Design of Label-Free DNA Light-Up Aptaswitches for Multiplexed Biosensing

We present a straightforward design approach to develop DNA-based light-up aptasensors. We performed the first systematic comparison of DNA fluorescent light-up aptamers (FLAPs), revealing key differences in affinity and specificity for their target dyes. Based on our analysis, two light-up aptamers emerged with remarkable specificity, fluorescence enhancement, and functionality in diverse environments. We then established generalizable design rules to couple the DNA FLAPs to small molecule-binding aptamers, creating 13 novel aptaswitches with reliable turn-on or turn-off aptaswitching in a dose-response manner. We developed new aptaswitches for ochratoxin A and ATP biosensing with up to a seven-fold response and low background. Finally, we demonstrated the orthogonal activity of our aptaswitch platforms. As a result, we introduce fluorescent light-up aptaswitches for one-pot detection of different targets in diverse sample matrices.

A simple and label-free fluorescent DNA sensor for visual detection of aptamer-based berberine

The intrinsic fluorescence of berberine is very weak, which can be enhanced by its interaction with specific aptamers. A simple and sensitive DNA sensor for visual detection of berberine has here been established. When using this sensor, there was a good linear relationship between the change in fluorescence intensity of berberine and the concentration of berberine in the range of 16-2000 nM, with a detection limit of 5.1 nM. The change in fluorescence intensity was caused by the addition of aptamers. A detection limit of 170.1 nM was acquired by reading the RGB values of fluorescent images with a smartphone for the quantification of berberine. Common antibiotics did not interfere with the measurement of the berberine concentration. The molecular ion peaks of the complexes formed by the aptamer and berberine could be clearly observed by electrospray ionization mass spectrometry. The UV-vis absorption spectra, circular dichroism spectra, and fluorescence spectra indicated a strong interaction between berberine and the aptamer. The dissociation constant (Kd) between berberine and the aptamer was 1.91 μM. This sensor was both simple and sensitive, requiring only a 21-base oligonucleotide. It realized a visual quantitative analysis with a smartphone. This method could also be used for similar fluorescence visualization determination of aptamer-based drug molecules.

An aptamer-based fluorometric method for the rapid berberine detection in Kampo medicines

BACKGROUND

Berberine (BBR), a key component in Kampo medicine, is a cationic benzylisoquinoline alkaloid whose detection plays a critical role in the quality control of these traditional remedies. Traditional methods for detecting BBR often involve complex procedures, which can be time-consuming and costly. To address this challenge, our study focuses on developing a simpler, faster, and more efficient detection method for BBR in Kampo medicine formulations.

RESULTS

We successfully developed a rapid fluorometric detection method for BBR using colloidal gold nanoparticle-based systematic evolution of ligands by exponential enrichment (GOLD-SELEX). Initially, specific single-stranded DNA (ssDNA) sequences were selected for their ability to enhance BBR's fluorescence intensity. The optimal ssDNA sequence, identified as BBR38, was further truncated to produce BBR38S, a stem-loop ssDNA that improved fluorescence upon interaction with BBR. To further enhance the fluorescence, the BBR38S aptamer underwent additional modifications, including stem truncation and nucleotide mutations, resulting in the higher fluorescence variant BBR38S-3 A10C. The final product, TetBBR38S, a tetramer version of BBR38S-3 A10C, exhibited a linear detection range of 0.780-50.0 μg mL-1 and a limit of detection of 0.369 μg mL-1. The assay demonstrated sufficient selectivity and was successfully applied to analyze 128 different Kampo medicine formulations, accurately detecting BBR content with high precision.

SIGNIFICANCE

This study represents an advancement in Kampo medicine research, marking the first successful application of an aptamer-based approach for BBR detection in complex matrices. The developed method is not only simple and rapid (with a detection time of 5 min) but also cost-effective, which is crucial for widespread application.

