Bispyrenyl Excimer Fluorescence: A Sensitive Oligonucleotide Probe

DNA Strand Displacement with Base Pair Stabilizers: Purine-2,6-Diamine and 8-Aza-7-Bromo-7-Deazapurine-2,6-Diamine Oligonucleotides Invade Canonical DNA and New Fluorescent Pyrene Click Sensors Monitor the Reaction

Purine-2,6-diamine and 8-aza-7-deaza-7-bromopurine-2,6-diamine 2'-deoxyribonucleosides (1 and 2) were implemented in isothermal DNA strand displacement reactions. Nucleoside 1 is a weak stabilizer of dA-dT base pairs, nucleoside 2 evokes strong stabilization. Strand displacement reactions used single-stranded invaders with single and multiple incorporations of stabilizers. Displacement is driven by negative enthalpy changes between target and displaced duplex. Toeholds are not required. Two new environmental sensitive fluorescent pyrene sensors were developed to monitor the progress of displacement reactions. Pyrene was connected to the nucleobase in the invader or to a dendritic linker in the output strand. Both new sensors were constructed by click chemistry; phosphoramidites and oligonucleotides were prepared. Sensors show monomer or excimer emission. Fluorescence intensity changes when the displacement reaction progresses. Our work demonstrates that strand displacement with base pair stabilizers is applicable to DNA, RNA and to related biopolymers with applications in chemical biology, nanotechnology and medicinal diagnostics.

Applications of the Reversible Boronic Acids/Boronate Switch to Nucleic Acids

Over the last decades, boron and nucleic acids chemistries have gained a lot of attention for biological, medicinal and analytical applications. Our laboratory has a long-standing interest in both chemistries and owing to the ability of boronic acids to react with cis-diol function in aqueous media we developed over the years a variety of applications ranging from molecular recognition and sensing to the development of reversible dynamic systems in which the natural phosphodiester linkage was replaced by a boronate. In this account, we summarize research results from our group from our preliminary studies on molecular recognition of ribonucleosides to the dynamic assembly of functional DNAzymes. In particular, the various parameters influencing the dynamic nature of these reversible covalent bonds able to respond to external stimuli are discussed. Finally, current challenges and opportunities for boron-based nucleic acids are also addressed.

Technical Evaluation of Commercial Sperm DFI Quality Control Products in SCSA Testing

With the increase in population and the advancement of medicine, people even more hope that their offspring will be healthier. DNA fragmentation rate is currently one of the more common indicators for evaluating sperm fertility and predicting the outcome of pregnancy. In order to evaluate the technical performance and application value of commercial sperm DFI (DNA fragmentation index) quality control products in the flow cytometry sperm chromatin structure analysis (SCSA), this paper uses flow cytometry to test commercial sperm DFI quality control products (Celula) and laboratory routine self-made DFI quality control products. In this paper, the quality control of new commercial sperm DFI and laboratory-made quality control were compared and tested for 30 consecutive days. And this paper monitors the response of commercial quality control products to the interference of key reagent parameters. This paper compares the stability of the test results of two quality control products and their sensitivity to the interference of key performance parameters of the detection reagent. Experimental results show that commercial sperm DFI quality control products can simulate sperm DNA damage to achieve accurate detection of DNA integrity. The stability of commercial sperm DFI quality control (CV = 2.47%) is better than that of laboratory-made quality control (CV = 11.22%). The new commercial sperm DFI quality control product can sensitively detect changes in the concentration of acidified solution and staining solution at the same time. It can effectively control the quality of detection reagents and experimental procedures. The new commercial sperm DFI quality control product can effectively control sperm DNA integrity testing. It can be used as an external quality control product for quality control of test results to ensure that more accurate test results are provided to the clinic.

Pyrene based materials as fluorescent probes in chemical and biological fields

Molecules that experience a change in their fluorescence emission due to the effect of fluorescence enhancement upon binding events, like chemical reactions or a change in their immediate environment, are regarded as fluorescent probes.

