Molecular beacon: a multitask probe

Advanced diagnostic methods for identification of bacterial foodborne pathogens: contemporary and upcoming challenges

It is a public health imperative to have safe food and water across the population. Foodborne infections are one of the primary causes of sickness and mortality in both developed and developing countries. An estimated 100 million foodborne diseases and 120 000 foodborne illness-related fatalities occur each year in India. Several factors affect foodborne illness, such as improper farming methods, poor sanitary and hygienic conditions at all levels of the food supply chain, the lack of preventative measures in the food processing industry, the misuse of food additives, as well as improper storage and handling. In addition, chemical and microbiological combinations also play a key role in disease development. But recent disease outbreaks indicated that microbial pathogens played a major role in the development of foodborne diseases. Therefore, prompt, rapid, and accurate detection of high-risk food pathogens is extremely vital to warrant the safety of the food items. Conventional approaches for identifying foodborne pathogens are labor-intensive and cumbersome. As a result, a range of technologies for the rapid detection of foodborne bacterial pathogens have been developed. Presently, many methods are available for the instantaneous detection, identification, and monitoring of foodborne pathogens, such as nucleic acid-based methods, biosensor-based methods, and immunological-based methods. The goal of this review is to provide a complete evaluation of several existing and emerging strategies for detecting food-borne pathogens. Furthermore, this review outlines innovative methodologies and their uses in food testing, along with their existing limits and future possibilities in the detection of live pathogens in food.

Oncogene-targeting nanoprobes for early imaging detection of tumor

Malignant tumors have been one of the major reasons for deaths worldwide. Timely and accurate diagnosis as well as effective intervention of tumors play an essential role in the survival of patients. Genomic instability is the important foundation and feature of cancer, hence, in vivo oncogene imaging based on novel probes provides a valuable tool for the diagnosis of cancer at early-stage. However, the in vivo oncogene imaging is confronted with great challenge, due to the extremely low copies of oncogene in tumor cells. By combining with various novel activatable probes, the molecular imaging technologies provide a feasible approach to visualize oncogene in situ, and realize accurate treatment of tumor. This review aims to declare the design of nanoprobes responded to tumor associated DNA or RNA, and summarize their applications in detection and bioimaging for tumors. The significant challenges and prospective of oncogene-targeting nanoprobes towards tumors diagnosis are revealed as well.

Molecular Beacon Probe (MBP)-Based Real-Time PCR

In the advancement of molecular biology techniques, several probe-based techniques, like molecular beacon probe (MBP) assay, TaqMan probe, and minor groove binder (MGB) probe assay, have been reported to identify specific sequences through real-time polymerase chain reaction (PCR). All probe-based methods are more sensitive than the conventional PCR for the detection and quantification of target genes. MBP is a hydrolysis probe that emits fluorescence when getting the specific sequences on the gene. Here, we describe the application of MBP for the identification of the motif sequences present in the promoters of differentially expressed genes.

Super-Resolution Tension PAINT Imaging with a Molecular Beacon

DNA-PAINT enabled super-resolution imaging through the transient binding of fluorescently-labelled single-stranded DNA (ssDNA) imagers to target ssDNA. However, its performance is constrained by imager background fluorescence, resulting in relatively long image acquisition and potential artifacts. We designed a molecular beacon (MB) as the PAINT imager. Unbound MB in solution reduces the background fluorescence due to its natively quenched state. They are fluorogenic upon binding to target DNA to create individual fluorescence events. We demonstrate that MB-PAINT provides localization precision similar to traditional linear imager DNA-PAINT. We also show that MB-PAINT is ideally suited for fast super-resolution imaging of molecular tension probes in living cells, eliminating the potential of artifacts from free-diffusing imagers in traditional DNA-PAINT at the cell-substrate interface.

Efficient multiplexing and variant discrimination in reverse-transcription loop-mediated isothermal amplification with sequence-specific hybridization probes

Loop-mediated isothermal amplification (LAMP) has proven a robust and reliable nucleic acid amplification method that is well suited for simplified and rapid molecular diagnostics. Various approaches have emerged for sequence-specific detection of LAMP products, but with limitations to their widespread utility or applicability for single-nucleotide polymorphism detection and multiplexing. Here we demonstrate the use of simple hybridization probes (as used for qPCR) that enable simple multiplexing and SARS-CoV-2 variant typing in reverse-transcription LAMP. This approach requires no modification to the LAMP primers and is amenable to the detection of single-nucleotide polymorphisms and small sequence changes, which is usually difficult in LAMP. By extending LAMP’s ability to be utilized for multitarget and single-base change detection, we hope to increase its potential to enable more and better molecular diagnostic testing.