Fluorogenic RNA-Based Biosensors of Small Molecules: Current Developments, Uses, and Perspectives

Small molecules are highly relevant targets for detection and quantification. They are also used to diagnose and monitor the progression of disease and infectious processes and track the presence of contaminants. Fluorogenic RNA-based biosensors (FRBs) represent an appealing solution to the problem of detecting these targets. They combine the portability of molecular systems with the sensitivity and multiplexing capacity of fluorescence, as well as the exquisite ligand selectivity of RNA aptamers. In this review, we first present the different sensing and reporting aptamer modules currently available to design an FRB, together with the main methodologies used to discover modules with new specificities. We next introduce and discuss how both modules can be functionally connected prior to exploring the main applications for which FRB have been used. Finally, we conclude by discussing how using alternative nucleotide chemistries may improve FRB properties and further widen their application scope.

Plasmon-enhanced fluorescence combined with aptamer sensor based on Ag nanocubes for signal-amplified detection of berberine hydrochloride

Plasmon enhanced fluorescent (PEF) with more "hot spots" play a critical role in signal amplified technology to avoid the intrinsic limitation of fluorophore which ascribed to a strong electromagnetic field at the tip structure. However, application of PEF technique to obtain a highly sensitive analysis of medicine was still at a very early stage. Herein, a simple but versatile Ag nanocubes (Agcubes)-based PEF sensor combined with aptamer (Agcubes@SiO2-QDs-Apt) was proposed for highly sensitive detection of berberine hydrochloride (BH). The distance between the plasma Agcubes and the red-emitted CdTe quantum dots (QDs) were regulated by the thickness of silica spacer. The three-dimensional finite-difference time-domain (3D-FDTD) simulation further revealed that Agcubes have a higher electromagnetic field than Ag nanospheres. Compared with PEF sensor, signal QDs-modified aptamer without Agcubes (QDs-Apt) showed a 10-fold higher detection limit. The linear range and detection limit of the Agcubes@SiO2-QDs-Apt were 0.1-100 μM, 87.3 nM, respectively. Furthermore, the PEF sensor was applied to analysis BH in the berberine hydrochloride tablets, compound berberine tablet and urine with good recoveries of 98.25-102.05%. These results demonstrated that the prepared PEF sensor has great potential for drug quality control and clinical analysis.

Fluorescence "light-up" sensor based on ligand/SiO2@NH2@cyanuric chloride nanoparticle interactions in alliance with salt dehydration for berberine detection

Berberine (BBR) is an important anti-inflammatory drug for the treatment of intestinal diseases. The quantification of BBR is required in clinical medicine because long-term or excessive intake can lead to drug resistance and adverse effects. In this study, SiO2@NH2@cyanuric chloride (CNCl) nanoparticles (NPs) were successfully prepared by covalently incorporating CNCl onto the surface of SiO2 NPs. Furthermore, a novel fluorescence "light-up" sensor for assaying BBR was established based on the interaction between BBR and SiO2@NH2@CNCl NPs. Although BBR was non-emissive in aqueous media, its fluorescence was considerably augmented because of the interaction with the as-prepared SiO2@NH2@CNCl NPs, and the enhancement factor was approximately three times larger than that of pure SiO2 NPs. Compared with SiO2 NPs, SiO2@NH2@CNCl NPs can interact with BBR through electrostatic interactions and π-π stacking. These interactions restricted the intramolecular motion and charge transfer of BBR, resulting in fluorescence enhancement. The sensor was sensitive, with a linear response over a concentration range of 25-2500 nM (R2 = 0.9905) and a detection limit (3σ/k) of 4.7 nM, and it had good selectivity for BBR in the presence of bovine serum albumin, amino acids, and metal ions. When the sensor was applied to real serum samples, rapid extraction and salt dehydration occurred to improve the efficiency of pretreatment, and satisfactory standard recovery rates (95%-96%) were achieved even when only small amounts of acetonitrile was used for protein precipitation. This strategy could serve as a reference for other studies requiring the analysis of drugs in biological samples.