Organic Dots Embedded in Mesostructured Silica Xerogel as High-Performance ECL Emitters: Preparation and Application for MicroRNA-126 Detection

Unlike the organic micro/nanocrystals prepared using an emerging reprecipitation method, a novel method of embedding 1-pyrenecarboxaldehyde dots (PycDs) into a mesostructured silica xerogel (PycDs@MSX) for use as electrochemiluminescence (ECL) emitters was first proposed to achieve an extremely strong ECL response, with peroxydisulfate (S₂O₈^2-) used as a coreactant. In this method, (i) PycDs@MSX could ensure the reversal of the PycDs environment from hydrophobic to hydrophilic and (ii) PycDs@MSX could provide massive porous channels, allowing for access of hydrophilic reactive intermediates (i.e., sulfate anion radicals, SO₄^•-), which could accelerate the rate of mass transfer and electron transfer between S₂O₈^2- and PycDs. Using Ag nanoparticles as a coreaction accelerator and a 3D DNA nanomachine as a signal amplification strategy, the proposed ECL biosensing platform was constructed and achieved ultrasensitive detection of microRNA-126 with an excellent linear range (from 100 aM to 100 pM) and a low detection limit (13.0 aM). More importantly, this work not only developed an innovative avenue to improve the ECL efficiency of organic emitters in aqueous phases but also provided a powerful strategy for biochemical analysis and disease diagnosis applications.

Sensitive discrimination of glycoproteins and cell differentiation with an array sensing platform exploiting pyrene-derived amphiphile/surfactant assemblies

An array sensing platform exploiting phenyl boronic acid-functionalized pyrene amphiphile/surfactant assemblies is constructed for glycoprotein discrimination, achieving a discrimination sensitivity of 50 nM. Gastric cancer cell lines of various differentiation grades are successfully discriminated, demonstrating its great potential in sensitive differentiation of glycoprotein-related samples in biomedical diagnosis.

Photophysical Properties of an Azine-Linked Pyrene-Cinnamaldehyde Hybrid: Evidence of Solvent-Dependent Charge-Transfer-Coupled Excimer Emission

We report the photophysical properties of a synthetic asymmetric azine-based compound (17Z,18E)-4'-((E)-3-phenylallylidene)-1'-(dimethylamino)-1-((pyren-8-yl)methylene)hydrazine (PYNC). The molecule PYNC shows an appreciable red shift in the emission maximum in a wide range of solvents. In water, PYNC shows the characteristic feature of excimer formation exclusively. However, in all other solvents, the excimer band is present alongside the charge transfer emission band. The assignment of charge transfer and excimer bands has been established by various steady-state emission spectral data. PYNC, owing to this novel excimer-coupled charge transfer phenomenon, can be a potential probe for studying various supramolecular assemblies of biological interest.

Spectroscopic study of fluorescent probes based on G-quadruplex oligonucleotides labeled with ethynylpyrenyldeoxyuridine

The design, synthesis, and spectral properties of four pyrene labeled oligonucleotide probes with G-quadruplex structure (Tel22-Tpy, Tel22-Upy, Tel22-6Upy, Tel22-18Upy) based on the 22-mer human telomeric sequence (Tel22) have been reported. Pyrene labels in the form of ethynylpyrenyldeoxyuridine have been inserted efficiently into oligodeoxynucleotides probes using phosphoramidite chemistry. The probes exhibited abilities to fold into G-quadruplex structures and to bind metal cations (Na⁺ and K⁺). Folding properties of probes and their spectral behavior were examined by recording the UV-vis, fluorescence, and CD spectra as well as by analyzing melting profiles. Fluorescence characteristics and G-quadruplex folding of probes were also studied at the interface of cationic dioctadecyldimethylammonium bromide (DODAB) monolayer. Investigations included film balance measurements (π-A isotherms) and fluorescence spectra recording using a fiber optic accessory interfaced with a spectrofluorimeter.

Diverse size approach to incorporate and extend highly fluorescent unnatural nucleotides into DNA

We have prepared a series of size-diverse unnatural nucleotides containing fluorescent (dApyrTP, dUpyrTP, dUantTP, dUthiTP) and quencher (dUazoTP) units, as well as nucleotides presenting small functional groups (dAethTP, dAoctTP, dUethTP, dUiodTP), all based on deoxyadenosine and deoxyuridine, and examined their suitability for use in enzymatic incorporation and extension into DNA. We observed a size-dependence of the incorporation and extension capability (following the order dUiodTP=dUethTP=dUthiTP>dUazoTP>dUpyrTP>dUantTP) during primer extension. This result was supported by circular dichroism (CD) spectra, which revealed a trend in the different B-form DNA structures depending on the size of the unit at the 5-position of the deoxyuridine (dUiodTP>dUethTP>dUthiTP>dUpyrTP), obtained from the PCR products. Interestingly, dUthiTP could be incorporated and extended into long DNA strands during primer extension and even PCR amplification, with CD spectroscopy confirming a stable secondary B-form duplex DNA structure. We observed full-length extension products even when combining dUthiTP with a template containing 24 continuous dA units during the primer extension. Thus, we believe that dUthiTP is a promising fluorescent nucleotide for a diverse range of biological applications requiring multiple incorporation and extension directly without disruption of B-form DNA structures.