An Advanced Detection System for In Situ Hybridization Using a Fluorescence Resonance Energy Transfer-based Molecular Beacon Probe

In situ hybridization (ISH) is a powerful method for detecting specific RNAs at the cellular level. Although conventional ISH using hapten-labeled probes are useful for detecting multiple RNAs, the detection procedures are still complex and required longer time. Therefore, we introduced a new application of fluorescence resonance energy transfer (FRET)-based molecular beacon (MB) probes for ISH. MCF-7 cells and C57BL/6J mouse uterus were used for ISH. MB probes for ERα mRNA and 28S rRNA were labeled with Cy3/BHQ-2 and 6-FAM/DABCYL, and conventional probes were labeled with digoxigenin. Fluorescence measurements revealed that of more-rapid hybridization kinetics compared to conventional probes. In MCF-7 cells, 28S rRNA was detected in nucleolus and cytoplasm of all cells, whereas ERα mRNA was detected in some nucleolus. In the uterus, 28S rRNA was clearly detected using complementary MB probe, but there were no signals in control slides. Moreover, 28S rRNA was detected in all cells, whereas ERα mRNA was detected mainly in the epithelium. Fluorescence intensity of 28S rRNA was decreased significantly in 1 or 2 base-mismatched sequences, that indicates highly specific detection of target RNAs. In conclusion, the FRET-based MB probes are very useful for ISH, providing rapid hybridization, high sensitivity and specificity.

Potential Method of Autophagy Imaging with Cationized Gelatin Nanospheres Incorporating Molecular Beacon

The objective of this research is to develop an imaging method with cationized gelatin nanospheres incorporating molecular beacon (cGNS_MB) to visualize an autophagy activity in living cells. Cationized gelatin nanospheres (cGNS) were prepared by the conventional coacervation method, and then molecular beacon (MB) was incorporated into them. The cGNS_MB prepared were internalized into cells at a high efficiency. In this study, a starvation medium of serum and amino acids-free was used to induce autophagy. The autophagy activity was confirmed by an immunofluorescence staining for microtubule-associated proteins light chain 3B (LC3B) of an autophagy specific protein. With the autophagy induction time, the number of LC3 fluorescent dots increased, which indicated an increased autophagy activity. As the autophagy-related genes, sequestosome 1 (SQSTM1) and cathepsin F (CTSF), which up-regulate after autophagy induction, were chosen as the targets of cGNS_MB. The fluorescence intensity of cGNS_MB targeting to SQSTM1 and CTSF increased with the starvation treatment time, which well corresponded with the gene expression results. When applied to cells in different autophagy conditions, the cGNS_MB visualized the autophagy activity corresponding with the autophagy condition of cells. From the results obtained, it was concluded that the cGNS_MB provide a promising method to visualize the autophagy of cells. The advantage of cGNS_MB visualization is to obtain the temporal and spatial information without destroying sample cells.

Paving the way towards continuous biosensing by implementing affinity-based nanoswitches on state-dependent readout platforms

Combining affinity-based nanoswitches with state-dependent readout platforms allows for continuous biosensing and acquisition of real-time information about biochemical processes occurring in the environment of interest.

Molecular Beacon Assay Development for Severe Acute Respiratory Syndrome Coronavirus 2 Detection

The fast spread of SARS-CoV-2 has led to a global pandemic, calling for fast and accurate assays to allow infection diagnosis and prevention of transmission. We aimed to develop a molecular beacon (MB)-based detection assay for SARS-CoV-2, designed to detect the ORF1ab and S genes, proposing a two-stage COVID-19 testing strategy. The novelty of this work lies in the design and optimization of two MBs for detection of SARS-CoV-2, namely, concentration, fluorescence plateaus of hybridization, reaction temperature and real-time results. We also identify putative G-quadruplex (G4) regions in the genome of SARS-CoV-2. A total of 458 nasopharyngeal and throat swab samples (426 positive and 32 negative) were tested with the MB assay and the fluorescence levels compared with the cycle threshold (Ct) values obtained from a commercial RT-PCR test in terms of test duration, sensitivity, and specificity. Our results show that the samples with higher fluorescence levels correspond to those with low Ct values, suggesting a correlation between viral load and increased MB fluorescence. The proposed assay represents a fast (total duration of 2 h 20 min including amplification and fluorescence reading stages) and simple way of detecting SARS-CoV-2 in clinical samples from the upper respiratory tract.

Recent Advances in the Molecular Beacon Technology for Live-Cell Single-Molecule Imaging

Nucleic acids, aside from being best known as the carrier of genetic information, are versatile biomaterials for constructing nanoscopic devices for biointerfacing, owing to their unique properties such as specific base pairing and predictable structure. For live-cell analysis of native RNA transcripts, the most widely used nucleic acid-based nanodevice has been the molecular beacon (MB), a class of stem-loop-forming probes that is activated to fluoresce upon hybridization with target RNA. Here, we overview efforts that have been made in developing MB-based bioassays for sensitive intracellular analysis, particularly at the single-molecule level. We also describe challenges that are currently limiting the widespread use of MBs and provide possible solutions. With continued refinement of MBs in terms of labeling specificity and detection accuracy, accompanied by new development in imaging platforms with unprecedented sensitivity, the application of MBs is envisioned to expand in various biological research fields.

Isolation of Cardiomyocytes Undergoing Mitosis With Complete Cytokinesis

RATIONALE

Adult human cardiomyocytes do not complete cytokinesis despite passing through the S-phase of the cell cycle. As a result, polyploidization and multinucleation occur. To get a deeper understanding of the mechanisms surrounding division of cardiomyocytes, there is a crucial need for a technique to isolate cardiomyocytes that complete cell division/cytokinesis.

