Traditional Molecular Beacons Research Articles

Development and analysis of a universal label-free micro/nano component for three-channel detection of silver ions, mercury ions, and tetracycline

In this paper, an enzyme-free and label-free fluorescent nanomodule is proposed for rapid, simple and sensitive detection of Ag+, Hg2+ and tetracycline (TC). The strategy is cleverly designed to enable multiple-purpose detection with as little as 31 nt of ssDNA. Both the embedded dye SYBR Green I and the nanomaterial graphene oxide (GO) are able to distinguish single-stranded DNA from double-stranded DNA; thus, the combination of the two instead of using traditional molecular beacon (MB)-labeled fluorophores and quencher groups can effectively reduce the cost of experiments while efficiently reducing the background noise. Performance testing experiments confirmed the stability and selectivity of the platform; the limits of detection (LODs) of Ag+ and Hg2+ were 1.41 nM and 1.79 nM, respectively, and the detection range were within the WHO standards. In addition, only some base sequences in the flexible functional domain of the nanoloop needed to be programmed to build a universal platform, which was feasible using TC as a target. Therefore, the designed nanomodule has the potential to detect various types of targets, such as antibiotics, proteins, and target genes, and has broad application prospects in environmental monitoring, food testing, and disease diagnosis.

Cubic DNA nanocage-based three-dimensional molecular beacon for accurate detection of exosomal miRNAs in confined spaces

In situ nondestructive bioanalysis of targets in nanoscale confined space, e.g. exosomes, poses a high challenge to analytical technologies, especially to molecular fluorescent probes, because it is required to enter the confined space to recognize the target, and maintain independent and stable signal output. The unexpected fluorescence quenching and fluorescence resonance energy transfer (FRET) caused by high-frequency Brownian motion and collision in confined space are the main limiting factors. Herein, we constructed a well-defined and programmable cubic DNA nanocage-based three-dimensional molecular beacon (ncMB), which successfully broke through the above dilemma, and realized the detection of miRNA in exosomes. Specifically, steric hindrance and electrostatic repulsion derived from the unique three-dimensional structure of ncMB result in a barrier between fluorescent probes, thus eliminating unexpected fluorescence quenching during single exosomal miRNA detection and unexpected FRET during dual exosomal miRNA detection. Benefiting from the excellent anti-fluorescence and anti-FRET performance of ncMB, compared with traditional molecular beacons (MB), the detected fluorescence signal in exosomes can be improved by an order of magnitude. Moreover, ncMB is proven to have powerful programmability and anti-interference capability. Overall, it is believed that the ncMB can eliminate the signal distortion that was usually associated with commonly used MB, especially in the confined space. The ncMB is considered as a powerful and versatile tool for accurate in situ signal output in exosomes and maybe other confined spaces.

A novel adenosine-based molecular beacon probe for room temperature nucleic acid rapid detection in cotton thread device

We used cotton thread as substrate to develop a novel room temperature DNA detection device for low-cost, sensitive and rapid detection of a human genetic disease, hereditary tyrosinemia type I related DNA sequences. A novel adenosine based molecular beacon (ABMB) probe modified on gold nanoparticle was used as reporter probe. In the presence of coralyne, a small molecule which can react with adenosines, the ABMB would form a hairpin structure just like traditional molecular beacon used extensively. In the presence of target DNA sequences, the hairpin structure of ABMB modified on gold nanoparticles will be opened and the biotin group modified at one end of the DNA probes will be released and react with the streptavidin immobilized on the test zone of the cotton thread. The response of the thread based DNA test device is linear over the range of 2.5–100nM complementary DNA. The ability of our developed device for discriminating the single base mismatched DNA related to a human genetic disease, hereditary tyrosinemia type I, was improved comparing with previous report. It is worth mentioning that the whole assay procedure for DNA test is performed under room temperature which simplified the assay procedures greatly.

A graphene oxide-based enzyme-free signal amplification platform for homogeneous DNA detection.

A graphene oxide (GO) based enzyme-free signal amplification platform for homogeneous DNA sensing is developed with simplicity and high sensitivity. In the absence of the target DNA, labeled hairpin probe 1 (H1) and probe 2 (H2) were adsorbed on the surface of GO, resulting in the fluorescence quenching of the dyes and minimizing the background fluorescence. The addition of the target DNA facilitated the formation of double-stranded DNA (dsDNA) between H1 and H2, causing the probes to separate from GO and release the target DNA through a strand displacement reaction. Meanwhile, the whole reaction started anew. This is an excellent isothermal signal amplification technique without the involvement of enzymes. By monitoring the change of the fluorescence intensity, the target DNA not only can be determined in buffer solution, but also can be detected in 1% serum solution spiked with a series of concentrations of the target DNA. In addition, the consumption amount of the probes in this method is lower than that in traditional molecular beacon methods.