Two-step FRET mediated metal ion induced signalling responses in a probe appended with three fluorophores

A tri-fluorophore appended Tren receptor based probe exhibited chelation induced ratiometric fluorescence signalling through a two-step FRET process; enhancement of F_An→ F_Rhenergy transfer efficiency through an F_NBDintermediate was observed.

A single thiazole orange molecule forms an exciplex in a DNA i-motif

A fluorescent exciplex of thiazole orange (TO) is formed in a single-dye conjugated DNA i-motif. The exciplex fluorescence exhibits a large Stokes shift, high quantum yield, robust response to pH oscillation and little structural disturbance to the DNA quadruplex, which can be used to monitor the folding of high-order DNA structures.

An intermolecular pyrene excimer in the pyrene-labeled N-thiophosphorylated thiourea and its nickel(ii) complex

(1-pyrene)NHC(S)NHP(S)(OiPr)₂ (HL) and its Ni^II complex ([NiL2]) have been synthesized. Both HL and [NiL2] were found to be emissive in solution of CH₂Cl₂, which is due to the concentration dependent emission of the pyrene monomer and excimer.

Hetero-Selective DNA-Like Duplex Stabilized by Donor-Acceptor Interactions

We report on the characterization of a novel hetero-selective DNA-like duplex of pyrene and anthraquinone pseudo base pairs. The pyrene/anthraquinone pairs showed excellent selectivity in hetero-recognition and even trimers were found to form a hetero-duplex. Pyrene and anthraquinone moieties were tethered on acyclic D-threoninol linkers and linked to adjacent residues by using standard phosphoramidite chemistry. When pyrene and anthraquinone were incorporated at pairing positions in complementary strands of natural DNA oligonucleotides, the duplex was stabilized significantly. Moreover, a pyrene hexamer and an anthraquinone hexamer formed a stable artificial hetero-duplex without the assistance of natural base pairs. The pyrene/anthraquinone pair was so stable that even trimers formed a hetero-duplex under conditions in which natural DNA strands of three residues do not.

Ratiometric sensing of lysine through the formation of the pyrene excimer: experimental and computational studies

Lysine assisted ratiometric monomer to excimer conversion of pyrene derivatives allows intracellular lysine detections.

Non-natural G-quadruplex in a non-natural environment

The biocompatibility as well as the sustainability of a deep eutectic solvent makes it a good substitute for aqueous media in studying biomolecules. Understanding the structure and stability of natural and non-natural G-quadruplexes in aqueous and highly viscous media will be useful in biological and nanodevice applications. We report the synthesis and conformational analysis of a model G-rich oligonucleotide G3T3 and non-natural G-rich sequences Pyr1-Pyr3 in aqueous and highly viscous media. Progressive increases in the loop replacement with a non-natural pyrene linker leads to a systematic increase of the thermal denaturation temperature of the modified G-rich oligonucleotides Pyr1-Pyr3 in 10 mM cacodylate buffer (pH 7.2) containing 100 mM KCl, as monitored using UV-Vis spectroscopy. A circular dichroism signal clearly revealed the formation of a predominantly anti-parallel vs. parallel conformation in the natural G-rich oligonucleotide G3T3 as well as the non-natural G-rich oligonucleotides Pyr1-Pyr3 in 10 mM cacodylate buffer (pH 7.2) containing 100 mM KCl. On the other hand, we observed thermodynamic destabilization of G-rich oligonucleotides in a deep eutectic solvent (DES; 1 : 2 choline chloride-urea) containing 100 mm KCl with an increase in loop replacements. Interestingly, we observed an exclusively parallel G-quadruplex conformation in the case of G3T3 in DES containing 100 mm KCl. While pyrene containing G-rich oligonucleotides Pyr1-Pyr3 exhibited a predominantly parallel vs. anti-parallel G-quadruplex conformation in DES containing 100 mM KCl.

A bispyrene derivative as a selective fluorescent probe for RNA

A novel bispyrene compound was synthesized to selectively detect RNA through excimer emission “turn-on” at physiological pH.

Highly emissive water-soluble tetraazaperopyrenes as fluorescent markers

Synthesis of highly fluorescent water-soluble tetraazaperopyrene (TAPP) derivatives is reported; these act as fluorescent markers for cell nuclei.