OBJECTIVE

Markers of cell cycle progression based on DNA content cannot distinguish between mitotic cardiomyocytes that fail to complete cytokinesis from those cells that undergo true cell division. With the use of molecular beacons (MBs) targeting specific mRNAs, we aimed to identify truly proliferative cardiomyocytes derived from human induced pluripotent stem cells.

METHODS AND RESULTS

Fluorescence-activated cell sorting combined with MBs was performed to sort cardiomyocyte populations enriched for mitotic cells. Expressions of cell cycle specific genes were confirmed by means of reverse transcription-quantitative polymerase chain reaction and single-cell RNA sequencing (scRNA-seq) combined with gene signatures of cell cycle progression. We characterized the sorted groups by proliferation assays and time-lapse microscopy which confirmed the proliferative advantage of MB-positive cell populations relative to MB-negative and G2/M populations. Gene expression analysis revealed that the MB-positive cardiomyocyte subpopulation exhibited patterns consistent with the processes of nuclear division, chromosome segregation, and transition from M to G1 phase. The use of dual-MBs targeting CDC20 and SPG20 mRNAs enabled the enrichment of cytokinetic events (CDC20^highSPG20^high). Interestingly, cells that did not complete cytokinesis and remained binucleated were found to be CDC20^lowSPG20^high while polyploid cardiomyocytes that replicated DNA but failed to complete karyokinesis were found to be CDC20^lowSPG20^low.

CONCLUSIONS

This study demonstrates a novel alternative to existing DNA content-based approaches for sorting cardiomyocytes with true mitotic potential that can be used to study the unique dynamics of cardiomyocyte nuclei during mitosis. Our technique for sorting live cardiomyocytes undergoing cytokinesis would provide a basis for future studies to uncover mechanisms underlying the development and regeneration of heart tissue.

Supramolecular Microgels with Molecular Beacons at the Interface for Ultrasensitive, Amplification-Free, and SNP-Selective miRNA Fluorescence Detection

In this study, a supramolecular structure with femtomolar biorecognition properties is proposed for use in analytical devices. It is obtained by an innovative interface between synthetic hydrogel polymers and molecular beacon (mb) probes. Supramolecularly structured microgels are synthetized with a core-shell architecture with specific dyes polymerized in a desired compartment. Mb probes are opportunely conjugated at the microgel interface so that their recognition mechanism is preserved and their spatial distribution is optimized to avoid crowding effects. The miR-21, a microRNA involved in various biological processes and usually used as a biomarker in early cancer diagnosis, has been selected as the target. The results demonstrate that by tuning the spatial distribution of molecular probes immobilized on the microgel and/or the amount of microgels, the assay shows scalable sensitivity reaching a limit of detection down to about 10 fM, without amplification steps and with detection time as short as 1 h. The assay results specific toward single mutated targets, and it is stable in the presence of high-interfering oligonucleotides concentrations. The miRNA target is also detected in human serum with performances similar to those observed in PBS buffer because of microgel antifouling properties without the need of any surface treatment. All tests were performed in a low sample volume (20 μL). As a result, mb-microgel represents an innovative biosensor to precisely quantify microRNAs in a direct (mix&read), scalable, and selective way. Such an approach paves the way for creating innovative biosensing interfaces with other probes, such as hairpins, aptamers, and PNA.

Fluorescence amplified sensing platforms enabling miRNA detection by self-circulation of a molecular beacon circuit

We have proposed a novel strategy for miRNA detection through enzyme-free signal amplification by self-circulation of the hybridization between the miRNAs and molecular beacon (MB) circuits. Unlike general MB-based miRNA detection based on the one-to-one (1 : 1) hybridization between MBs and miRNA, our system consists of four species of MBs (MBs A, B, C and D) (MB circuits) and is activated by a hybridization chain reaction. MBs stably coexist as hairpin structures that hardly show fluorescence signals in the absence of target miRNA. After miRNA detection, this MB circuit is able to generate fluorescence signals and amplify the fluorescence signal, contributing to improvement in detection sensitivity under iso-thermal conditions without an enzyme. Furthermore, in vitro and in vivo studies have proven that MB circuits can detect low levels of miRNA with high sensitivity, compared to when only one MB alone is used. Therefore, the MB circuits can provide a useful platform for target miRNA detection.

A fast and visual method for duplex shrimp pathogens detection with high specificity using rapid PCR and molecular beacon

Molecular diagnosis of genome is one of the major methods for pathogens detection. The commonly used PCR method can realize an exponential amplification of the target gene but is time-consuming. In this work, we proposed a duplex and visual method using rapid PCR combined with molecular beacons to specifically detect two kinds of shrimp pathogens in one reaction tube. We only need to observe the fluorescence change of the reaction tube with naked eye to determine the result. A home-made automatic transfer equipment allows reaction tubes shuttling quickly between two water baths to achieve rapid PCR amplification. A simple device was also designed to present the detection results easily determined with naked eye. This duplex and visual detection method is fast, low-cost and of high specificity. From DNA extraction to results judgment, only 15 min was enough. Infectious Hypodermal and Hematopoietic Necrosis Virus (IHHNV) and Vibrio parahaemolyticus (VP) are two common shrimp pathogens which were chosen as our detection objects. This method may give a possibility to conduct end-point visual duplex detection, which may make a positive influence on the pathogen prevention.