A General Strategy for Label-Free Sensitive DNA Detection Based on Quantum Dot Doping

Development of rapid, sensitive, and cost-effective DNA detection is of great significance to meet the growing demand of disease diagnostics. Herein, we report a new general strategy for label-free sensitive in-solution DNA detection using quantum dot (QD) doping-induced photoluminescence as a fluorogenic reporter system. The dopant mercury (Hg(II)) ions are initially sequestered in the hairpin-structured probe through T-Hg(2+)-T mismatch formation. Upon hybridization with the DNA target, the hairpin is disrupted and Hg(2+) ions are released and incorporated into ZnSe QDs, leading to a dopant-specific emission peak at 560 nm for DNA detection. Unlike the other methods, this method does not require any chemical modification of the DNA probe. It could provide high signal-to-noise ratio, robust single-base mismatch discrimination capability, and 3 orders of magnitude lower limit of detection (LOD) than the traditional molecular beacon (MB)-based fluorescence spectroscopy without any type of amplification. The method could be used for the detection of a variety of clinical significant DNA targets containing single mutations. To the best of our knowledge, this is the first study on applying chemical transformation of inorganic nanostructures to sensitive DNA detection.

A novel room temperature nucleic acid detection method based on immobilization of adenosine-based molecular beacon

We developed a novel room temperature fluorescence DNA biosensor based on immobilization of well designed adenosine-based molecular beacon (ABMB). In the presence of coralyne, a small molecule which can react with adenosines, the ABMB would form a hairpin structure just like traditional molecular beacon used extensively. In our experiments, two kinds of adenosine-based molecular beacon probes with twelve adenosines bases at each end (A12-MB1-A12 and A12-MB2-A12), and their complementary target DNA, non-complementary target DNA and single base mismatched DNAs were used as models to demonstrate the proof-of-concept. Under optimized conditions, the detection limit was estimated to be 50pM based on S/N=3. The ability of our developed biosensor for discriminating the single base mismatched DNA related to a human genetic disease, hereditary tyrosinemia type I, was improved undoubtedly once A12-MB2-A12 was used as capture probe comparing with previous report. It is worth to mention that the whole assay procedures were conducted under room temperature.

DNA nanomachines as evolved molecular Beacons for in vitro and in vivo detection

Modern biosensors require high sensitivity, great signal enhancement and extensive applicability for detection and diagnostic purposes. Traditional molecular beacons (MBs) do not meet these requirements because of the lack of signal amplification. The current amplification pathways using enzymes, DNAzymes and nanoparticles are usually quite sophisticated and are limited to specific applications. Herein, we developed simple biosensors based on the structure of kissing-hairpin. Through hybridization amplification of these nanomachines, the evolved MBs could greatly enhance the detected signals (approximately 10-fold higher than the signals generated by traditional molecular beacons), reduce the sensing limits for targets and, remarkably, distinguish single-base mismatches specifically for nucleic acid detection. In addition, these new MBs can be directly applied in living cells. By introducing aptamer sequences, these novel sensors can also detect proteins and small molecules. These properties were exemplified by the detection of both the β-actin gene and thrombin. The simplicity, sensitivity and flexibility of these devices make them appropriate for more expansive applications.

Graphene Oxide-Based Fluorescent “on/off” Switch for Visual Bioassay Using “Molecular Beacon”-Hosted Hoechst Dyes

In this study, the fluorescence of Hoechst dyes is significantly lit up by addition of our designed MB probe, forming a complex of "molecular beacon"-hosted Hoechst dyes (HMB). Combined with this property, a novel graphene oxide (GO)-based fluorescent "on/off" switch was developed to visually follow bioassay utilizing HMB as signal indicators and GO as an excellent energy acceptor to efficiently quench the fluorescence of HMB in a label-easy format. We have demonstrated its application for label-easy fluorescence "turn on" detection of sequence-specific DNA and "turn off" detection of exonuclease with sensitivity and selectivity in a single step in homogeneous solution. Compared to traditional molecular beacons, the proposed design is cost-effective and simple to prepare without fluorescence labeling or chemical modification.