Switching selectivity between Pb2+ and Hg2+ ions through variation of substituents at xanthene end; ‘turn-on’ signalling responses by FRET modulation

Substitution at amino groups attached to the xanthene core modulates the stereo-electronic situation to switch selectivity; a FRET mediated signalling with a distinctive coupling of fluorophores.

Observation of the rare chrysene excimer

Formation of the so far elusive chrysene excimer in solution is achieved by using DNA as a supramolecular scaffold.

Multipyrene tandem probes for point mutations detection in DNA

Here we report design, synthesis and characterization of highly sensitive, specific and stable in biological systems fluorescent probes for point mutation detection in DNA. The tandems of 3'- and 5'-mono- and bis-pyrene conjugated oligo(2'-O-methylribonucleotides), protected by 3'-"inverted" thymidine, were constructed and their potential as new instruments for genetic diagnostics was studied. Novel probes have been shown to exhibit an ability to form stable duplexes with DNA target due to the stabilizing effect of multiple pyrene units at the junction. The relationship between fluorescent properties of developed probes, the number of pyrene residues at the tandem junction, and the location of point mutation has been studied. On the basis of the data obtained, we have chosen the probes possessing the highest fluorescence intensity along with the best mismatch discrimination and deletion and insertion detection ability. Application of developed probes for detection of polymorphism C677T in MTHFR gene has been demonstrated on model systems.

New probe design strategy by cooperation of metal/DNA-ligation and supermolecule inclusion interaction: application to detection of mercury ions(II)

In this paper, the development is described of an efficient pyrene excimer signaling-based fluorescent sensor for the measurement of mercury ions in aqueous solutions based on thymine-Hg(2+)-thymine (T-Hg(2+)-T) coordination chemistry and the inclusion interaction of γ-cyclodextrin. Introduction of cyclodextrin can provide cooperation for the molecular level space proximity of the two labeled pyrene molecules, moreover the hydrophobic cavity of γ-cyclodextrin can also offer protection for the pyrene dimer's emission from the quenching effect of Hg(2+) and enhance the fluorescence intensity of the pyrene excimer. To demonstrate the feasibility of the design, a bis-pyrene-labeled thymine-rich DNA strand was used as the detection probe. In the presence of Hg(2+), stem-close-shaped DNA strands can be formed with the cooperation of γ-cyclodextrin and ideally predominantly emit the excimer fluorescence. The selectivity of the sensor for Hg(2+) against other biologically and environmentally related metal ions is outstanding due to the high specificity of T-Hg(2+)-T formation. In addition, the pyrene excimer has a long fluorescence lifetime, which can tolerate intense background fluorescence interference from complex biological components, making it potentially applicable in the analysis of complex biological samples.

Control of aggregation-induced emission by DNA hybridization

Aggregation-induced emission (AIE) was studied by hybridization of dialkynyl-tetraphenylethylene (DATPE) modified DNA strands. Molecular aggregation and fluorescence of DATPEs are controlled by duplex formation.

Fluorescent sensing and discrimination of ATP and ADP based on a unique sandwich assembly of pyrene-adenine-pyrene

It is still a challenging task to discriminate adenosine-5'-triphosphate (ATP) from various nucleoside triphosphates, such as GTP, CTP, UTP, and TTP. The ability to distinguish ATP from adenosine diphosphate (ADP) by fluorescent signals is also urgently desired. Herein, we report two pyrene-based zinc complexes as nucleoside polyphosphate receptors with high selectivity for ATP and ADP based on fluorescence and NMR studies. A unique pyrene-adenine-pyrene sandwich assembly was observed in the case of compound 1 with ATP or ADP, resulting in the increase of monomer fluorescence intensity; whereas the other bases of nucleoside triphosphates, such as GTP, CTP, UTP, and TTP were not sandwiched, resulting in a switch in the monomer-excimer fluorescence of pyrene. The different binding patterns of various nucleobases with a pyrene-pyrene assembly make 1 a highly selective fluorescent sensor for ANP (N=di, tri). In the case of compound 2, the first 0.5 equivalents of ATP induced a strong excimer emission, whilst ADP induced a large enhancement in the monomeric fluorescent peak. This fluorescence change makes 2 an efficient sensor to discriminate ATP from ADP.