Convenient Monitoring System of Intracellular microRNA Expression during Adipogenesis via Mechanical Stimulus-Induced Exocytosis of Lipovesicular miRNA Beacon

Noninvasive investigation of microRNAs (miRNAs) expression, which is deeply related to biological phenomena such as stem cell differentiation, in culture soup is particularly useful for monitoring of stem cell differentiation without phototoxicity of living cells, especially when cell morphologies remain unchanged during differentiation. However, real-time detection of miRNA in culture soup is not recommended because of insufficient miRNA amounts in culture soup. In this study, a convenient method is introduced for real-time assessing intracellular miRNA in culture soup by using lipovesicular miRNA beacon (Lipo-mB) and mechanical stimulus-mediated exocytosis. Pipetting-harvest of culture soup induces exocytosis-secretion of fluorescence signal of Lipo-mB from cytoplasm into culture soup. To demonstrate this method, Lipo-mB is applied for monitoring of adipogenesis by analyzing the expression levels of various intracellular miRNAs, which are related to adipogenesis regulators. The fluorescence intensity profile of the culture soup is correlated with the quantitative reverse-transcription-polymerase chain reaction data and absorbance of Oil Red O staining. These results demonstrate that Lipo-mB can successfully monitor stem cell differentiation by sensing changes in miRNA expression from culture soup of living cells. Lipo-mB can be further developed as an accurate sensing system for analyzing subtle differences in genotype, even when changes in phenotype cannot be observed.

Studying the influence of stem composition in pH-sensitive molecular beacons onto their sensing properties

Intracellular sensing using fluorescent molecular beacons is a potentially useful strategy for real-time, in vivo monitoring of important cellular events. This work is focused on evaluation of pyrene excimer signaling molecular beacons (MBs) for the monitoring of pH changes in vitro as well as inside living cells. The recognition element in our MB called pHSO (pH-sensitive oligonucleotide) is the loop enclosing cytosine-rich fragment that is able to form i-motif structure in a specific pH range. However, alteration of a sequence of the 6 base pairs containing stem of MB allowed the design of pHSO probes that exhibited different dynamic pH range and possessed slightly different transition midpoint between i-motif and open loop configuration. Moreover, this conformational transition was accompanied by spectral changes showing developed probes different pyrene excimer-monomer emission ratio triggered by pH changes. The potential of these MBs for intracellular pH sensing is demonstrated on the example of HeLa cells line.

Bright luminescent optically engineered core/alloyed shell quantum dots: an ultrasensitive signal transducer for dengue virus RNA via localized surface plasmon resonance-induced hairpin hybridization

A plasmon-mediated fluorescence molecular beacon biosensor probe has been developed for dengue virus with high sensitivity and specificity.

Peptide nucleic acid probe-based fluorescence melting curve analysis for rapid screening of common JAK2, MPL, and CALR mutations

BACKGROUND

We developed and evaluated the feasibility of peptide nucleic acid (PNA)-based fluorescence melting curve analysis (FMCA) to detect common mutations in myeloproliferative neoplasms (MPNs).

METHODS

We have set up two separate reactions of PNA-based FMCA: JAK2 V617F &CALR p.Leu367fs*46 (set A) and MPL W515L/K &CALR p.Lys385fs*47 (set B). Clinical usefulness was validated with allele-specific real-time PCR, fragment analysis, Sanger sequencing in 57 BCR-ABL1-negative MPNs.

RESULTS

The limit of detection (LOD) of PNA-based FMCA was approximately 10% for each mutation and interference reactions using mixtures of different mutations were not observed. Non-specific amplification was not observed in normal control. PNA-based FMCA was able to detect all JAK2 V617F (n=20), CALR p.Leu367fs*46 (n=10) and p.Lys385fs*47 (n=8). Three of six MPL mutations were detected except three samples with low mutant concentration in out of LOD. JAK2 exon 12 mutations (n=7) were negative without influencing V617F results. Among six variant CALR exon 9 mutations, two were detected by this method owing to invading of probe binding site.

CONCLUSIONS

PNA-based FMCA for detecting common JAK2, MPL, and CALR mutations is a rapid, simple, and sensitive technique in BCR-ABL1-negative MPNs with >10% mutant allele at the time of initial diagnosis.

Simple, rapid detection of influenza A (H1N1) viruses using a highly sensitive peptide-based molecular beacon

A peptide-based molecular beacon (PEP-MB) was prepared for the simple, rapid, and specific detection of H1N1 viruses using a fluorescence resonance energy transfer (FRET) system. The PEP-MB exhibited minimal fluorescence in its "closed" hairpin structure. However, in the presence of H1N1 viruses, the specific recognition of the hemagglutinin (HA) protein of H1 strains by the PEP-MB causes the beacon to assume an "open" structure that emits strong fluorescence. The PEP-MB could detect H1N1 viruses within 15 min or even 5 min and can exhibit strong fluorescence even at low viral concentrations, with a detection limit of 4 copies.

