA-controlled self-assembly of a 9,10-distyrylanthracene (DSA) probe with the aggregation-induced emission (AIE) property, thereby avoiding a sophisticated fabrication process and aggregation-caused quenching (ACQ) effect. Compared with previous technologies, this assay has some advantages. First, since the DSA probe can be synthesized through a simple and effective synthetic route and the sensing technology adopts the unlabelled ssDNA, this biosensor shows advantages of simplicity and cost efficiency. Besides, for the determination of ssDNA, S1 nuclease, and inhibitor, the DSA-based probe provides high sensitivity and a good linear relationship due to the AIE property. As a result, we determined the DNA 24-mer concentration as low as 150 pM, and we are able to detect ssDNA lengths with a linear range from 6mer to 24mer (R?=?0.998) as well as DNA 24-mer concentrations with a linear range from 0 to 200 nM (R?=?0.998) and S1 nuclease concentrations with a linear range from 6 to 32 U ml^?1 (R?=?0.995), respectively. Moreover, the fluorescent intensity with various concentrations of S1 nuclease becomes highly discriminating after 3–16 min. Thus, it is possible to detect nuclease activity within 3–16 min, which demonstrates another advantage of a quick response of the present biosensor system.     

A fluoride-selective PCT chemosensor based on formation of a static pyrene excimer

[reaction: see text] Calixarene-based fluorescent chemosensor 1 with two fluorogenic pyrene units conjugated to amide groups as guest recognition sites is synthesized. Complexation of F(-) by 1 causes a red shift of its absorption band to 400 nm (Deltalambda = 54 nm) and a blue shift of the excimer emission to 470 nm (Deltalambda = 12 nm) together with enhanced fluorescence intensity. The blue-shifted excimer emission is attributed to a pyrene dimer formed in the ground state, a so-called static excimer.     

Dual pyrene-labeled pyrrolidinyl peptide nucleic acid as an excimer-to-monomer switching probe for DNA sequence detection

The unique ability of pyrene to form excimers with distinct emission characteristic from monomer offers an attractive means to signal the interactions between biomolecules. In this work, dual pyrene-labeled pyrrolidinyl peptide nucleic acid probe with a d-prolyl-2-aminocyclopetanecarboxylic acid α,β-dipeptide backbone (acpcPNA) was designed as an excimer-to-monomer switching probe for DNA sequence detection. In single stranded state, the excimer emission at 470 nm was mainly observed in the fluorescence spectrum. In the presence of DNA target, the hybridization resulted in separation of the two pyrene units, therefore the spectrum displayed increased monomer emission at 380 nm with concomitant decreased excimer emission. Switching ratio, which is defined as the ratio of the monomer to excimer in the double stranded form [F₃₈₀/F₄₇₀(ds)] divided by the same value obtained from the single stranded form [F₃₈₀/F₄₇₀(ss)], was used to describe the performance of the probes. Switching ratios in the range of 5–30 were observed with various dual pyrene-labeled acpcPNA probes bearing pyrenebutyryl label attached five-base apart. Practically no excimer-to-monomer switching behavior was observed with DNA targets carrying a single mismatched base as shown by the small switching ratios of ∼1.     

Cu2+-induced blue shift of the pyrene excimer emission: a new signal transduction mode of pyrene probes

A pentiptycene-bispyrenyl system (1) has been synthesized and investigated as a fluorescent chemosensor for metal ions. A novel blue shift along with an intensity enhancement of the pyrene excimer emission is observed for 1 in the presence of Cu(2+). Such a new signal transduction mode of pyrene probes results from the formation of a static pyrene excimer that has very different characteristics from its dynamic counterpart.     

A self-assembled deoxyribonucleic acid concatemer for sensitive detection of single nucleotide polymorphism

Polymerase-free and label-free strategies for DNA detection have shown excellent sensitivity and specificity in various biological samples. Herein, we propose a method for single nucleotide polymorphism (SNP) detection by using self-assembled DNA concatemers. Capture probes, bound to magnetic beads, can joint mediator probes by T4 DNA ligase in the presence of target DNA that is complementary to the capture probe and mediator probe. The mediator probes trigger self-assembly of two auxiliary probes on magnetic beads to form DNA concatemers. Separated by a magnetic rack, the double-stranded concatemers on beads can recruit a great amount of SYBR Green I and eventually result in amplified fluorescent signals. In comparison with reported methods for SNP detection, the concatemer-based approach has significant advantages of low background, simplicity, and ultrasensitivity, making it as a convenient platform for clinical applications. As a proof of concept, BRAF^T1799A oncogene mutation, a SNP involved in diverse human cancers, was used as a model target. The developed approach using a fluorescent intercalator can detect as low as 0.1 fM target BRAF^T1799A DNA, which is better than those previously published methods for SNP detection. This method is robust and can be used directly to measure the BRAF^T1799A DNA in complex human serum with excellent recovery (94–103%). It is expected that this assay principle can be directed toward other SNP genes by simply changing the mediator probe and auxiliary probes.     

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.     

Unique blue shift due to the formation of static pyrene excimer: highly selective fluorescent chemosensor for Cu

New binaphthyl derivatives bearing pyrene groups have been synthesized and studied as fluorescent chemosensors for Cu²⁺ ions. A unique blue shift along with fluorescent enhancement in pyrene excimer emission was observed, which were induced by the formation of a static pyrene excimer.     

