Modulated drug release from the stem-and-loop structured oligodeoxynucleotide upon UV-A irradiation in the presence of target DNA

o-Nitrobenzyl photochemistry as induced by UV-A irradiation was applied to a photoactivated drug releasing system based on a molecular beacon strategy. A stem-and-loop structured oligodeoxynucleotide (ODN) possessing a photoreactive o-nitrobenzyl chromophore at the 3'-end and 1-aminonaphthalene quencher at the 5'-end underwent conformational change into a conventional double strand structure by hybridization with a specified target DNA. The intrinsic stem-and-loop structure suppressed photoactivated release of benzoic acid as a phantom drug from the o-nitrobenzyl chromophore because of intramolecular quenching by the 1-aminonaphthalene unit in close proximity to the chromophore. Formation of the double strand structure in the presence of perfectly matched target DNA minimized occurrence of intramolecular quenching and thereby enhanced the photoactivated drug release.     

Quencher-free molecular beacons: a new strategy in fluorescence based nucleic acid analysis

Molecular beacons (MBs) have been used as viable fluorescent probes in nucleic acid analysis. Many researchers around the world continue to modify the MBs to suit their needs. As a result, a number of nucleic acid probing systems with close resemblance to the MBs are being reported from time to time. Quencher-free molecular beacons (QF-MBs) are a significant modification of the conventional MB; in QF-MBs the quencher part has been eliminated. Despite the absence of the quencher, the QF-MBs can identify specific target DNA. They can also be used in SNP typing and in real-time PCR analysis for quantification of DNAs. The design, factors behind functioning and applications of different types of QF-MBs and closely related quencher-free nucleic acid probing systems (QF-NAPs) have been described in this tutorial review.     

Quencher as leaving group: efficient detection of DNA-joining reactions

We describe a new fluorescence reporting strategy in which dabsyl, a well-known quencher, activates a hydroxyl group in a probe to convert it to a leaving group. When a nucleophilic phosphorothioate probe binds adjacent to a dabsyl quenched probe, autoligation occurs, releasing the quencher, and lighting up the probes, This signal change can be used to detect single nucleotide differences in DNA without enzymes or reagents.     

Transverse location of new fluorene based depth dependent fluorescent probes in membranes--quenching studies with 9,10-dibromostearic acid

Fluorescence quenching technique has been used to determine the transverse location of the fluorescent fluorenyl fatty acids in single bilayer vesicles prepared from phosphatidylcholine. The fluorenyl fatty acids used here are 2-fluorenyl acetic, butyric, hexanoic and octanoic acid. In addition a new type of fluorescent probe, 7-n-butyl-fluorene-2-butyric acid, wherein a hydrophobic tail is attached to 2-fluorenyl-butyric acid has also been used to study its effect on alignment of these probes in the membrane. The association properties of the quencher 9,10-dibromostearic acid have been analysed. It is observed that the quencher association involves partitioning into the vesicles and does not involve any binding to the vesicles. The absolute partition coefficient of the 9,10-dibromostearic acid which partitions between the aqueous and the lipid phases of the phospholipid dispersion has been evaluated. Using this information the corrected Stern-Volmer plots were drawn and the bimolecular quenching constant evaluated.     

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。     

Intramolecular dimers: a new strategy to fluorescence quenching in dual-labeled oligonucleotide probes

Many genomics assays use profluorescent oligonucleotide probes that are covalently labeled at the 5' end with a fluorophore and at the 3' end with a quencher. It is generally accepted that quenching in such probes without a stem structure occurs through F?rster resonance energy transfer (FRET or FET) and that the fluorophore and quencher should be chosen to maximize their spectral overlap. We have studied two dual-labeled probes with two different fluorophores, the same sequence and quencher, and with no stem structure: 5'Cy3.5-beta-actin-3'BHQ1 and 5'FAM-beta-actin-3'BHQ1. Analysis of their absorption spectra, relative fluorescence quantum yields, and fluorescence lifetimes shows that static quenching occurs in both of these dual-labeled probes and that it is the dominant quenching mechanism in the Cy3.5-BHQ1 probe. Absorption spectra are consistent with the formation of an excitonic dimer, an intramolecular heterodimer between the Cy3.5 fluorophore and the BHQ1 quencher.     

