A polycation-chaperoned in-stem molecular beacon system

In the presence of poly(L-lysine)-graft-dextran, an in-stem molecular beacon involving three perylene-anthraquinone pairs in the stem region had a signal/background ratio of as high as 570. Response speed was also remarkable; equilibrium was attained within 5 minutes after addition of substrate DNA at 20 °C.     

Towards single-spot multianalyte molecular beacon biosensors

The separate developments of microarray patterning of DNA oligonucleotides, and of DNA hairpins as sensitive probes for oligonucleotide identification in solution, have had a tremendous impact on basic biological research and clinical applications. Herein, we will discuss several successful efforts to develop oligonucleotide sensors based on the surface immobilization of functionalized DNA hairpins. We also will discuss the development of prototypical single-spot multianalyte “Molecular Beacon” biosensors. Importantly, we show that organic fluorophores will likely be inadequate in moving this technology forward and new approaches, such as the use of nanotechnology, will be needed.     

The road to non-enzymatic molecular networks

This Minireview gives an overview of recent progress in the design and analysis of chemical systems that utilize template-directed autocatalytic and cross-catalytic processes as a means of wiring dynamically interacting molecules. Synthetic networks comprising two to nine replicating species are discussed. It is shown that for larger systems, more catalytic pathways must be manipulated to control the entire network topology and specific functionality of the individual species or subnetworks. Cellular biochemistry is an example of a natural functional molecular network; synthetic self-organized networks can provide additional models of complex systems.     

A highly discriminating quencher-free molecular beacon for probing DNA

We inserted a fluorene-labeled deoxyuridine derivative, synthesized using Sonogashira coupling, efficiently into the loop region of a DNA hairpin using phosphoramidite chemistry. This molecular beacon, which features no additional fluorescence quencher, discriminates between perfect and one-base-mismatched base pairing by changes in its fluorescence intensity. The discrimination factor is 14.7 for the recognition of a single (A/C) base mismatch.     

Dual nanocatalysts co-decorated three-dimensional,laser-induced graphene hybrid nanomaterials integrated with a smartphone portable electrochemical system for point-of-care non-enzymatic glucose diagnosis

Non-enzymatic biosensors based on various nanomaterials with large surface-volume ratios and high catalytic efficiencies have been proposed to compensate for the non-stability and high cost of enzymatic biosensors. However, the construction of a stable, highly sensitive, flexible, three-dimensional (3D), microstructured, non-enzymatic biosensor integrated with a smartphone-based portable system has been challenging. Herein, highly conductive laser-induced graphene (LIG) array with a honeycomb-like 3D microstructure co-decorated with copper(I) oxide and gold nanocatalysts was developed via simple and green electro-deposition and chemical reduction approaches for a miniaturized electrochemical flexible non-enzymatic biosensor. SEM, XRD, Raman and XPS analyzations indicated that the Cu₂O and Au nanocatalysts co-decorated three-dimensional, laser-induced graphene hybrid nanomaterials were developed successfully. The signal of the biosensor was improved by more than 10 fold compared to the LIG alone due to the co-decorated with copper(I) oxide and gold nanocatalysts. The fabricated electrochemical biochip was integrated with a smartphone-based microstation for glucose monitoring, presenting a larger linear interval of 1–20 mM with an excellent sensitivity of 236 μA/mM/cm² and a relatively low detection limit of 0.31 μM. Noticeably, the biochip could measure blood sugar on curved surfaces and still deliver stable sensing signals after being bent back-and-forth 25 times. The novel biosensor is a potentially valuable flexible electronic device. The hybrid nanomaterials developed in this work may be applicable to other biosensing, catalytic, and energy devices (supercapacitors and batteries).     