Selective and sensitive ratiometric detection of Hg(II) ions using a simple amino acid based sensor

Synthesis of a novel pyrene derivative sensor (Py-Met) based on amino acid and its fluorescent behavior for Hg(II) in water was investigated. Upon Hg(II) binding, the Py-Met-bearing sulfonamide group exhibited a considerable excimer emission at 480 nm along with a decrease of monomer emission at 383 nm. Py-Met allows a selective and sensitive ratiometric detection of Hg(II) without any interference from other metal ions.     

Fluorescence light-up recognition of DNA nucleotide based on selective abasic site binding of an excited-state intramolecular proton transfer probe

DNA single-nucleotide polymorphism (SNP) detection has attracted much attention due to mutation-related diseases. Various fluorescence methods for SNP detection have been proposed and many are already in use. However, fluorescence enhancement for signal-on SNP identification without label modification still remains a challenge. Here, we find that the abasic site (AP site) in a DNA duplex can be developed as a binding pocket favorable for the occurrence of the excited-state intramolecular proton transfer (ESIPT) of a 3-hydroxyflavone, fisetin, which is used as a proof of concept for effective SNP identification. Fisetin binding at the AP site is highly selective for target thymine or cytosine facing the AP site by observation of a drastic increase in the ESIPT emission band. In addition, the target recognition selectivity based on this ESIPT process is not affected by flanking bases of the AP site. The binding selectivity of fisetin at the AP site is also confirmed by measurements of fluorescence resonance energy transfer, emission lifetime and DNA melting. The fluorescent signal-on sensing for SNP based on this fluorophore is substantially advantageous over the previously used fluorophores such as the AP site-specific signal-off organic ligands with a similar fluorescing mechanism before and after binding to DNA with hydrogen bonding interaction. We expect that this approach will be employed to develop a practical SNP detection method by locating an AP site toward a target and employing an ESIPT probe as readout.     

Probe accessibility effects on the performance of electrochemical biosensors employing DNA monolayers

Surface-confined DNA probes are increasingly used as recognition elements (or presentation scaffolds) for detection of proteins, enzymes, and other macromolecules. Here we demonstrate that the density of the DNA probe monolayer on the gold electrode is a crucial determinant of the final signalling of such devices. We do so using redox modified single-stranded and double-stranded DNA probes attached to the surface of a gold electrode and measuring the rate of digestion in the presence of a non-specific nuclease enzyme. We demonstrate that accessibility of DNA probes for binding to their macromolecular target is, as expected, improved at lower probe densities. However, with double-stranded DNA probes, even at the lowest densities investigated, a significant fraction of the immobilized probe is inaccessible to nuclease digestion. These results stress the importance of the accessibility issue and of probe density effects when DNA-based sensors are used for detection of macromolecular targets.     

Fluorescent and Electrochemical Sensing of Polyphosphate Nucleotides by Ferrocene Functionalised with Two ZnII(TACN)(pyrene) Complexes

The [Fc? bis{Zn^II(TACN)(Py)}] complex, comprising two Zn^II(TACN) ligands (Fc=ferrocene; Py=pyrene; TACN=1,4,7‐triazacyclononane) bearing fluorescent pyrene chromophores linked by an electrochemically active ferrocene molecule has been synthesised in high yield through a multistep procedure. In the absence of the polyphosphate guest molecules, very weak excimer emission was observed, indicating that the two pyrene‐bearing Zn^II(TACN) units are arranged in a trans‐like configuration with respect to the ferrocene bridging unit. Binding of a variety of polyphosphate anionic guests (PPi and nucleotides di‐ and triphosphate) promotes the interaction between pyrene units and results in an enhancement in excimer emission. Investigations of phosphate binding by ³¹P NMR spectroscopy, fluorescence and electrochemical techniques confirmed a 1:1 stoichiometry for the binding of PPi and nucleotide polyphosphate anions to the bis(Zn^II(TACN)) moiety of [Fc? bis{Zn^II(TACN)(Py)}] and indicated that binding induces a trans to cis configuration rearrangement of the bis(Zn^II(TACN)) complexes that is responsible for the enhancement of the pyrene excimer emission. Pyrophosphate was concluded to have the strongest affinity to [Fc? bis{Zn^II(TACN)(Py)}] among the anions tested based on a six‐fold fluorescence enhancement and 0.1 V negative shift in the potential of the ferrocene/ferrocenium couple. The binding constant for a variety of polyphosphate anions was determined from the change in the intensity of pyrene excimer emission with polyphosphate concentration, measured at 475 nm in CH₃CN/Tris‐HCl (1:9) buffer solution (10.0 mM , pH 7.4). These measurements confirmed that pyrophosphate binds more strongly (K_b=(4.45±0.41)×10⁶ M ^?1) than the other nucleotide di‐ and triphosphates (K_b=1–50×10⁵ M ^?1) tested.     

荧光探针法研究壳聚糖水凝胶形成过程及其性能

基于芘(Py)单体荧光光谱结构对微观环境变化的敏感性,以及介质粘度及Py分子间距对Py激基络缔合物形成的影响,以戊二醛交联壳聚糖(CS)水凝胶体系为例研究了Py荧光探针法监测水凝胶形成过程及其溶胀性能的可行性。结果表明,Py荧光光谱精细结构的变化(以I~3/I~1为参量)或Py激基缔合物荧光强度与单体荧光强度之比(I~E/I~M)的变化与CS水凝胶的形成及溶胀程度有很好的对应关系。此外,CS凝胶网状结构中包埋的聚N-异丙基丙烯酰胺(PNIPAM)的构象变化也可由探针光谱变化反映出来。利用这种荧光探针方法有助于从分子水平上探知凝胶形成过程的微观本质。此外,这种方法也可作为光纤传导监测凝胶形成过程和溶胀的基础。