DNA-Aptamer-Based qPCR Using Light-Up Dyes for the Detection of Nucleic Acids

Quantitative polymerase chain reaction (qPCR) is widely used in detection of nucleic acids, but existing methods either lack sequence-specific detection or are costly because they use chemically modified DNA probes. In this work, we apply a DNA aptamer and light-up dye-based chemistry for qPCR for nucleic acid quantification. In contrast to the conventional qPCR, in our method, we observe an exponential decrease in fluorescence upon DNA amplification. The qPCR method we developed produced consistent Ct vs log10 (DNA amount) standard curves, which have a linearfit with R2 value > 0.99. This qPCR technique was validated by quantifying gene targets from Streptococcus zooepidemicus (SzhasB) and Mycobacterium tuberculosis (MtrpoB). We show that our strategy is able to successfully detect DNA at as low as 800 copies/μL. To the best of our knowledge, this is the first study demonstrating the application of light-up dyes and DNA aptamers in qPCR.

Portable dual-aptamer microfluidic chip biosensor for Bacillus cereus based on aptamer tailoring and dumbbell-shaped probes

As food-borne pathogens, Bacillus cereus not only produce toxins that contaminate food and threaten human health, but also rely on spores to resist extreme environments. At present, the detection of B. cereus is still at the genome level and it is not easily distinguished from other Bacilli of the same group. Herein, we obtained the aptamers of B. cereus in different phases through Cell-SELEX technology. Then, through step-by-step tailoring and molecular docking, the two best performing aptamers were ascertained and the interaction revealed between the repeated G bases in the aptamer and the polar amino acids in the α-helix of the epiprotein. Based on these aptamers, a multifunctional dumbbell-shaped probe and an ultrasensitive microfluidic chip biosensor were designed. Tests showed that the novel sensor is able to complete detection within 1 h with a limit of detection (LOD) of 9.27 CFU/mL. Moreover, the sensor can be used in complex food environments, such as milk and rice, is able to detect both vegetative cells and spores, and it can also distinguish B. thuringiensis from the same flora. This study can provide a reference for the future development of food-borne pathogenic bacteria aptamer selecting, target interaction analysis, detection methods and equipment.

A self-assembling split aptamer multiplex assay for SARS-COVID19 and miniaturization of a malachite green DNA-based aptamer

Multiplex assays often rely on expensive sensors incorporating covalently linked fluorescent dyes. Herein, we developed a self-assembling aptamer-based multiplex assay. This multiplex approach utilizes a previously established split aptamer sensor in conjugation with a novel split aptamer sensor based upon a malachite green DNA aptamer. This system was capable of simultaneous fluorescent detection of two SARS COVID-19-related sequences in one sample with individual sensors that possesses a limit of detection (LOD) in the low nM range. Optimization of the Split Malachite Green (SMG) sensor yielded a minimized aptamer construct, Mini-MG, capable of inducing fluorescence of malachite green in both a DNA hairpin and sensor format.

A DNAzyme-based label-free fluorescent probe for guanosine-5'-triphosphate detection

Guanosine-5'-triphosphate (GTP) plays a key role in many important biological processes of cells. It is not only a primer for DNA replication and one of the four essential nucleoside triphosphates for mRNA synthesis, but also an energy source for translation and other important cellular processes. It can be converted to adenine nucleoside triphosphate (ATP), and the intracellular GTP level is closely related to the specific pathological state, so it is crucial to establish a simple and accurate method for the detection of GTP. Deoxyribozymes have unique catalytic and structural properties. One of the deoxyribozymes which is named DK2 with self-phosphorylation ability can transfer a phosphate from GTP to the 5' end in the presence of manganese(ii), while lambda exonuclease (λexo) catalyzes the gradual hydrolysis of double-stranded DNA molecules phosphorylated at the 5'-end from 5' to 3', but cannot cleave the 5'-OH end. The fluorescent dye SYBR Green I (SG I) can bind to dsDNA and produce significant fluorescence, but it can only give out weak fluorescence when it is mixed with a single strand. Here, we present a novel unlabeled fluorescence assay for GTP based on the self-phosphorylation of deoxyribozyme DK2 and the specific hydrolysis of λexo. Owing to the advantages of simple operation, high sensitivity, good specificity, low cost and without fluorophore (quenching group) labeling, this method has great potential in biological applications.