One-Step, Multiplexed Fluorescence Detection of microRNAs Based on Duplex-Specific Nuclease Signal Amplification

Traditional molecular beacons, widely applied for detection of nucleic acids, have an intrinsic limitation on sensitivity, as one target molecule converts only one beacon molecule to its fluorescent form. Herein, we take advantage of the duplex-specific nuclease (DSN) to create a new signal-amplifying mechanism, duplex-specific nuclease signal amplification (DSNSA), to increase the detection sensitivity of molecular beacons (Taqman probes). DSN nuclease is employed to recycle the process of target-assisted digestion of Taqman probes, thus, resulting in a significant fluorescence signal amplification through which one target molecule cleaves thousands of probe molecules. We further demonstrate the efficiency of this DSNSA strategy for rapid direct quantification of multiple miRNAs in biological samples. Our experimental results showed a quantitative measurement of sequence-specific miRNAs with the detection limit in the femtomolar range, nearly 5 orders of magnitude lower than that of conventional molecular beacons. This amplification strategy also demonstrated a high selectivity for discriminating differences between miRNA family members. Considering the superior sensitivity and specificity, as well as the multiplex and simple-to-implement features, this method promises a great potential of becoming a routine tool for simultaneously quantitative analysis of multiple miRNAs in tissues or cells, and supplies valuable information for biomedical research and clinical early diagnosis.

High-Precision, In Vitro Validation of the Sequestration Mechanism for Generating Ultrasensitive Dose-Response Curves in Regulatory Networks

Our ability to recreate complex biochemical mechanisms in designed, artificial systems provides a stringent test of our understanding of these mechanisms and opens the door to their exploitation in artificial biotechnologies. Motivated by this philosophy, here we have recapitulated in vitro the “target sequestration” mechanism used by nature to improve the sensitivity (the steepness of the input/output curve) of many regulatory cascades. Specifically, we have employed molecular beacons, a commonly employed optical DNA sensor, to recreate the sequestration mechanism and performed an exhaustive, quantitative study of its key determinants (e.g., the relative concentrations and affinities of probe and depletant). We show that, using sequestration, we can narrow the pseudo-linear range of a traditional molecular beacon from 81-fold (i.e., the transition from 10% to 90% target occupancy spans an 81-fold change in target concentration) to just 1.5-fold. This narrowing of the dynamic range improves the sensitivity of molecular beacons to that equivalent of an oligomeric, allosteric receptor with a Hill coefficient greater than 9. Following this we have adapted the sequestration mechanism to steepen the binding-site occupancy curve of a common transcription factor by an order of magnitude over the sensitivity observed in the absence of sequestration. Given the success with which the sequestration mechanism has been employed by nature, we believe that this strategy could dramatically improve the performance of synthetic biological systems and artificial biosensors.

Detection of C677T mutation of MTHFR in subject with coronary heart disease by hairpin probe with enzymatic color on microarray

Molecular beacon (MB) is especially suited for detection of single nucleotide polymorphism (SNP), and the type of MB immobilized on the surface of microarray in particular, may detect multi-sample and multi-locus. However, the majority of MB needs to be labeled with fluorescence and quenching molecules on the two ends of the probe, and observed the reaction of fluorescence or complicated electrochemical signal produced hybridization of MB and target sequence by complex and expensive instruments. The “molecular beacon” and microarray designed appropriately in our study can produce visible light response signal induced by amplification effect of enzymatic color, and are avoided with the marker of fluorescence and quenching molecules and expensive instruments. The “molecular beacon” without fluorescence and quenching molecules is entitled as “hairpin DNA probe” by us for only the “hairpin” structure of traditional molecular beacon is adopted. The merits of two techniques, molecular beacon and amplification effect of enzymatic color, are successfully combined, and the technique is simple, sensitive and specific, to detect and compare the methylenetetrahydrofolate reductase (MTHFR) Gene C677T mutation of subjects between coronary heart disease (CHD) and control group. The results showed that MTHFR Gene C677T polymorphism is an independent risk factor for CHD.

A versatile graphene-based fluorescence “on/off” switch for multiplex detection of various targets

We have designed a versatile molecular beacon (MB)-like probe for the multiplex sensing of targets such as sequence-specific DNA, protein, metal ions and small molecule compounds based on the self-assembled ssDNA–graphene oxide (ssDNA–GO) architecture. The probe employs fluorescence “on/off” switching strategy in a single step in homogeneous solution. Compared to traditional molecular beacons, the proposed design is simple to prepare and manipulate and has little background interference, but still gives superior sensitivity and rapid response. More importantly, this ssDNA–GO architecture can serve as a universal beacon platform by simply changing the types of ssDNA sequences for the different targets. In this work, the ssDNA–GO architecture probe has been successfully applied in the multiplex detection of sequence-specific DNA, thrombin, Ag +, Hg 2+ and cysteine, and the limit of detection was 1 nM, 5 nM, 20 nM, 5.7 nM and 60 nM, respectively. The results demonstrate that the ssDNA–GO architecture can be an excellent and versatile platform for sensing multiplex analytes, easily replacing the universal molecular beacon.

