A highly sensitive fluorescence-enhanced aptasensor based on polyAn-aptamer nanostructure

Arboviruses: the hidden danger of the tropics

Arboviruses are viruses that are transmitted by arthropods such as mosquitoes, ticks, and flies, and most of them are RNA viruses. Vector-borne transmission occurs when an infected arthropod bites a vertebrate host, allowing the virus to enter the bloodstream and initiate infection. Arboviruses are known to cause significant morbidity and mortality in mammals, and at least a hundred of them have been identified as human pathogens. In this review, we provide an updated overview of four prominent arboviruses that are present in Southeast Asia (SEA): dengue virus (DENV), Japanese encephalitis virus (JEV), Zika virus (ZIKV), and chikungunya virus (CHIKV). The epidemiology and pathogenesis of these viruses and the currently used methods for diagnosis, prevention, and treatment of arbovirus infections are discussed in detail. Finally, we summarise the concerns and future considerations for combating these dangerous pathogens.

DNAzyme-mediated fluorescence signal variation of DNA-Ag nanoclusters and construction of an aptasensor for ATP

DNA-templated silver nanoclusters (DNA-AgNCs) are novel nanomaterials with unique fluorescence characteristics. DNAzyme is a functional oligonucleotide that can catalyze the disruption of nucleic acid substrates. In this research, the effect of DNAzyme digestion on the fluorescence property of DNA-AgNCs was explored for the first time. A significant reduction in the fluorescence intensity of DNA-AgNCs after cleavage by DNAzyme was discovered. Further research found that the DNAzyme-catalyzed cleavage reduced the stability of DNA-AgNCs and led to their aggregation, accounting for a decline in fluorescence intensity up to 84%. Inspired by the above finding, a fluorescent aptasensor that integrates the benefits of DNA-AgNCs, exonuclease III (Exo III)-assisted signal amplification and DNAzyme was developed for sensitive detection of adenosine triphosphate (ATP). Under optimal conditions, the linear range was from 25 μM to 1000 μM and the detection limit was estimated to be 4.46 μM. Furthermore, this fluorescent aptasensor was effectively employed to quantify ATP levels in human serum samples, demonstrating its practicality in detecting ATP in biological matrices. The elucidation of DNAzyme-based fluorescence characteristic variation of DNA-AgNCs may provide insights into the interactions between DNAzyme and nanomaterials and has great prospects in the construction of fluorescent biosensors.

Development of a highly sensitive ampicillin sensor utilizing functionalized aptamers

To develop a sensitive and simple ampicillin (AMP) sensor for trace antibiotic residue detection, the influencing factors of the modification effect of nanogold-functionalized nucleic acid sequences (Adenine: A, Thymine: T) were comprehensively analyzed in this study, including the modification method, base length and type. It was found that under the same base concentration, longer chains are more likely to reach saturation than shorter chains; and when the base concentration and length are both the same, A exhibits a higher saturation modification level compared to T. Based on these research findings, a highly sensitive fluorescence aptamer sensor for detecting ampicillin was constructed using the optimized functionalized sequence (ployA6-aptamer) and experimental conditions (6 hours binding time between nucleic acid aptamer and complementary strand, pH 7 working solution, 20 minutes detection time) based on the principle of fluorescence resonance energy transfer. The sensor has a detection range of 0.18 ng ml-1 to 3.11 ng ml-1 for ampicillin, with a detection limit of 0.04 ng ml-1. It exhibits significant selectivity and achieves an average recovery rate of 98.71% in tap water and 91.83% in milk. This method can be used not only for residual ampicillin detection, but also for highly sensitive detection of various antibiotics and small biological molecules by replacing the aptamer type. It provides a research basis for the design of highly sensitive fluorescence aptamer sensors and further applications of nanogold@DNA composite structures.

