Colorimetric detection of clinical DNA samples using an intercalator-conjugated polydiacetylene sensor

Highly selective detection of deoxyribonucleic acid in living cells using RecA-green fluorescent protein-single-stranded deoxyribonucleic acid filament fluorescence resonance energy transfer probe

A fluorescence resonance energy transfer (FRET) method was developed for double-stranded deoxyribonucleic acid (dsDNA) detection in living cells using the RecA-GFP (green fluorescent protein) fusion protein filament. In brief, the thiol-modified single-stranded DNA (ssDNA) was attached to gold nanoparticles (AuNPs); on the contrary, the prepared RecA-GFP fusion protein interacted with ssDNA. Due to the FRET between AuNPs and RecA-GFP, fluorescence of RecA-GFP fusion protein was quenched. In the presence of homologous dsDNA, homologous recombination occurred to release RecA-GFP fusion protein. Thus, the fluorescence of RecA-GFP was recovered. The dsDNA concentration was detected using fluorescence intensity of RecA-GFP. Under optimal conditions, this method could detect dsDNA activity as low as 0.015 optical density (OD) Escherichia coli cells, with a wide linear range from 0.05 to 0.9 OD cells, and the regression equation was ΔF = 342.7c + 78.9, with a linear relationship coefficient of 0.9920. Therefore, it provided a promising approach for the selective detection of dsDNA in living cells for early clinical diagnosis of genetic diseases.

A Chitosan-Based Fluorescent Probe Combined with Smartphone Technology for the Detection of Hypochlorite in Pure Water

Using chitosan as a raw material, 1,8-naphthimide as the fluorescent chromophore, and sulfur-containing compounds as the recognition groups, a novel naphthimide-functionalized chitosan probe, CS-BNS, for the detection of ClO- was successfully synthesized. The modification of chitosan was verified by SEM, XRD, FTIR, mapping, 13C-NMR, TG and the structure of the probe molecule was characterized. The identification performance of the probes was studied using UV and fluorescence spectrophotometers. The results show that CS-BNS exhibits a specific response to ClO- based on the oxidative reaction of ClO- to the recognition motifs, as well as a good resistance to interference. And the probe has high sensitivity and fast response time, and can complete the detection of ClO- in a pure water system within 60 s. The probe can also quantify ClO- (y = 30.698x + 532.37, R2 = 0.9833) with a detection limit as low as 0.27 μM. In addition, the combination of the probe with smartphone technology enables the visualization and real-time monitoring of ClO-. Moreover, an identification system for ClO- was established by combining the probe with smartphone technology, which realized the visualization and real-time monitoring of ClO-.

Polydiacetylene-based colorimetric and fluorometric sensors for lead ion recognition

Development of novel sensors for the detection of lead ions (Pb2+) has attracted increasing interest due to their inherent toxic effects on human health and the environment. In this study, we describe two new polydiacetylene (PDA)-based liposome sensors for the colorimetric and fluorometric recognition of Pb2+ in aqueous solution. In the sensor system, a thymine-1-acetic acid (TAA) or orotic acid (OA) group was reasonably introduced into the diacetylene monomer to work as a strong binding site for Pb2+. The TAA- or OA-functionalized monomer and 10,12-pentacosadiynoic acid (PCDA) were incorporated into PDA liposomes in aqueous solution. After UV light-induced polymerization, deep blue colored liposome solutions were obtained. Upon the addition of a series of transition metal cations into the liposome solutions, only Pb2+ could induce a color change from blue to red observable by the naked eye and a large fluorescence enhancement. The results clearly showed that the PDA-EDEA-TAA and PDA-EDEA-OA liposomes could act as highly selective and sensitive probes to detect Pb2+ in aqueous solution. The detection limits of PDA-EDEA-TAA and PDA-EDEA-OA systems are 38 nM and 25 nM, respectively. The excellent selectivity of PDA liposomes could be attributed to the stronger complexation behavior of Pb2+ with TAA (or OA) and the carboxylic acid at the lipid-solution interface which could perturb the PDA conjugated backbone. In addition, the proposed sensors were successfully applied to detect trace amounts of Pb2+ in real water samples with excellent recovery, indicating that the developed method had a good accuracy and precision for the analysis of trace Pb2+ in practical samples.

