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.     

Capillary electrophoresis and fluorescence studies on molecular beacon-based variable length oligonucleotide target discrimination

Molecular beacons (MBs) are oligonucleotide probes having a compact hairpin structure, with a fluorophore attached to one end and a quencher molecule attached to the other end. In its native state, the fluorophore is quenched by virtue of its proximity to the quencher molecule. Upon hybridization with its complementary oligonucleotide target, fluorescence is elicited due to a conformational change that results in separation of the fluorophore and quencher molecule. The present study describes the hybridization interaction of an MB to various complementary target sequences. The effects of temperature and length of complementary target sequences on hybridization were investigated using capillary electrophoresis and solution-based fluorescence techniques. Hybridization efficiency was dependent on the ability of the target sequences to destabilize the stem region by binding directly to the stem region. Optimal hybridization occurred between 40 and 50 degrees C for all targets tested, with the true target forming a more stable hybrid complex.     

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.     

Magnetic beads as versatile tools for electrochemical DNA and protein biosensing

Magnetic beads (MBs) are versatile tools in the separation of nucleic acids, proteins and other biomacromolecules, their complexes and cells. In this article recent application of MBs in electrochemical biosensing and particularly in the development of DNA hybridization sensors is reviewed. In these sensors MBs serve not only for separation but also as a platform for optimized DNA hybridization. A hybridization event is detected separately at another surface, which is an electrode. The detection is based either on the intrinsic DNA electroactivity or on various kinds of DNA labeling, including chemical modification, enzyme tags, nanoparticles, electroactive beads, etc., greatly amplifying the signals measured. In addition to DNA hybridization, other kinds of biosensing in combination with MBs, such as DNA-protein interactions, are reviewed.     

Metal-organic approach to binary optical memory

Two new Ru(II) diimine chromophores, each containing a single photochromic dianthryl unit, have been prepared and characterized. The photoluminescence from the Ru(II) complexes is modulated by the photochromic action of the dianthryl species, which serves as a triplet energy transfer quencher in one photochromic state. The coupling of the dianthryl photochromic action to the Ru(II) complex emission permits nondestructive photoluminescence readout of binary information photochemically recorded on the molecular level. Luminescent images stored on polystyrene films that contain these molecules maintained their integrity for periods of months with no apparent degradation or variation in the image resolution, suggesting their durability for long-term storage in read-only memory applications.     

INTRAMOLECULAR FLUORESCENCE QUENCHING IN COVALENT ACRYLAMIDE-INDOLE ADDUCTS

Abstract— Indole derivatives have been prepared which have a covalently linked quencher, acrylamide. One of these adducts, N-acrylyltryptamine, has a flexible linkage and the other, N-acrylyl-1,2,3,4-tetrahydropyridoindole, has a rigid bridge between indole and the quencher. The intensity decays of these adducts were obtained using multi-frequency phase and modulation fluorometry. The fluorescence of these adducts appears to be dynamically quenched; dominant lifetimes of 64 ps and 31 ps are found for the flexible and rigid adducts. This indicates that very rapid intramolecular quenching occurs, even when the quencher and fluorophore cannot collide. Quenching in the rigid molecule probably involves electron transfer through two sigma bonds. Anisotropy decay data were also collected and rotational correlation times of 62 ps and 163 ps are reported for the flexibile and rigid adducts, respectively.     

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.     

Multiplexed Immunosensing Platform Coupled to Hybridization Chain Reaction for Electrochemical Determination of MicroRNAs in Clinical Samples

There is an urgent need for development of rapid and inexpensive techniques for detection of microRNAs (miRNAs), which are potential biomarkers of various types of cancer. In this paper, we describe a multiplexed electrochemical platform for determination of three cancer‐relevant miRNAs: miR‐21, let‐7a and miR‐31. The strategy combines the use of magnetic beads (MBs) modified with a commercial antibody for the efficient capture of the heteroduplexes formed by hybridization of the target miRNA with DNA probe. Free non‐hybridized region of the DNA probe was thereafter hybridized with two biotin‐labeled auxiliary DNA probes in a process of hybridization chain reaction (HCR), resulting in a long hybrid bearing a large number of biotin molecules. Labeling of these multiple biotin units with streptavidin‐peroxidase conjugates allowed an amplification of the amperometric signal measured after capturing the modified MBs at a screen‐printed carbon electrode array of eight electrodes. The combined strategy demonstrated in a similar assay time significantly higher sensitivity than those previously described using modified MBs with the same capture antibody (without amplification by HCR) or a HCR strategy implemented on the surface of MBs, respectively. The methodology exhibits a good selectivity for discriminating single mismatches and was applied to the determination of the three target miRNAs in total RNA (RNA_t) extracted from various cancer cell lines and from cervical precancerous lesions.     