Fluorescence-Based Strategies to Investigate the Structure and Dynamics of Aptamer-Ligand Complexes

In addition to the helical nature of double-stranded DNA and RNA, single-stranded oligonucleotides can arrange themselves into tridimensional structures containing loops, bulges, internal hairpins and many other motifs. This ability has been used for more than two decades to generate oligonucleotide sequences, so-called aptamers, that can recognize certain metabolites with high affinity and specificity. More recently, this library of artificially-generated nucleic acid aptamers has been expanded by the discovery that naturally occurring RNA sequences control bacterial gene expression in response to cellular concentration of a given metabolite. The application of fluorescence methods has been pivotal to characterize in detail the structure and dynamics of these aptamer-ligand complexes in solution. This is mostly due to the intrinsic high sensitivity of fluorescence methods and also to significant improvements in solid-phase synthesis, post-synthetic labeling strategies and optical instrumentation that took place during the last decade. In this work, we provide an overview of the most widely employed fluorescence methods to investigate aptamer structure and function by describing the use of aptamers labeled with a single dye in fluorescence quenching and anisotropy assays. The use of 2-aminopurine as a fluorescent analog of adenine to monitor local changes in structure and fluorescence resonance energy transfer (FRET) to follow long-range conformational changes is also covered in detail. The last part of the review is dedicated to the application of fluorescence techniques based on single-molecule microscopy, a technique that has revolutionized our understanding of nucleic acid structure and dynamics. We finally describe the advantages of monitoring ligand-binding and conformational changes, one molecule at a time, to decipher the complexity of regulatory aptamers and summarize the emerging folding and ligand-binding models arising from the application of these single-molecule FRET microscopy techniques.

Recent progress on colloidal metal nanoparticles as signal enhancers in nanosensing

Colloidal metal nanoparticles present very special optical and electromagnetic properties at the nanoscale range. Such plasmonic properties have derived in a huge research field that encompasses the understanding of nanoparticle formation mechanisms for the ultimate goal of developing novel materials for real-life applications. Plasmonic sensing is experiencing a rapid transition by taking advantage of the characteristic properties of colloidal metal nanoparticles. However, a rational design of novel nanoplasmonic substrates, which gathers as much as the required properties for a substrate to be a 'good' sensor is critical through the development of applications that can be effectively transferred as applied technologies. Also, the chosen sensing technique is a key factor when planning the design of a new plasmonic-based sensor. Several factors such as composition, shape, size, particle interactions or stability among others will define the final quality of the nanomaterial as sensing platform. Herein, we review the latest and most promising state-of-the art of nanoplasmonic-based sensors in four differentiated areas regarding the surface-enhanced spectroscopy detection technique being LSPR-, SERS- and SEIRA-, and SEF based platforms.

Separation of Mycobacterium abscessus into subspecies or genotype level by direct application of peptide nucleic acid multi-probe- real-time PCR method into sputa samples

Background

Recently, we introduced a novel peptide nucleic acid (PNA) multi-probe real time PCR method targeting the hsp65 gene (hsp65 PNA RT-PCR) to distinguish Mycobacterium abscessus groups.

Methods

Here, we evaluated the usefulness of the hsp65 PNA RT-PCR for the direct identification of the M. abscessus group at the subspecies and genotype levels from sputa samples. The method was applied to total sputa DNA from 60 different patients who were identified as having mycobacterial infections via rpoB PCR restriction analysis of the same cultures.

Results

The hsp65 PNA RT-PCR method had higher sensitivity than the multi-probe real-time PCR assay targeting hsp65 (HMPRT-PCR) for the detection of M. abscessus from sputum [96.7 % (29/30 samples) vs. 70 % (21/30 samples); 100 % specificity].

Conclusions

These results suggest that the PNA-based method is feasible for the detection of M. abscessus members not only from cultures but also directly from sputa.

Electronic supplementary material

The online version of this article (doi:10.1186/s12879-015-1076-8) contains supplementary material, which is available to authorized users.

Pyrene functionalized molecular beacon with pH-sensitive i-motif in a loop

In this work, we present a spectral characterization of pH-sensitive system, which combines the i-motif properties with the spatially sensitive fluorescence signal of pyrene molecules attached to hairpin ends. The excimer production (fluorescence max. ∼480 nm) by pyrene labels at the ends of the molecular beacon is driven by pH-dependent i-motif formation in the loop. To illustrate the performance and reversible work of our systems, we performed the experiments with repeatedly pH cycling between pH values of 7.5±0.3 and 6.5±0.3. The sensor gives analytical response in excimer-monomer switching mode in narrow pH range (1.5 pH units) and exhibits high pH resolution (0.1 pH unit).