"Turn-on" and pinhole-free ultrathin core-shell Au@SiO2 nanoparticle-based metal-enhanced fluorescent (MEF) chemodosimeter for Hg2

This study reports a metal-enhanced fluorescence chemodosimeter for highly sensitive detection of Hg2+ ions. Silica-coated Au nanoparticles (Au@SiO2 NPs) with a pinhole-free 4-5 nm shell were synthesized and functionalized with a monolayer of turn-on fluorescent probes. Compared to other organic fluorescent probes suffering from poor biocompatibility and detection limits, this design of a monolayer of turn-on fluorescent probes immobilized on the Au@SiO2 NPs with a pinhole-free 4-5 nm shell avoids fluorescence quenching and allows the fluorescent probe within the field of the inner Au NPs to experience metal-enhanced fluorescence. With this design, the chemodosimeter permits fluorescence emission in the presence of Hg2+ ions, because they trigger the ring-opening reaction of the fluorescent probe immobilized on the Au@SiO2 NPs. Additionally, the fluorescent probe is distanced by the thin SiO2 shell from directly attaching to the metallic Au NPs, which not only avoids fluorescence quenching but allows the fluorescent probe within the long-ranged field of the inner Au NPs to experience metal-enhanced fluorescence. As a result, the detection limit for the chemodosimeter can reach up to 5.0 × 10-11 M, nearly two orders of magnitude higher than that achieved for the free fluorescent probe. We also demonstrate the acquisition of images of Hg2+ in HTC116 cells and zebrafish using a simple fluorescence confocal imaging technique. The fluorescence response results for HTC116 cells and zebrafish show that the probes can permeate into cells and organisms. Considering the availability of the many organic fluorescent probes that have been designed, the current designed metal-enhanced fluorescence chemodosimeter holds great potential for fluorescence detection of diverse species and fluorescence imaging.

Wavelength-Dependent Metal-Enhanced Fluorescence Biosensors via Resonance Energy Transfer Modulation

Fluorescence can be enhanced or quenched depending on the distance between the surface of a metal nanoparticle and the fluorophore molecule. Fluorescence enhancement by nearby metal particles is called metal-enhanced fluorescence (MEF). MEF shows promising potential in the field of fluorescence-based biological sensing. MEF-based biosensor systems generally fall into two platform categories: (1) a two/three-dimensional scaffold, or (2) a colloidal suspension. This review briefly summarizes the application studies using wavelength-dependent carbon dots (UV-VIS), noble metals (VIS), and upconversion nanoparticles (NIR to VIS), representative nanomaterials that contribute to the enhancement of fluorescence through the resonance energy transfer modulation and then presents a perspective on this topic.

Recent Advances in DNA Nanotechnology for Plasmonic Biosensor Construction

Since 2010, DNA nanotechnology has advanced rapidly, helping overcome limitations in the use of DNA solely as genetic material. DNA nanotechnology has thus helped develop a new method for the construction of biosensors. Among bioprobe materials for biosensors, nucleic acids have shown several advantages. First, it has a complementary sequence for hybridizing the target gene. Second, DNA has various functionalities, such as DNAzymes, DNA junctions or aptamers, because of its unique folded structures with specific sequences. Third, functional groups, such as thiols, amines, or other fluorophores, can easily be introduced into DNA at the 5′ or 3′ end. Finally, DNA can easily be tailored by making junctions or origami structures; these unique structures extend the DNA arm and create a multi-functional bioprobe. Meanwhile, nanomaterials have also been used to advance plasmonic biosensor technologies. Nanomaterials provide various biosensing platforms with high sensitivity and selectivity. Several plasmonic biosensor types have been fabricated, such as surface plasmons, and Raman-based or metal-enhanced biosensors. Introducing DNA nanotechnology to plasmonic biosensors has brought in sight new horizons in the fields of biosensors and nanobiotechnology. This review discusses the recent progress of DNA nanotechnology-based plasmonic biosensors.

Signal enhancing strategies in aptasensors for the detection of small molecular contaminants by nanomaterials and nucleic acid amplification

Small molecular contaminants (such as mycotoxins, antibiotics, pesticide residues, etc.) in food and environment have given rise to many biological and ecological toxicities, which has attracted worldwide attention in recent years. Meanwhile, due to the advantages of aptamers such as high specificity and stability, easy synthesis and modification, as well as low cost and immunogenicity, various aptasensors for the detection of small molecular contaminants have been flourishing. An aptasensor as a whole is composed of an aptamer-based target recognizer and a signal transducer, which are fields of concentrated research. In the practical detection applications, in order to achieve the quantitative detection of small molecular contaminants at low abundance in real samples, a large number of signal enhancing strategies have been utilized in the development of aptasensors. Recent years is a vintage period for efficient signal enhancing strategies of aptasensors by the aid of nanomaterials and nucleic acid amplification that are applied in the elements for target recognition and signal conversion. Therefore, this paper meticulously reviews the signal enhancing strategies based on nanomaterials (including the (quasi-)zero-dimensional, one-dimensional, two-dimensional and three-dimensional nanomaterials) and nucleic acid amplification (including enzyme-assisted nucleic acid amplification and enzyme-free nucleic acid amplification). Furthermore, the challenges and future trends of the abovementioned signal enhancing strategies for application are also discussed in order to inspire the practitioners in the research and development of aptasensors for small molecular contaminants.