Bifunctional ligand-mediated amplification of polydiacetylene response to biorecognition of diethylstilbestrol for on-site smartphone detection

Polydiacetylene (PDA) is very suited for sensitively detecting large biomolecules, and its unique chromatic properties enable visual read-out. However, application to the selective detection of small molecules remains challenging. Here, bifunctional ligands are studied to amplify the color change of PDA for biorecognition of small molecules for the smartphone-based detection of diethylstilbestrol (DES). PDA is decorated with streptavidin (PDA-SA, blue), and biotin-modified DES (bio-DES) is prepared as a bifunctional ligand to couple with PDA-SA and DES antibody. Since multiple bio-DES can bind to a single SA, then multiple SAs on PDA lead to an increased surface coverage of the vesicle. In samples without DES, PDA-SA-bio-DES-DES antibody complexes will form, leading to a color transition (blue to red); this color transition is greatly amplified by antibody-induced aggregation of the complexes. When DES is present, aggregation is inhibited due to competition for the antibody and PDA-SA-bio-DES retains its blue color. A linear relationship (0.4-1250 ng mL^-1) is found between the colorimetric response and the logarithmic DES concentration, with adequate selectivity, accuracy (82.24-118.64%), and precision (below 8.24%). Finally, a paper-based DES PDA biosensor is developed with visual and smartphone-based detection limits of 10 ng mL^-1 and 0.85 ng mL^-1 in water, respectively.

The application of DNA-HRP functionalized AuNP probes in colorimetric detection of citrus-associated Alternaria genes

The monitoring of the fungal genus Alternaria, which causes destructive brown spot disease in citruses worldwide and produces highly toxic mycotoxins, is extremely important to protect citrus and human health. In this work, we describe an ultrasensitive colorimetric method for the detection of genomic DNA of Alternaria from citrus fruit samples, using a system consisting of five groups of reporter probes. Each reporter probe is prepared by coupling recognition DNA and horseradish peroxidase (HRP) on the surface of gold nanoparticle (AuNP) through a convenient and low-cost freezing-assisted method. Meanwhile, the capture DNA is immobilized on magnetic bead (MB) via biotin-streptavidin reaction. Then, the capture DNA, target DNA, and five groups of AuNP-based reporter probes form a stable DNA-heptamer sandwich structure on the MB, and then HRP generates a blue signal for the subsequent colorimetric detection. It should be noted that AuNP with a large specific surface area drives abundant HRP anchoring, resulting in significant signal amplification. In addition, there are five groups of AuNP-based reporter probes, which further amplify the detection signal. As a result, the detection limit of the artificial target DNA is as low as 15.6 pM. Because the detection signal can be recorded visually without any special equipment, and its sensitivity is high, this method represents a suitable diagnostic tool for Alternaria genetic detection.

Integrating multiple hybridization chain reactions on gold nanoparticle and alkaline phosphatase-mediated in situ growth of gold nanobipyramids: An ultrasensitive and high color resolution colorimetric method to detect the mecA gene of Staphylococcus aureus

Colorimetry has been considered as a potential instrument-free platform for point-of-care genomic detection. However, it is limited by the poor sensitivity and low color resolution. Herein, we report a high-resolution colorimetric biosensor based on multiple hybridization chain reactions (HCRs) on gold nanoparticle (AuNP) and alkaline phosphatase (ALP)-mediated in situ growth of gold nanobipyramids (AuNBPs) for ultrasensitive detection of the Staphylococcus aureus (S. aureus) mecA gene. In our design, target DNA is hybridized with capture hairpin DNA on magnetic beads and then amplified by multiple HCRs on AuNP. Since biotin-labeled hairpin-structured nucleic acids are utilized to conduct HCRs, together with the large specific surface area of AuNP, the biotin- and streptavidin- based reaction results in a large amount of ALP on AuNP. With the aid of NADPH, ALP-mediated in situ growth of AuNBPs is observed, and a series of rainbow-like colors are associated with different target DNA concentrations. Through the multiple-amplification strategy produced by AuNP, HCRs, and enzymatic reactions, the target DNA as low as 2.71 pM can be detected with high specificity. Moreover, this method has been successfully applied to detect the mecA gene extracted from S. aureus. Therefore, the proposed method holds great potential in clinical diagnosis.