Sensitive and Selective Amplified Fluorescence DNA Detection Based on Exonuclease III-Aided Target Recycling

A limitation of many traditional approaches to the detection of specific oligonucleotide sequences, such as molecular beacons, is that each target strand hybridizes with (and thus activates) only a single copy of the relevant probe sequence. This 1:1 hybridization ratio limits the gain of most approaches and thus their sensitivity. Here we demonstrate a nuclease-amplified DNA detection scheme in which exonuclease III is used to "recycle" target molecules, thus leading to greatly improved sensitivity relative to, for example, traditional molecular beacons without any significant restriction in the choice of target sequences. The exonuclease-amplified assay can detect target DNA at concentrations as low as 10 pM when performed at 37 degrees C, which represents a significant improvement over the equivalent molecular beacon alone. Moreover, at 4 degrees C we can obtain a detection limit as low as 20 aM, albeit at the cost of a 24 h incubation period. Finally, our assay can be easily interrogated with the naked eye and is thus amenable to deployment in the developing world, where fluorometric detection is more problematic.

A single-label phenylpyrrolocytidine provides a molecular beacon-like response reporting HIV-1 RT RNase H activity.

6-Phenylpyrrolocytidine (PhpC), a structurally conservative and highly fluorescent cytidine analog, was incorporated into oligoribonucleotides. The PhpC-containing RNA formed native-like duplex structures with complementary DNA or RNA. The PhpC-modification was found to act as a sensitive reporter group being non-disruptive to structure and the enzymatic activity of RNase H. A RNA/DNA hybrid possessing a single PhpC insert was an excellent substrate for HIV-1 RT Ribonuclease H and rapidly reported cleavage of the RNA strand with a 14-fold increase in fluorescence intensity. The PhpC-based assay for RNase H was superior to the traditional molecular beacon approach in terms of responsiveness, rapidity and ease (single label versus dual). Furthermore, the PhpC-based assay is amenable to high-throughput microplate assay format and may form the basis for a new screen for inhibitors of HIV-RT RNase H.

Homogeneous DNA Detection Based on Fluorescence Quenching by Nanoparticles in Single‐step Format: Target‐Induced Configuration Transform

AbstractA new strategy for homogeneous detection of DNA hybridization in single‐step format was developed based on fluorescence quenching by gold nanoparticles. The gold nanoparticle is functionalized with 5′‐thiolated 48‐base oligonucleotide (probe sequence), whose 3′‐terminus is labeled with fluorescein (FAM), a negatively charged fluorescence dye. The oligonucleotide adopts an extended configuration due to the electrostatic repulsion between negatively charged gold nanoparticle and the FAM‐attached probe sequence. After addition of the complementary target sequence, specific DNA hybridization induces a conformation change of the probe from an extended structure to an arch‐like configuration, which brings the fluorophore and the gold nanoparticle in close proximity. The fluorescence is efficiently quenched by gold nanoparticles. The fluorescence quenching efficiency is related to the target concentration, which allows the quantitative detection for target sequence in a sample. A linear detection range from 1.6 to 209.4 nmol/L was obtained under the optimized experimental conditions with a detection limit of 0.1 nmol/L. In the assay system, the gold nanoparticles act as both nanoscaffolds and nanoquenchers. Furthermore, the proposed strategy, in which only two DNA sequences are involved, is not only different from the traditional molecular beacons or reverse molecular beacons but also different from the commonly used sandwich hybridization methods. In addition, the DNA hybridization detection was achieved in homogenous solution in a single‐step format, which allows real‐time detection and quantification with other advantages such as easy operation and elimination of washing steps.

Surface-Enhanced Raman Nanoparticle Beacons Based on Bioconjugated Gold Nanocrystals and Long Range Plasmonic Coupling

We have developed a new class of surface-enhanced Raman scattering beacons (SERS beacons) that can be turned on and off by long-range plasmonic coupling, induced by biomolecular recognition and binding events. The beacons are based on colloidal gold nanocrystals in two sizes (40 and 60 nm) and are prepared by spectral encoding with a Raman reporter molecule, functionalized with thiolated DNA probes, and stabilized and protected by low molecular weight poly(ethylene glycol)s (PEGs). The results show the SERS signal intensities increase by 40-200-fold when the nanoparticle beacons are activated by plasmonic coupling, much higher than the bright-to-dark intensity ratios reported for traditional molecular beacons. Multivalent gold nanoparticles also have exquisite specificity and are able to recognize single-base mismatches or mutations. This class of SERS nanoparticle beacons has novel mechanisms for molecular detection and signal amplification, and its long-range coupling nature raises new opportunities in developing plasmonic probes to detect proteins, cells, and intact viruses.