Ligand Fishing with Cellular Membrane-Coated Magnetic Beads: A New Method for the Screening of Potentially Active Compounds from Natural Products

Ligand fishing with target biomolecule-immobilized magnetic beads (MBs) has been established and developed for nearly 10 years. Advantages of this technique, such as the ease of operation, associated with a diversity of automated online approaches, make it a valuable tool for affinity studies. However, transmembrane proteins have not been used as the target biomolecules in the assay, since they are usually not available in a purified and bioactive form. In addition, few publications have reported the use of this method for screening active compounds derived from natural products. In this work, for the first time, cellular membrane-coated MBs, which to a large extent maintain the activity of the transmembrane proteins, were used for the fishing assay. We demonstrated application of red blood cell membrane-coated MBs for fishing potential active components from a natural product (Angelica dahurica). The potential active compounds, such as imperatorin, bergapten, and pabulenol, were detected. The result correlated well with cell membrane chromatography (CMC) coupled with HPLC. Comparisons of the developed MBs fishing assay with the CMC method showed the noteworthy advantages of the fishing technique regarding the consumption of cellular membranes, buffers as well as length of operation time.     

Studies of the photo-oxidation of polydienes: Part 1—Photo-stabilising effect of some derivatives of diacetyl-monooxime benzoylhydrazone nickel(II) chelates on cis-1,4-polybutadiene

Three derivatives of diamagnetic diacetyl-monooxime benzoylhydrazone nickel(II) chelates were evaluated as uv stabilisers for cis-1,4-polybutadiene (BR) in solution and in films. In the presence of methylene blue (MB) as singlet oxygen sensitiser, such chelates inhibit the effect of singlet oxygen formed during irradiation by visible light. The photo-stabilising mechanism of the chelates is discussed in terms of their action as singlet oxygen quencher as well as their action as uv absorbers. Further, a stabilising mechanism which involves the trapping of alkyloxy and/or alkylperoxy radicals has also been suggested for two of the chelates. Combination of the most effective chelate and β-carotene as singlet oxygen quencher exhibits synergistic behaviour. The polymer samples which were irradiated in its presence were examined using the Differential Scanning Calorimeter (DSC) technique. The results obtained also demonstrate the photo-stabilising effect of the chelate.     

Covalent attachment of biotinylated molecular beacons via thiol-ene coupling. A study on conformational changes upon hybridization and streptavidin binding

The authors describe a method for the detection of DNA by using immobilized molecular beacons (MBs) on the surface of silicon, with a view on possible application in biosensing. MB hybridization and protein recognition were interrogated on silicon-on-insulator (SOI) surfaces by using fluorescently tagged probes. In order to better understand the conformational changes that occur to MBs upon hybridization, the process was studied by using dual polarization interferometry (DPI). A model system was developed that matches thickness, mass, and density parameters. The results experimentally demonstrate that hybridization promotes the displacement of a protein away from the surface. This finding may be further exploited in techniques such as photonic sensors, thereby paving the way to the design of more sensitive biosensors based on the use of MBs.

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Graphical abstract Schematic of a new DNA/RNA detection scheme by using immobilized molecular beacons (MBs) on silicon, with a view on possible application in biosensing. A study was performed on the conformational changes that occur to MBs upon hybridization by Dual Polarization Interferometry (DPI).