Constitutional Dynamic Chemistry-based New Concept of Molecular Beacons for High Efficient Development of Fluorescent Probes

Inspired by the concept of constitutional dynamic chemistry, we propose a new and well-adaptable strategy for developing molecular beacon (MB)-like fluorescent probes. To demonstrate the strategy, we synthesized and used an amino group containing pyrenyl derivative of cholesterol (CP) for the construction of new fluorescent probes with EDTA and sulfuric acid. The probes as created were successfully used for n-hexane purity checking and Ba(2+)and Pb(2+)sensing, respectively.

One-strand oligonucleotide probe for fluorescent label-free “turn-on” detection of T4 polynucleotide kinase activity and its inhibition

Thioflavin T (ThT), as one of the most exciting fluorogenic molecules, boasts the “molecular-rotor” ability to induce DNA sequences containing guanine repeats to fold into G-quadruplex structures.

Inside single cells: quantitative analysis with advanced optics and nanomaterials

Single-cell explorations offer a unique window to inspect molecules and events relevant to mechanisms and heterogeneity constituting the central dogma of biology. A large number of nucleic acids, proteins, metabolites, and small molecules are involved in determining and fine-tuning the state and function of a single cell at a given time point. Advanced optical platforms and nanotools provide tremendous opportunities to probe intracellular components with single-molecule accuracy, as well as promising tools to adjust single-cell activity. To obtain quantitative information (e.g., molecular quantity, kinetics, and stoichiometry) within an intact cell, achieving the observation with comparable spatiotemporal resolution is a challenge. For single-cell studies, both the method of detection and the biocompatibility are critical factors as they determine the feasibility, especially when considering live-cell analysis. Although a considerable proportion of single-cell methodologies depend on specialized expertise and expensive instruments, it is our expectation that the information content and implication will outweigh the costs given the impact on life science enabled by single-cell analysis.

Label-free molecular beacons for biomolecular detection

Biomolecular detection and imaging methods provide quantitative measurements essential for biological research. In this context, molecular beacon based sensors have emerged as powerful, no-wash imaging agents, providing target-specific fluorescent activation for nucleic acids, proteins, and small molecules. Conventional molecular beacons require double-labeled DNA sequences, which are costly and time-consuming to prepare. To address this issue, we developed DNA based label-free molecular beacons consisting of two regions: a signal-generating region based on human telomeric G-quadruplex sequence that activates Thioflavin T fluorescence and a target recognition sequence designed to interact in a molecular beacon format. We demonstrated the utility of these probes for the selective detection of DNA, RNA, and protein. Multiple probes were applied against a single target to achieve improved brightness in fluorescence detection of nucleic acid targets. This label-free strategy provides a straightforward, cost-effective alternative to fluorescently labeled oligonucleotides in biomolecular detection and imaging.

Multilayer graphene-gold nanocomposite modified stem-loop DNA biosensor for peanut allergen-Ara h1 detection

In this study, we developed an electrochemically-amplified, stem-loop DNA biosensor to detect the peanut allergen Ara h1. Specifically, we electrodeposited a multilayer graphene-gold nanocomposite onto a glassy carbon electrode and then immobilised a thiolated hairpin DNA-biotin probe onto the modified electrode surface. The multilayer graphene-gold composite has good dispersion ability, and can amplify the electrochemical signal due to its high electron-transfer efficiency. The probe was switched to an "off" state in the presence of target DNA. The prepared biosensor demonstrated a linear response ranging from 10(-16) to 10(-13)M, with an ultrasensitive detection limit of 0.041 fM. Moreover, the biosensor showed excellent selectivity, as well as the ability to discriminate between a complementary target and a one-base mismatch or non-complementary sequence. Results show that this prepared DNA biosensor can be successfully used to detect the peanut allergen Ara h1 in a peanut milk beverage. Findings can be applied to the prevention of allergic reactions, thus improving human health and safety.

The quantitative real-time PCR applications in the monitoring of marine harmful algal bloom (HAB) species

In the last decade, various molecular methods (e.g., fluorescent hybridization assay, sandwich hybridization assay, automatized biosensor detection, real-time PCR assay) have been developed and implemented for accurate and specific identification and estimation of marine toxic microalgal species. This review focuses on the recent quantitative real-time PCR (qrt-PCR) technology developed for the control and monitoring of the most important taxonomic phytoplankton groups producing biotoxins with relevant negative impact on human health, the marine environment, and related economic activities. The high specificity and sensitivity of the qrt-PCR methods determined by the adequate choice of the genomic target gene, nucleic acid purification protocol, quantification through the standard curve, and type of chemical detection method make them highly efficient and therefore applicable to harmful algal bloom phenomena. Recent development of qrt-PCR-based assays using the target gene of toxins, such as saxitoxin compounds, has allowed more precise quantification of toxigenic species (i.e., Alexandrium catenella) abundance. These studies focus only on toxin-producing species in the marine environment. Therefore, qrt-PCR technology seems to offer the advantages of understanding the ecology of harmful algal bloom species and facilitating the management of their outbreaks.