Structures and strategies for enhanced sensitivity of polydiacetylene(PDA) based biosensor platforms

Polydiacetylene (PDA) is a versatile polymer that has been studied in numerous fields because of its unique optical properties derived from alternating multiple bonds in the polymer backbone. The conjugated structure in the polymer backbone enables PDA to possess the ability of blue-red colorimetric transition when π-π interactions in the PDA backbone chain are disturbed by the external environment. The chromatic property of PDA disturbed by external stimuli can also emit fluorescence in the red region. Owing to the unique characteristics of PDA, it has been widely studied in facile and label-free sensing applications based on colorimetric or fluorescence signals for several decades. Among the various PDA structures, membrane structures assembled by amphiphilic molecules are widely used as a versatile platform because facile modification of the synthetic membrane provides extensive applications, such as receptor-ligand interactions, resulting in potent biosensors. To use PDA as a sensory material, several methods have been studied to endow the specificity to PDA molecules and to amplify the signal from PDA supramolecules. This is because selective and sensitive detection of target materials is required at an appropriate level corresponding to each material for applicable sensor applications. This review focuses on factors that affect the sensitivity of PDA composites and several strategies to enhance the sensitivity of the PDA sensor to various structures. Owing to these strategies, the PDA sensor system has achieved a higher level of sensitivity and selectivity, enabling it to detect multiple target materials for a full field of application.

Recent advances in nanomaterials for colorimetric cancer detection

The early diagnosis of cancer can significantly improve patient survival rates. Colorimetric methods for real-time naked-eye detection have aroused growing interest owing to their low cost, simplicity, and practicability. With the rapid development of nanotechnology, compared with conventional diagnostic methods, nanomaterials with unique physical and chemical properties were applied to improve selectivity and sensitivity in colorimetric detection of cancer biomarkers, such as MUC1 aptamer conjugated PtAuNPs to specifically recognize MUC1 proteins on the cancer cell surfaces, etching of silver nanoprisms to detect prostate-specific antigen, and aggregation or dispersion of AuNPs to sense prostate cancer antigen gene 3 or glutathione, by which the limit of detection (LOD) could approach values down to a few cancer cells per mL, several fg per mL proteins, several ng of nucleic acids, or even tens of nM of organic molecules. Herein, we review the recent progress achieved in developing colorimetric nanosensors for cancer diagnosis, particularly providing an overview of the sensing principles, target biomarkers, advanced nanomaterials employed in the fabrication of sensing platforms, and strategies for improving signal sensitivity and specificity. Finally, we sum up the nanomaterial-based colorimetric cancer detection as well as existing challenges that should be resolved to extend their clinical application.

Pyronaridine: An update of its pharmacological activities and mechanisms of action

Pyronaridine (PYR) is an erythrocytic schizonticide with a potent antimalarial activity against multidrug-resistant Plasmodium. The drug is used in combination with artesunate for the treatment of uncomplicated P. falciparum malaria, in adults and children. The present review briefly retraces the discovery of PYR and recent antimalarial studies which has led to the approval of PYR/artesunate combination (Pyramax) by the European Medicines Agency to treat uncomplicated malaria worldwide. PYR also presents a marked antitumor activity and has revealed efficacy for the treatment of other parasitic diseases (notably Babesia and Trypanosoma infections) and to mitigate the Ebola virus propagation. On the one hand, PYR functions has an inhibitor of hemozoin (biomineral malaria pigment, by-product of hemoglobin digestion) formation, blocking the biopolymerization of β-hematin and thus facilitating the accumulation of toxic hematin into the digestive vacuole of the parasite. On the other hand, PYR is a bona fide DNA-intercalating agent and an inhibitor of DNA topoisomerase 2, leading to DNA damages and cell death. Inhibition of hematin polymerization represents the prime mechanism at the origin of the antimalarial activity, whereas anticancer effects relies essentially on the interference with DNA metabolism, as with structurally related anticancer drugs like amsacrine and quinacrine. In addition, recent studies point to an immune modulatory activity of PYR and the implication of a mitochondrial oxidative pathway. An analogy with the mechanism of action of artemisinin drugs is underlined. In brief, the biological actions of pyronaridine are recapitulated to shed light on the diverse health benefits of this unsung drug.

Carbon dot-based fluorometric optical sensors: an overview

Fluorescent carbon dots (CDs) are a new class of carbon nanomaterials and have demonstrated excellent optical properties, good biocompatibility, great aqueous solubility, low cost, and simple synthesis. Since their discovery, various synthesis methods using different precursors were developed, which were mainly classified as top-down and bottom-up approaches. CDs have presented many applications, and this review article mainly focuses on the development of CD-based fluorescent sensors. The sensing mechanisms, sensor design, and sensing properties to various targets are summarized. Broad ranges of detection, including temperature, pH, DNA, antibiotics, cations, cancer cells, and antibiotics, have been discussed. In addition, the challenges and future directions for CDs as sensing materials are also presented.