     

Strongly photoluminescent Eu(III) tetrazolate ternary complexes with phosphine oxides as powerful sensitizers

The Eu(III) cation forms electrically neutral photoluminescent complex with 5-(2-pyridyl-1-oxide)tetrazolate (PTO) anion. Although the photoluminescence properties of such tertiary Eu(III) and Tb(III) complexes were not as high (13 and 31% photoluminescence quantum yield, respectively) as reported for other diketonate lanthanide complexes probably because of high number of nitrogen atoms involved in PTO which leads to attachment of water molecules, reducing the luminescence quantum yield with vibrational and rotational quenching. Here, we report the removal of quencher molecules from the coordination sphere of tris–europium tetrazolate oxide complex by replacing them with various phosphine oxides which leads to improved photoluminescence quantum yield for the complexes by acting as auxiliary co-ligands with that of the main antenna 5-(2-pyridyl-1-oxide)tetrazolate. The coordination sphere in these complexes can be complemented by aromatic phosphine oxides to provide highly photoluminescent Eu(III) complexes. The highest quantum yield was 38% in 3 [Eu(PTO)₃·DPEPO](H₂O)₅ containing bis(2-(diphenylphosphino)phenyl) ether oxide (DPEPO) as compared to tris–europium complex with 5-(2-pyridyl-1-oxide)tetrazolate.     

A probabilistic derivation of the partial least-squares algorithm

Traditionally the partial least-squares (PLS) algorithm, commonly used in chemistry for ill-conditioned multivariate linear regression, has been derived (motivated) and presented in terms of data matrices. In this work the PLS algorithm is derived probabilistically in terms of stochastic variables where sample estimates calculated using data matrices are employed at the end. The derivation, which offers a probabilistic motivation to each step of the PLS algorithm, is performed for the general multiresponse case and without reference to any latent variable model of the response variable and also without any so-called "inner relation". On the basis of the derivation, some theoretical issues of the PLS algorithm are briefly considered: the complexity of the original motivation of PLS regression which involves an "inner relation"; the original motivation behind the prediction stage of the PLS algorithm; the relationship between uncorrelated and orthogonal latent variables; the limited possibilities to make natural interpretations of the latent variables extracted.     

Probing the permeability of polyelectrolyte multilayer capsules via a molecular beacon approach

Application of polyelectrolyte multilayer (PEM) capsules as vehicles for the controlled delivery of substances, such as drugs, genes, pesticides, cosmetics, and foodstuffs, requires a sound understanding of the permeability of the capsules. We report the results of a detailed investigation into probing capsule permeability via a molecular beacon (MB) approach. This method involves preparing MB-functionalized bimodal mesoporous silica (BMSMB) particles, encapsulating the BMSMB particles within the PEM film to be probed, and then incubating the encapsulated BMSMB particles with DNA target sequences of different lengths. Permeation of the DNA targets through the capsule shell causes the immobilized MBs to open due to hybridization of the DNA targets with the complementary loop region of the MBs, resulting in an increase in the MB fluorescence. The assay conditions (BMSMB particle concentration, MB loading within the BMS particles, DNA target concentration, DNA target size, pH, sodium chloride concentration) where the MB-DNA sensing process is effective were first examined. The permeability of DNA through poly(sodium 4-styrenesulfonate) (PSS)/poly(allylamine hydrochloride) (PAH) multilayer films, with and without a poly(ethyleneimine) (PEI) precursor layer, was then investigated. The permeation of the DNA targets decreases considerably as the thickness of the PEM film encapsulating the BMSMB particles increases. Furthermore, the presence of a PEI precursor layer gives rise to less permeable PSS/PAH multilayers. The diffusion coefficients calculated for the DNA targets through the PEM capsules range from 10-19 to 10-18 m2 s-1. This investigation demonstrates that the MB approach to measuring permeability is an important new tool for the characterization of PEM capsules and is expected to be applicable for probing the permeability of other systems, such as membranes, liposomes, and emulsions.     

Molecular beacon-based fluorescence biosensor for the detection of gene fragment and PCR amplification products related to chronic myelogenous leukemia