Use of flow cytometry for rapid, quantitative detection of poliovirus-infected cells via TAT peptide-delivered molecular beacons

Rapid and efficient detection of viral infection is crucial for the prevention of disease spread during an outbreak and for timely clinical management. In this paper, the utility of Tat peptide-modified molecular beacons (MBs) as a rapid diagnostic tool for the detection of virus-infected cells was demonstrated. The rapid intracellular delivery mediated by the Tat peptide enabled the detection of infected cells within 30 s, reaching saturation in signal in 30 min. This rapid detection scheme was coupled with flow cytometry (FC), resulting in an automated, high-throughput method for the identification of virus-infected cells. Because of the 2-order-of-magnitude difference in fluorescence intensity between infected and uninfected cells, as few as 1% infected cells could be detected. Because of its speed and sensitivity, this approach may be adapted for the practical diagnosis of multiple viral infections.

Design and development of an in-house multiplex RT-PCR assay for simultaneous detection of HIV-1 and HCV in plasma samples

BACKGROUND AND OBJECTIVES

HIV-1 and HCV infections are life threatening problems in patients who receive blood products. Serological methods have proven useful in detecting these infections, but there are setbacks that make it challenging to detect these infectious agents. By the advent of Nucleic Acid Testing (NAT) methods, especially in multiplex format, more precise detection is possible.

MATERIALS AND METHODS

We have developed a multiplex RT-PCR assay for simultaneous detection of HIV-1 and HCV. Primers were designed for highly conserved region of genome of each virus. Using these primers and standard plasmids, we determined the limit of detection, clinical and analytical specificity and sensitivity of the assay. Monoplex and multiplex RT-PCR were performed.

RESULTS

Analytical sensitivity was considered to be 100 and 200 copies/ml for HIV-1 and HCV, respectively. High concentration of one virus had no significant effect on the detection of the other one with low concentration. By analysis of 40 samples, clinical sensitivity of the assay was determined to be 97.5%. Using different viral and human genome samples, the specificity of the assay was evaluated to be 100%.

CONCLUSIONS

The aim of this study was to develop a reliable, rapid and cost effective method to detect HIV-1 and HCV simultaneously. Results showed that this simple and rapid method is perfectly capable of detecting two viruses in clinical samples.

Detection of prolactin inducible protein mRNA, a biomarker for breast cancer metastasis, using a molecular beacon-based assay

Mortality due to breast cancer is increasingly linked to early, undetected metastasis, making methods for earlier detection acutely necessary. We describe the development of an assay based on molecular beacon (MB) chemistry with fluorescence detection to monitor a breast cancer biomarker for the analysis of breast cancer metastasis. The MB assay is based on the complementary base-pairing interactions of the MB nucleic acid with mRNA indicative of breast cancer metastasis. The presence of mRNA is characterized by an increase in the fluorescence intensity of the molecular beacon. The assay gives a linear, reproducible response to prolactin inducible protein mRNA, with a limit of detection in the high picomolar range. This method sensitively and specifically identifies a biomarker directly in serum samples in minimal time and with a straightforward procedure, dramatically reducing the total time for sample analysis over current methods from days to hours. The potential impact of this work in detection and understanding of breast cancer metastasis lies in improvements in simplicity, accuracy, and speed over current methods, which could allow for improved patient treatment and prognoses. Ultimately, additional sample throughput will result in better understanding of disease progression.

Mercury/homocysteine ligation-induced ON/OFF-switching of a T-T mismatch-based oligonucleotide molecular beacon

A molecular beacon (MB) with stem-loop (hairpin) DNA structure and with attached fluorophore-quencher pair at the ends of the strand has been applied to study the interactions of Hg(2+) ions with a thymine-thymine (T-T) mismatch in Watson-Crick base-pairs and the ligative disassembly of MB·Hg(2+) complex by Hg(2+) sequestration with small biomolecule ligands. In this work, a five base-pair stem with configuration 5'-GGTGG...CCTCC-3' for self-hybridization of MB has been utilized. In this configuration, the four GC base-pair binding energy is not sufficient to hybridize fully at intermediate temperatures and to form a hairpin MB conformation. The T-T mismatch built-in into the stem area can effectively bind Hg(2+) ions creating a bridge, T-Hg-T. We have found that the T-Hg-T bridge strongly enhances the ability of MB to hybridize, as evidenced by an unusually large MB melting temperature shift observed on bridge formation, ΔT(m) = +15.1 ± 0.5 °C, for 100 nM MB in MOPS buffer. The observed ΔT(m) is the largest of the ΔT(m) found for other MBs and dsDNA structures. By fitting the parameters of the proposed model of reversible MB interactions to the experimental data, we have determined the T-Hg-T bridge formation constant at 25 °C, K(1) = 8.92 ± 0.42 × 10(17) M(-1) from mercury(II) titration data and K(1) = 1.04 ± 0.51 × 10(18) M(-1) from the bridge disassembly data; ΔG° = -24.53 ± 0.13 kcal/mol. We have found that the biomarker of oxidative stress and cardiovascular disease, homocysteine (Hcys), can sequester Hg(2+) ions from the T-Hg-T complex and withdraw Hg(2+) ions from MB in the form of stable Hg(Hcys)(2)H(2) complexes. Both the model fitting and independent (1)H NMR results on the thymidine-Hg-Hcys system indicate also the high importance of 1:1 complexes. The high value of K(1) for T-Hg-T bridge formation enables analytical determinations of low concentrations of Hg(2+) (limit of detection LOD = 19 nM or 3.8 ppb, based on 3σ method) and Hcys (LOD = 23 nM, 3σ method). The conditional stability constants for Hg(Hcys)H(2)(2+) and Hg(Hcys)(2)H(2) at 52 °C have been determined, β(112) = 5.37 ± 0.3 × 10(46) M(-3), β(122) = 3.80 ± 0.6 × 10(68) M(-4), respectively.