Polydiacetylene (PDA) Liposome-Based Immunosensor for the Detection of Exosomes

Exosomes are extracellular vesicles (EVs) that have attracted attention because of their important biological roles in intercellular communication and transportation of various biomolecules, including proteins and genetic materials. However, due to difficulties in their selective capture and detection, further application of exosomes remains challenging. To detect EVs, we fabricated a liposomal biosensor based on polydiacetylene (PDA), a conjugate polymer that has been widely used in sensing applications derived from its unique optical properties. To confer selectivity and sensitivity to the sensory material, antibodies targeting CD63, a membrane protein exclusively found in exosomes, were attached to the PDA liposomes and phospholipid molecules were incorporated into the PDA vesicles. Signal analysis derived from PDA liposomes for exosome detection and quantification was performed by observing colorimetric changes triggered by the ligand-receptor interaction of PDA vesicles. Visual, UV-visible, and fluorescence spectroscopic methods were used to obtain signals from the PDA lipid immunosensor, which achieved a detection limit of 3 × 10⁸ vesicles/mL, the minimum concentration that can be used in practical applications. The strategies used in the system have the potential to expand into the field of dealing with exosomes.

Utilization of chromic polydiacetylene assemblies as a platform to probe specific binding between drug and RNA

Recognition of nucleic acids remains an important endeavor in biology. Nucleic acids adopt shapes ranging from A-form (RNA and GC rich DNA) to B-form (AT rich DNA). We show, in this contribution, shape-specific recognition of A-U rich RNA duplex by a neomycin (Neo)-polydiacetylene (PDA) complex. PDA assemblies are fabricated by using a well-known diacetylene (DA) monomer, 10,12-pentacosadiynoic acid (PCDA). The response of poly(PCDA) assemblies is generated by mixing with a modified neomycin-PCDA monomer (Neo-PCDA). The functionalization by neomycin moiety provides specific binding with homopolyribonucleotide poly (rA) - poly (rU) stimulus. Various types of alcohols are utilized as additives to enhance the sensitivity of poly(PCDA)/Neo-PCDA assemblies. A change of absorption spectra is clearly observed when a relatively low concentration of poly (rA)-poly (rU) is added into the system. Furthermore, poly(PCDA)/Neo-PCDA shows a clear specificity for poly (rA)-poly (rU) over the corresponding DNA duplex. The variation of linker between neomycin moiety and conjugated PDA backbone is found to significantly affect its sensitivity. We also investigate other parameters including the concentration of Neo-PCDA and the DA monomer structure. Our results provide here preliminary data for an alternative approach to improve the sensitivity of PDA utilized in biosensing and diagnostic applications.

Selective and sensitive detection of MiRNA-21 based on gold-nanorod functionalized polydiacetylene microtube waveguide

Development of rapid, highly selective and sensitive miRNA detection in a complex biological environment has attracted considerable attention. Herein, we describe a novel two step method to construct gold-nanorod functionalized polydiacetylene (PDA) microtube for miRNA detection. In PDA microtube, with a one-dimensional (1D) waveguide nature, the excitation position and emission out-coupling position are far apart, thus helpful in reducing contribution of auto-fluorescence from biological sample. The use of specially designed toehold-mediated strand displacement reaction enables the reliable and selective discrimination of miRNA sequences with high sequence homology. Based on the condensing enrichment effect, the detection limit of the proposed PDA microtube system is as low as 0.01nM, and it can be applied directly to detect disease-specific miRNA targets in human serum. This PDA microtube waveguide system can be further integrated into the chip for the potential applications in minimally invasive, portable clinical diagnostic equipment.

Photopatterned Polydiacetylene Images Using a DNA Bio-Photomask

We describe a novel strategy to fabricate a well-defined polydiacetylene (PDA) supramolecular pattern on polyvinylidene fluoride (PVDF) membrane utilizing a DNA bio-photomask. By focusing on that, the absorption spectrum of DNA molecules having a λmax at 260 nm overlaps with the wavelength at which the photopolymerization of the diacetylene monomer occurs, DNA molecules are used to define specific patterns on PVDF membranes coated with diacetylene lipids by shielding the applied 254 nm UV light and consequently preventing the photopolymerization of the lipids. As a result, the DNA-covered regions retain the original white color on the membrane while the regions uncovered by DNA molecules undergo the color change to blue through the photopolymerization by 254 nm UV irradiation. On the basis of the selective illumination through a DNA photomask, we precisely manufacture specific patterns using a microarray spotting method and also demonstrate the capability of this strategy to achieve a novel colorimetric DNA sensor without any complicated process.