An aptamer-based and pyrene-labeled fluorescent biosensor for homogeneous detection of potassium ions

A simple and homogeneous method based on aptamer and pyrene moieties for the detection of K(+) was developed. The aptamer was labeled by pyrene moiety at 3' end as the molecular recognition element. In the presence of K(+), the complementary oligonucleotide labeled by pyrene moiety at 5' end was displaced from the aptamer, which was accompanied by a dramatic decrease of the excimer fluorescence of pyrene. However, the excimer fluorescence remains in the absence of the target. With optimum conditions, relative changes of the pyrene excimer fluorescence intensity were proportional to the concentrations of K(+) in the range of 6.3 × 10(-4) to 1.0 × 10(-2) M with a detection limit of 5.0 × 10(-4) M. Importantly, in the presence of Na(+), NH(4)(+), Mg(2+) and Ca(2+) cations of biological fluids, this method was able to detect K(+) with high selectivity. In a word, the assay seems to have great potential applications, especially in biological fluids due to its simplicity, specificity and homogeneous detection.

Supramolecular chemical sensors based on pyrene monomer-excimer dual luminescence

The past ten years have seen a spectacular development of chemical sensors based on the monomer-excimer dual luminescence of aromatic systems, such as pyrene. Either in the form of integrated or multicomponent molecular devices these chemosensors have been attracting a high interest above all because of their unique ratiometric properties. This review will focus on the latter systems, which can be classified into two classes: Firstly, the assembly of receptor-effector conjugates is triggerred by the analyte of interest. As a result, the sensor shows monomer to excimer fluorescence switching upon substrate binding. Secondly, the supramolecular assembly that constitutes the sensor is perturbed by interaction with the analyte. This induces a conformational change or the exchange of a component of the system, which is the cause of the luminescence switch effect.

Fluorescent and electrochemical sensing of polyphosphate nucleotides by ferrocene functionalised with two Zn(II)(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 (31)P 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 CH(3)CN/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) x 10(6) M(-1)) than the other nucleotide di- and triphosphates (K(b)=1-50 x 10(5) M(-1)) tested.

Homogeneous assays using aptamers

Aptamers are DNA or RNA oligonucleotides that can bind with high affinity and specificity to a wide range of targets such as proteins, metal ions or pathogenic microorganisms. Soluble aptamers and aptazymes have been used as sensing elements for developing homogeneous assays in a solution phase, the whole sensing process being carried out in a homogeneous solution. Contrary to most conventional heterogeneous assays that are time-consuming and labor-intensive, aptamer-based homogeneous assays are simple, easy-to-perform, rapid and do not require immobilization nor washing steps. To our knowledge, this review is the first entirely dedicated to aptamer-based homogeneous assays. Optical detection appears as the most developed technique. Colorimetry represents the simplest sensing mode that occupies a very important position among aptamer-based assays, involving gold nanoparticle aggregation (with unmodified or aptamer-modified gold NPs), the formation of HRP-mimicking DNAzyme with hemin, dye displacement or interactions with a cationic polymer. Fluorescence that is highly sensitive offers the most developed detection mode. Aptamers can be labeled or not, to give rise to turn-on or usually less sensitive turn-off fluorescent assays. Newly reported and thus less developed non-conventional magnetic resonance imaging (MRI) and electrochemistry also recently appeared in the literature, thrombin still remains the main detected target. Homogeneous assays based on aptazyme, an aptamer sequence connected to a known ribozyme motif, are also described in this review, involving optical detection, by colorimetry or fluorescence.

A new fluorescent sensor based on 1H-pyrazolo[3,4-b]quinoline skeleton. Part 2

A novel fluorescent dye bis-(pyridin-2-yl-methyl)-(1,3,4-triphenyl-1H-pyrazolo[3,4-b]quinolin-6-ylmethyl)-amine (P1) has been synthesized and investigated by means of steady state and time-resolved fluorescence techniques. This compound acts as sensor for fluorescence detection of small inorganic cations (lithium, sodium, barium, magnesium, calcium, and zinc) in highly polar solvents such as acetonitrile. The mechanism which allows application of this compound as sensor is an electron transfer from the electron-donative part of molecule (amine) to the acceptor part (pyrazoloquinoline derivative), which is retarded upon complexation of the electro-donative part by inorganic cations. The binding constants are strongly dependent on the charge density of the analyzed cations. The 2/1 complexes of P1 with Zn⁺⁺ and Mg⁺⁺ cations posses large binding constants. Moreover, in the presence of these cations a significant bathochromic shift of fluorescence is observed. The most probable explanation of such behaviour is the formation of intramolecular excimer. This is partially supported by the quantum chemical calculations.