Visual detection of single-base mismatches in DNA using hairpin oligonucleotide with double-target DNA binding sequences and gold nanoparticles

We describe a hairpin oligonucleotide (HO) with double-target DNA binding sequences in the loop and 11-base in the stem for visual detection of single-base mismatches (SBM) in DNA with highly specificity. The thiol-modified HO was immobilized on gold nanoparticle (Au-NP) surface through a self-assembling process. The strategy of detecting SBM depends on the unique molecular recognition properties of HO to the perfect-matched DNA and SBM to generate different quantities of duplex DNA on the Au-NP surface, which are captured on the test zone of lateral flow test strip via the DNA hybridization reaction between the duplex DNA and preimmobilized DNA probe. Accumulation of Au-NPs produces the characteristic red bands, enabling visual detection of SBM. It was found that the ability of HO to differentiate perfect-matched DNA and SBM was increased dramatically by incorporating double-target DNA binding sequences in the loop of HO. The signal ratio between perfect-matched DNA and SBM was up to 28, which is much higher than that of conventional HO or molecular beacon. The approach was applied to detect the mutation sites, Arg142Cys and Gly529Ile, of transglutaminase 1 gene in autosomal recessive congenital ichthyosis. The results presented here show that the new HO is a potential molecular recognition probe for the future development of nucleic acid-based biosensors and bioassays. The approach can be used for point-of-care diagnosis of genetic diseases and detecting infectious agents or warning against bio-warfare agents.

Ligand-induced changes in T box antiterminator RNA stability

The T box antiterminator RNA element is an important component of the T box riboswitch that controls the transcription of vital genes in many Gram-positive bacteria. A series of 1,4-disubstituted 1,2,3-triazoles was screened in a fluorescence-monitored thermal denaturation assay to identify ligands that altered the stability of antiterminator model RNA. Several ligands were identified that significantly increased or decreased the melting temperature (T(m) ) of the RNA. The results indicate that this series of triazole ligands can alter the stability of antiterminator model RNA in a structure-dependent manner.

Bioluminescent stem-loop probes for highly sensitive nucleic acid detection

Here, we report the first bioluminescent stem-loop probe, which is 50 times more sensitive and able to achieve a LOD 25 times lower than fluorescent stem-loop probes. Chemical generation of a signal from Renilla luciferase reduces background noise for improved quantitative utility in nucleic acid biomarker detection.

Detecting RNA viruses in living mammalian cells by fluorescence microscopy

Traditional methods that rely on viral isolation and culture techniques continue to be the gold standards used for detection of infectious viral particles. However, new techniques that rely on visualization of live cells can shed light on understanding virus-host interaction for early stage detection and potential drug discovery. Live-cell imaging techniques that incorporate fluorescent probes into viral components provide opportunities for understanding mRNA expression, interaction, and virus movement and localization. Other viral replication events inside a host cell can be exploited for non-invasive detection, such as single-virus tracking, which does not inhibit viral infectivity or cellular function. This review highlights some of the recent advances made using these novel approaches for visualization of viral entry and replication in live cells.

Enumeration of methanogens with a focus on fluorescence in situ hybridization

Methanogens, the members of domain Archaea are potent contributors in global warming. Being confined to the strict anaerobic environment, their direct cultivation as pure culture is quite difficult. Therefore, a range of culture-independent methods have been developed to investigate their numbers, substrate uptake patterns, and identification in complex microbial communities. Unlike other approaches, fluorescence in situ hybridization (FISH) is not only used for faster quantification and accurate identification but also to reveal the physiological properties and spatiotemporal dynamics of methanogens in their natural environment. Aside from the methodological aspects and application of FISH, this review also focuses on culture-dependent and -independent techniques employed in enumerating methanogens along with associated problems. In addition, the combination of FISH with micro-autoradiography that could also be an important tool in investigating the activities of methanogens is also discussed.

Polymer-functionalized gold nanoparticles as versatile sensing materials

In this brief review, gold nanoparticles conjugated with functional polymers are described from the viewpoint of application to sensing materials. The optical properties of gold nanoparticles, the synthesis of polymer-functionalized gold nanoparticles, and their analytical applications are discussed. Polymer-functionalized gold nanoparticles are categorized into two classes: biopolymer-conjugated gold nanoparticles and artificial-polymer conjugated gold nanoparticles. Fluorometric and colorimetric sensing using gold nanoparticles are focused; fluorometric detection enables us to exploit sensitive assays for practical use. Furthermore, chemical amplification using gold nanoparticles is also discussed for the sensitive probing.