DNA adsorbed on graphene and graphene oxide: Fundamental interactions,desorption and applications

Interfacing DNA oligonucleotides with graphene-based materials, especially graphene oxide, has produced many new sensors and devices. Since graphene oxide is an excellent fluorescence quencher, fluorescently labeled DNAs (probes) are nearly fully quenched upon adsorption. Addition of the complementary DNA results in probe desorption and fluorescence enhancement. Aside from its analytical applications, this system provides a fascinating topic for biointerface science. DNA can be adsorbed by graphene oxide via π–π stacking and hydrogen bonding, while it must overcome electrostatic repulsion at the same time. The mechanism of DNA-induced probe desorption has also been a topic of extensive discussion. In this article, DNA adsorption and desorption reactions and interactions with graphene oxide and related materials (e.g. graphene) are reviewed based on the current understandings. A few representative applications based on these processes are also described briefly.     

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.     

A new approach for the detection of carbon-centered radicals in enzymatic processes using prefluorescent probes

In this communication we propose a novel application for prefluorescent probes in the detection of free carbon-centered radicals in enzymatic processes. Prefluorescent probes combine a fluorescent moiety tethered to a paramagnetic nitroxide that acts as a fluorescence quencher. Trapping of a radical by the nitroxide group restores the fluorescence properties. The increase in fluorescence intensity with time reflects the formation and quenching of carbon-centered radicals and can be used for the quantitative evaluation of yields and kinetics. As a test system we used horseradish peroxidase, an oxidoreductase that is widely accepted to operate by a radical-mediated mechanism. We used the prefluorescent probe (quinoline-TEMPO), where a quinoline moiety has been tethered to 2,2,6,6-tetramethylpiperidin-1-oxyl.     

Time gating improves sensitivity in energy transfer assays with terbium chelate/dark quencher oligonucleotide probes

Lanthanides are attractive as biolabels because their long luminescence decay rates allow time-gated detection, which separates background scattering and fluorescence from the lanthanide emission. A stable and highly luminescent terbium complex based on a tetraisophthalamide (TIAM) chelate is paired with a polyaromatic-azo dark quencher (referred to as a Black Hole Quencher or BHQ) to prepare a series of 5'TIAM(Tb)/3'BHQ dual-labeled oligonucleotide probes with no secondary structure. Luminescence quenching efficiency within terbium/BHQ probes is very dependent on the terbium-BHQ distance. In an intact probe, the average terbium-BHQ distance is short, and Tb --> BHQ energy transfer is efficient, decreasing both the terbium emission intensity and lifetime. Upon hybridization or nuclease digestion, which spatially separate the Tb and BHQ moieties, the Tb luminescence intensity and lifetime increase. As a result, time-gated detection increases the emission intensity ratio of the unquenched probe/quenched probe due to the shorter lifetime of the quenched species. A 40-mer probe that has a 3-fold increase in steady-state luminescence upon digestion has a 50-fold increase when gated detection is used. This study demonstrates that time gating with lanthanide/dark quencher probes in energy transfer assays is an effective means of improving sensitivity.     

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.     

A new dark quencher for use in genetic analysis

A novel, long-wavelength, non-fluorescent quencher (LQ), based on 1,4-diaminoanthraquinone, has been incorporated at the 3' and 5'-termini of oligonucleotides. The quencher has been used in Molecular beacons, efficiently quenching the long wavelength fluorophore, Cy5.     