Inhibited aptazyme-based catalytic molecular beacon for amplified detection of adenosine

Combining the inhibited aptazyme and molecular beacon(MB),we developed a versatile sensing strategy for amplified detection of adenosine.In this strategy,the adenosine aptamer links to the 8-17 DNAzyme to form an aptazyme.A short sequence,denoted as inhibitor,is designed to form a duplex spanning the aptamer–DNAzyme junction,which blocks the catalytic function of the DNAzyme.Only in the presence of target adenosine,the aptamer binds to adenosine,thus the inhibitor dissociates from the aptamer portion of the aptazyme and can no longer form the stable duplex required to inhibit the catalytic activity of the aptazyme.The released DNAzyme domain will hybridize to the MB and catalyze the cleavage in the presence of Zn2+,making the fluorophore separate from the quencher and resulting in fluorescence signal.The results showed that the detection method has a dynamic range from 10 nmol/L to 1 nmol/L,with a detection limit of 10 nmol/L.     

A versatile molecular beacon-like probe for multiplexed detection based on fluorescence polarization and its application for a resettable logic gate

A versatile molecular beacon (MB)-like probe was developed for multiplexed detection based on fluorescence polarization by target-induced allosteric effect and furthermore for resettable logic gate operation.     

Structure Elucidator: a versatile expert system for molecular structure elucidation from 1D and 2D NMR data and molecular fragments

StrucEluc is an expert system that allows the computer-assisted elucidation of chemical structures based on the inputs of a series of spectral data including 1D and 2D NMR and mass spectra. The system has been enabled to allow a chemist to utilize fragments stored in a fragment database as well as user-defined fragments submitted by the chemist in the structure elucidation process. The association of fragments in this way has been shown to dramatically speed up the process of structure generation from 2D NMR data and has helped to minimize or eliminate the need for user intervention thereby further enabling the vision of automated elucidation. The use of fragments has frequently transformed very difficult 2D NMR elucidation challenges into easily solvable tasks. A strategy to utilize molecular fragments has been developed and optimized based on specific challenging examples. This strategy will be described here using real world examples. Experience gained by solving more than 150 structure elucidation problems from a variety of literature sources is also reviewed in this work.     

A molecular peptide beacon for the ratiometric sensing of nucleic acids

A pyrene-functionalized cationic oligopeptide 1 efficiently binds to double-stranded DNA, as shown by different spectrophotochemical studies. Upon binding, the conformation of 1 changes from a folded to an extended form, which leads to a distinct change in the fluorescence properties. Thus, 1 functions as a molecular peptide beacon, and as it is easily taken up by cells, 1 can also be used for imaging of nucleic acids within cells.     

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.     

Dendrimer as a versatile platform for biomedical application: A review

Modern chemistry is vastly fascinated by dendrimer chemistry, an area that is rapidly expanding and brimming with potential applications. Dendrimers are highly branched polymers that have multiple peripheral groups, interior cavities and they have many structural properties therefore Dendrimers play a crucial role in the fields of nanotechnology, pharmaceuticals, and medicinal chemistry. The terminal functional groups of dendrimers may be chemically linked to other moieties in order to adjust surface properties for applications such as biomimetic nanodevices. A variety of biologically active agents can be incorporated into dendrimers to create biologically active conjugates, including novel drug carriers, by utilizing the homogeneity of their three-dimensional architecture. The purpose of this review is to provide a brief overview of bio-inspired dendrimer applications, highlighting their use as drug and gene delivery agents, and biomedical diagnostic agents. In addition, the review mentions briefly some dendrimer applications in cosmetics, agrochemicals, and catalyst.     

Design of a novel G-quenched molecular beacon: a simple and efficient strategy for DNA sequence analysis

G-quenched MBs are devised from readily available starting materials and used for sequence specific DNA detection with high efficiency.     

A room-temperature adenosine-based molecular beacon for highly sensitive detection of nucleic acids

This study developed a simple, sensitive, and selective molecular beacon for detecting nucleic acids at room temperature based on coralyne induced conformational change of a MB through A(2)-coralyne-A(2) coordination.     