Modulating Optical Characteristics of Nanoimprinted Plasmonic Device by Re-Shaping Process of Polymer Mold

Metal nanostructures exhibit specific optical characteristics owing to their localized surface plasmon resonance (LSPR) and have been studied for applications in various optical devices. The LSPR property strongly depends on the size and shape of metal nanostructures; thus, plasmonic devices must be designed and fabricated according to their uses. Nanoimprint lithography (NIL) is an effective process for repeatedly fabricating metal nanostructures with controlled sizes and shapes and require optical properties. NIL is a powerful method for mass-producible, low-cost, and large-area fabrication. However, the process lacks flexibility in adjusting the size and shape according to the desirable optical characteristics because the size and shape of metal nanostructures are determined by a single corresponding mold. Here, we conducted a re-shaping process through the air-plasma etching of a polymer's secondary mold (two-dimensional nanopillar array made of cyclo-olefin polymer (COP)) to modulate the sizes and shapes of nanopillars; then, we controlled the spectral characteristics of the imprinted plasmonic devices. The relationship between the structural change of the mold, which was based on etching time, and the optical characteristics of the corresponding plasmonic device was evaluated through experiments and simulations. According to evaluation results, the diameter of the nanopillar was controlled from 248 to 139 nm due to the etching time and formation of a pit structure. Consequently, the spectral properties changed, and responsivity to the surrounding dielectric environment was improved. Therefore, plasmonic devices based on the re-shaped COP mold exhibited a high responsivity to a refractive index of 906 nm/RIU at a wavelength of 625 nm.

Single-stranded DNA probe paired aptasensor with extra dye binding sites to enhance its fluorescence response in the presence of a target compound

The purpose of this study is to investigate the possibility of improving the performance of a DNA binding dye water quenching based aptasensor without changing or truncating the aptamer. To demonstrate the possibility of increasing the change in fluorescence of the aptasensor by pairing it with a suitable ssDNA probe, three ssDNA probes (probe 1, 2, and 3) were employed and the fluorescence from the bound dyes was measured. This showed that ssDNA probe 2 created the most additional binding sites. By varying the target compound concentration (0, 0.05, 0.5, 5, 50, and 500 mg L⁻¹ 4-n-nonylphenol), the corresponding change in the fluorescence signal of the unpaired and ssDNA probe paired aptasensors were measured and compared over a range of emission wavelengths. The response of all three ssDNA probe paired aptasensors showed good fit (R² = 0.88–0.92) to a logarithmic response. The sensitivity of the aptasensor paired with ssDNA probe 2 was improved by ∼60%, whereas that of the aptasensor paired with ssDNA probe 3 was only improved by a marginal ∼3%. This study is a demonstration of using an appropriate ssDNA probe to increase the number of binding sites and hence the performance of a DNA binding dye and water quenched aptasensor. It is a possibility that can be extended to similar aptasensors without having to change or truncate the aptamer.

Principle of an ssDNA paired aptasensor where extra dye binding sites are created to enhance its fluorescence response.

Aptamers used for biosensors and targeted therapy

Aptamers are single-stranded nucleic acid sequences that can bind to target molecules with high selectivity and affinity. Most aptamers are screened in vitro by a combinatorial biology technique called systematic evolution of ligands by exponential enrichment (SELEX). Since aptamers were discovered in the 1990s, they have attracted considerable attention and have been widely used in many fields owing to their unique advantages. In this review, we present an overview of the advancements made in aptamers used for biosensors and targeted therapy. For the former, we will discuss multiple aptamer-based biosensors with different principles detected by various signaling methods. For the latter, we will focus on aptamer-based targeted therapy using aptamers as both biotechnological tools for targeted drug delivery and as targeted therapeutic agents. Finally, challenges and new perspectives associated with these two regions were further discussed. We hope that this review will help researchers interested in aptamer-related biosensing and targeted therapy research.