Application of Single—labelled Probe—primer in PCR Amplification to the Detection of Hepatitis B Virus DNA

A new method based on the incorporation of a single-lablled probe-primer into polymerase chain reaction(PCR) for the detection of PCR-amplified DNA in a closed system is reported.The probeprimerc consists of a specific probe sequence on the 5‘‘‘‘‘‘‘‘-end and a primer sequence on the 3‘‘‘‘‘‘‘‘-end.A flurophore is located at the 5‘‘‘‘‘‘‘‘end.The primeR-quencher is an oligonucleotide,which is complementary to the probe sequence of probe-primer and labelled with a quencher at the 3‘‘‘‘‘‘‘‘-end.In the duplex formed by probe-primer and primer-quencher.the fluorophore and quencher are kept in close proximity to each other.Therefore the fluorescence is quenched.During PCR amplificatio,the specific probe sequence of probeprimer binds to its complement within the same strand of DNA,and is cleaved by Taq DNA polymerase,resulting in the restoration of fluorescence.This system has the same energy transfer mechanism as molecular beacons,and a good quenching effciency can be ensured.Following optimization of PCR conditions,this method was used to detect hepatitis b virus(HBV) dna in patient sera.This technology eliminates the risk of carry-over contamination,simplifies the amplification assay and opens up new possibilities for the real-time detection of the amplified DNA.     

Tail-labelling of DNA probes using modified deoxynucleotide triphosphates and terminal deoxynucleotidyl transferase. Application in electrochemical DNA hybridization and protein-DNA binding assays

A simple approach to DNA tail-labelling using terminal deoxynucleotidyl transferase and modified deoxynucleoside triphosphates is presented. Amino- and nitrophenyl-modified dNTPs were found to be good substrates for this enzyme giving 3'-end stretches of different lengths depending on the nucleotide and concentration. 3-Nitrophenyl-7-deazaG was selected as the most useful label because its dNTP was efficiently incorporated by the transferase to form long tail-labels at any oligonucleotide. Accumulation of many nitrophenyl tags per oligonucleotide resulted in a considerable enhancement of voltammetric signals due to the nitro group reduction, thus improving the sensitivity of electrochemical detection of the tail-labelled probes. We demonstrate a perfect discrimination between complementary and non-complementary target DNAs sequences by tail-labelled hybridization probes as well as the ability of tumour suppressor p53 protein to recognize a specific binding site within tail-labelled DNA substrates, making the methodology useful in electrochemical DNA hybridization and DNA-protein interaction assays.     

Distribution of fluorocarbon quencher among micelles via pyrene fluorescence probe method

 Fluorescence-quenching of pyrene in micellar system has been investigated using 1,1,2,2-tetrahydroheptadecafluorodecylpyridinium chloride (HFDePC). The new fluorocarbon quencher has a similar quenching ability as hexadecyl-pyridinium chloride (CPC) towards pyrene in hydrocarbon micelles if only a quencher molecule is solubilized in a micelle. The fluorocarbon quencher randomly distributed among micelles if the average occupancy number of probes per a micelle was small enough. The fluorescence behavior of pyrene was examined for hexadecyl-trimethylammonium chloride (CTAC) and HFDePC mixtures. The variation of fluorescence intensity gave second cmc, reflecting the micellar immiscibility of fluorocarbon and hydrocarbon surfactants. The second cmc can be simulated by material balances of both surfactants supposing the coexistence of two kinds of mixed micelles. The fluorescence-quenching behavior suggested the enhanced micellar immiscibility probably due to nonrandom distribution of fluorocarbon quenchers among micelles. Received: 13 March 1997 Accepted: 24 May 1997     

RNA-templated single-base mutation detection based on T4 DNA ligase and reverse molecular beacon

A novel RNA-templated single-base mutation detection method based on T4 DNA ligase and reverse molecular beacon (rMB) has been developed and successfully applied to identification of single-base mutation in codon 273 of the p53 gene. The discrimination was carried out using allele-specific primers, which flanked the variable position in the target RNA and was ligated using T4 DNA ligase only when the primers perfectly matched the RNA template. The allele-specific primers also carried complementary stem structures with end-labels (fluorophore TAMRA, quencher DABCYL), which formed a molecular beacon after RNase H digestion. One-base mismatch can be discriminated by analyzing the change of fluorescence intensity before and after RNase H digestion. This method has several advantages for practical applications, such as direct discrimination of single-base mismatch of the RNA extracted from cell; no requirement of PCR amplification; performance of homogeneous detection; and easily design of detection probes.     