Reagentless, reusable, ultrasensitive electrochemical molecular beacon aptasensor

A bifunctional derivative of the thrombin-binding aptamer with a redox-active Fc moiety and a thiol group at the termini of the aptamer strand was synthesized. The ferrocene-labeled aptamer thiol was self-assembled through S-Au bonding on a polycrystalline gold electrode surface and the surface was blocked with 2-mercaptoethanol to form a mixed monolayer. By use of a fluorescent molecular beacon, the effect of counterions on quadruplex formation was established. The aptamer-modified electrode was characterized electrochemically by cyclic voltammetry (CV), differential pulse voltammetry (DPV), and electrochemical impedance spectroscopy (EIS). The modified electrode showed a voltammetric signal due to a one-step redox reaction of the surface-confined ferrocenyl moiety of the aptamer immobilized on the electrode surface in 10 mM N-(2-hydroxyethyl)piperazine-N'-2-ethanesulfonic acid (HEPES) buffer of pH 8.0. An increase in the DPV current signal was evident after blocking with 2-mercaptoethanol, effectively removing aptamer nonspecifically absorbed rather than bound to electrode surface or due to the formation of the aptamer-thrombin affinity interaction. The impedance measurement, in agreement with the differential pulse voltammetry (DPV), showed decreased Faradaic resistances in the same sequence. The "signal-on" upon thrombin association could be attributed to a change in conformation from random coil-like configuration on the probe-modified film to the quadruplex structure. The DPV of the modified electrode showed a linear response of the Fc oxidation signal to the increase in the thrombin concentration in the range between 5.0 and 35.0 nM with a linear correlation of r = 0.9988 and a detection limit of 0.5 nM. The molecular beacon aptasensor was amenable to full regeneration by simply unfolding the aptamer in 1.0 M HCl, and could be regenerated 25 times with no loss in electrochemical signal upon subsequent thrombin binding.     

Gold nanoparticle fluorescent molecular beacon for low-resolution DQ2 gene HLA typing

Coeliac disease is an inflammation of the small intestine triggered by gluten ingestion. We present a fluorescent genosensor, exploiting molecular-beacon-functionalized gold nanoparticles, for the identification of human leukocyte antigen (HLA) DQ2 gene, a key genetic factor in coeliac disease. Optimization of sensor performance was achieved by tuning the composition of the oligonucleotide monolayer immobilized on the gold nanoparticle and the molecular beacon design. Co-immobilization of the molecular beacon with a spacing oligonucleotide (thiolated ten-thymine oligonucleotide) in the presence of ten-adenine oligonucleotides resulted in a significant increase of the sensor response owing to improved spacing of the molecular beacons and extension of the distance from the nanoparticle surface, which renders them more available for recognition. Further increase in the response (approximately 40%) was shown to be achievable when the recognition sequence of the molecular beacon was incorporated in the stem. Improvement of the specificity of the molecular beacons was also achieved by the incorporation within their recognition sequence of a one-base mismatch. Finally, gold nanoparticles functionalized with two molecular beacons targeting the DQA1*05* and DQB1*02* alleles allowed the low-resolution typing of the DQ2 gene at the nanomolar level.     

Rapid DNA hybridization analysis using a PDMS microfluidic sensor and a molecular beacon.

A rapid DNA analysis has been developed based on a fluorescence intensity change of a molecular beacon in a PDMS microfluidic channel. Recently, we reported a new analytical method of DNA hybridization involving a PDMS microfluidic sensor using fluorescence energy transfer (FRET). However, there are some limitations in its application to real DNA samples because the target DNA must be labelled with a suitable fluorescent dye. To resolve this problem, we have developed a new DNA microfluidic sensor using a molecular beacon. By monitoring the change in the restored fluorescence intensity along the channel length, it is possible to rapidly detect any hybridization of the molecular beacon to the target DNA. In this case, the target DNA does not need to be labelled. Our experimental results demonstrate that this microfluidic sensor using a molecular beacon is a promising diagnostic tool for rapid DNA hybridization analysis.