A novel fluorescence method has been established for the determination of gene fragment and PCR amplification products related to chronic myelogenous leukemia (CML). A molecular beacon (MB) which comprises a DNA loop section, a pair of fluorophore (tetramethoxyl rhodamine, TAMRA), and a quencher (4-(2-methyl-on-amino-azobenzene) benzoate, DABCYL) was designed. The loop sequence of MB was designed according to the DNA sequence relating to CML (type b3a2) which contained a single-stranded oligonucleotide. Before hybridization, the fluorescence from the TAMRA had been quenched by the DABCYL. After hybridization with the complementary DNA, the quencher will become far away from the TAMRA, and the fluorescence intensity detected will increase. Changes in the fluorescence intensity have a linear relationship with the concentration of complementary DNA (C) in the range of 4.0 × 10⁻⁹–3.2 × 10⁻⁸ mol/L, with a correlation coefficient of 0.9973; the detection limit was 6.0 × 10⁻¹⁰ mol/L (S/N = 3). The developed method has high selectivity, which can be used to discriminate single-base mismatch sequence. The method has been applied to detect the short-stranded CML DNA fragment (278 bp) with high sensitivity. This approach is a promising method for the detection of CML in real samples for medical diagnostics.     

Fluorescent hybridization probes for nucleic acid detection

Due to their high sensitivity and selectivity, minimum interference with living biological systems, and ease of design and synthesis, fluorescent hybridization probes have been widely used to detect nucleic acids both in vivo and in vitro. Molecular beacons (MBs) and binary probes (BPs) are two very important hybridization probes that are designed based on well-established photophysical principles. These probes have shown particular applicability in a variety of studies, such as mRNA tracking, single nucleotide polymorphism (SNP) detection, polymerase chain reaction (PCR) monitoring, and microorganism identification. Molecular beacons are hairpin oligonucleotide probes that present distinctive fluorescent signatures in the presence and absence of their target. Binary probes consist of two fluorescently labeled oligonucleotide strands that can hybridize to adjacent regions of their target and generate distinctive fluorescence signals. These probes have been extensively studied and modified for different applications by modulating their structures or using various combinations of fluorophores, excimer-forming molecules, and metal complexes. This review describes the applicability and advantages of various hybridization probes that utilize novel and creative design to enhance their target detection sensitivity and specificity.     

Amperometric Magnetoimmunosensors for Direct Determination of D‐Dimer in Human Serum

Two different D‐dimer disposable amperometric immunosensing designs based on indirect competitive or sandwich formats and the use of carboxylic acid‐modified magnetic beads (COOH‐MBs) and screen‐printed carbon electrodes (SPCEs) have been developed and compared. In both approaches, the resulting modified MBs were magnetically captured on the surface of a SPCE which was used as the transducer for the electrochemical detection at ?0.20 V upon addition of H₂O₂, and hydroquinone (HQ). Both configurations exhibited linear ranges of clinical usefulness and detection limits quite below the clinical threshold (0.5 µg mL^?1 D‐dimer). The sandwich configuration has been successfully tested with serum samples.     

A new and efficient variable selection algorithm based on ant colony optimization. Applications to near infrared spectroscopy/partial least-squares analysis

A new variable selection algorithm is described, based on ant colony optimization (ACO). The algorithm aim is to choose, from a large number of available spectral wavelengths, those relevant to the estimation of analyte concentrations or sample properties when spectroscopic analysis is combined with multivariate calibration techniques such as partial least-squares (PLS) regression. The new algorithm employs the concept of cooperative pheromone accumulation, which is typical of ACO selection methods, and optimizes PLS models using a pre-defined number of variables, employing a Monte Carlo approach to discard irrelevant sensors. The performance has been tested on a simulated system, where it shows a significant superiority over other commonly employed selection methods, such as genetic algorithms. Several near infrared spectroscopic experimental data sets have been subjected to the present ACO algorithm, with PLS leading to improved analytical figures of merit upon wavelength selection. The method could be helpful in other chemometric activities such as classification or quantitative structure-activity relationship (QSAR) problems.     

Molecular Engineering of DNA: Molecular Beacons

Molecular beacons (MBs) are specifically designed DNA hairpin structures that are widely used as fluorescent probes. Applications of MBs range from genetic screening, biosensor development, biochip construction, and the detection of single‐nucleotide polymorphisms to mRNA monitoring in living cells. The inherent signal‐transduction mechanism of MBs enables the analysis of target oligonucleotides without the separation of unbound probes. The MB stem–loop structure holds the fluorescence‐donor and fluorescence‐acceptor moieties in close proximity to one another, which results in resonant energy transfer. A spontaneous conformation change occurs upon hybridization to separate the two moieties and restore the fluorescence of the donor. Recent research has focused on the improvement of probe composition, intracellular gene quantitation, protein–DNA interaction studies, and protein recognition.