A simple FRET-based modular design for diagnostic probes

In recent years, there has been a massive effort to develop molecular probes with optical modes of action. Probes generally produce detectable signals based on changes in fluorescence properties. Here, we demonstrate the potential of self-immolative molecular adaptors as a platform for Turn-On probes based on the FRET technique. The probe is equipped with identical fluorophore pairs or a fluorophore/quencher FRET pair and a triggering substrate. Upon reaction of the analyte of interest with the triggering substrate, the self-immolative adaptor spontaneously releases the two dye molecules to break off the FRET effect. As a result, a new measurable fluorescent signal is generated. The fluorescence obtained can be used to quantify the analyte. The modular structure of the probe design will allow the preparation of various chemical probes based on the FRET activation technique.     

AIEgens/Nucleic Acid Nanostructures for Bioanalytical Applications

DNA occupies significant roles in life processes, which include encoding the sequences of proteins and accurately transferring genetic information from generation to generation. Recent discoveries have demonstrated that a variety of biological functions are correlated with DNA′s conformational transitions. The non‐B form has attained great attention among the diverse forms of DNA over the past several years. The main reason for this is that a large number of studies have shown that the non‐B form of DNA is associated with gross deletions, inversions, duplications, translocations as well as simple repeating sequences, which therefore causes human diseases. Consequently, the conformational transition of DNA between the B‐form and the non‐B form is important for biology. Conventional fluorescence probes based on the conformational transitions of DNA usually need a fluorophore and a quencher group, which suffers from the complex design of the structure and tedious synthetic procedures. Moreover, conventional fluorescence probes are subject to the aggregation‐caused quenching (ACQ) effect, which limits their application toward imaging and analyte detection. Fluorogens exhibiting aggregation‐induced emission (AIE) have attracted tremendous attention over the past decade. By taking advantage of this unique behavior, plenty of fluorescent switch‐on probes without the incorporation of fluorescent quenchers/fluorophore pairs have been widely developed as biosensors for imaging a variety of analytes. Herein, the recent progress in bioanalytical applications on the basis of aggregation‐induced emission luminogens (AIEgens)/nucleic acid nanostructures are presented and discussed.     

Multiplexed in situ immunofluorescence using dynamic DNA complexes

DNA-based erasers: The designed strand-displacement reactions between dynamic DNA probes (carrying fluorescent dyes () and quencher domains (?)) and DNA-antibody conjugates generate detachable immunofluoresence-reporting complexes that can be assembled (first image) and disassembled (second image) reversibly within fixed cells. With this system, different protein targets can be imaged sequentially within the same cells (third image).     

Molecular beacons for bioanalytical applications

Molecular beacons (MBs) are hairpin-shaped oligonucleotides that contain both fluorophore and quencher moieties. They act like switches and are normally in a closed state, when the fluorophore and the quencher are brought together to turn "off" the fluorescence. When prompted to undergo conformational changes that open the hairpin structure, the fluorophore and the quencher are separated, and fluorescence is turned "on." This Education will outline the principles of MBs and discuss recent bioanalytical applications of these probes for in vitro RNA and DNA monitoring, biosensors and biochips, real-time monitoring of genes and gene expression in living systems, as well as the next generation of MBs for studies on proteins, the MB aptamers. These important applications have shown that MBs hold great potential in genomics and proteomics where real-time molecular recognition with high sensitivity and excellent specificity is critical.