Binary (Split) Light-up Aptameric Sensors

This Minireview discusses the design and applications of binary (also known as split) light-up aptameric sensors (BLAS). BLAS consist of two RNA or DNA strands and a fluorogenic organic dye added as a buffer component. When associated, the two strands form a dye-binding site, followed by an increase in fluorescence of the aptamer-bound dye. The design is cost-efficient because it uses short oligonucleotides and does not require conjugation of organic dyes with nucleic acids. In some applications, BLAS design is preferable over monolithic sensors because of simpler assay optimization and improved selectivity. RNA-based BLAS can be expressed in cells and used for the intracellular monitoring of biological molecules. BLAS have been used as reporters of nucleic acid association events in RNA nanotechnology and nucleic-acid-based molecular computation. Other applications of BLAS include the detection of nucleic acids, proteins, and cancer cells, and potentially they can be tailored to report a broad range of biological analytes.

A dual-function oligonucleotide-based ratiometric fluorescence sensor for ATP detection

Adenosine triphosphate (ATP) is the main energy currency of life that plays a vital role in supporting physiological activities in living organisms, including humans. Therefore, accurate and sensitive detection of ATP concentration is necessary in biochemical research and clinical diagnosis. Herein, a ratiometric fluorescence aptasensor was developed for ATP detection. A dual-function DNA strand comprising an ATP-binding aptamer (ABA) and berberine-binding aptamer (BBA) was designed and optimized, in which ABA can capture ATP and thioflavin T (ThT), whereas BBA can capture berberine. Interestingly, the fluorescence intensity of both berberine and ThT were enhanced as they were captured by this dual-function DNA strand. In the presence of ATP, the ABA on the 3'-end of the DNA bound specifically to its target, causing ThT release and a significant drop in ThT fluorescence. However, ATP had no significant effect on the interaction between berberine and DNA, remaining the enhanced fluorescence intensity of berberine stable. Based on this interesting phenomenon, a ratiometric fluorescence sensor was constructed that used the enhanced fluorescence intensity of berberine as reference to measure the fluorescence intensity of ThT for ATP detection. This ratiometric fluorescence strategy had excellent selectivity and high sensitivity towards ATP with a detection limit (3σ) as low as 24.8 nM. The feasibility of application of this method in biological samples was evaluated in human serum and urine samples, where it exhibited a good detection performance.

Progress in the isolation of aptamers to light-up the dyes and the applications

The progress in the selection of aptamers to light-up the dyes and the related applications are reviewed.

In vitro selection of ssDNA aptamers that can specifically recognize and differentiate riboflavin and its derivative FAD

It is very meaningful and useful to select specific aptamers with capacity to distinguish small structural analogues, but it is difficult to carry out by traditional affinity chromatography-SELEX (systematic evolution of ligands by exponential enrichment) based on immobilized target molecules. In this paper, as a proof of concept, we selected DNA aptamers that can specifically recognize and differentiate riboflavin and its derivative flavin adenine dinucleotide (FAD) by a modified method. Here, the random DNA library was indirectly immobilized on streptavidin functional agarose beads by hybridization with its biotinylated short complementary strand, and the specific affinity between aptamers and its target would induce the aptamers to release from beads. Binding specificity can be tailored by performing an additional negative SELEX with the structure analogue of target. After about 10 rounds of selection, 6 aptamers for riboflavin and 2 aptamers for FAD with good affinities were isolated, and their dissociation constants (K_ds) were all at low micromolar level. Moreover, as expected, most of these aptamers show high affinity and excellent selectivity for target molecules, almost no binding to structure analogues and purines, indicating this simple method could be used to select specific aptamers to distinguish small molecular targets with similar structures.

A light-up fluorescence assay for tumor cell detection based on bifunctional split aptamers

Light-up aptamers have attracted growing attention due to their advantages of being label-free and having low fluorescence background. In this work, we developed a light-up fluorescence assay for label-free detection of tumor cells based on a bifunctional split aptamer (BFSA) that contained two DNA strands (BFSA-a and BFSA-b). BFSA-a and BFSA-b were constructed by combining aptamers ZY11 and ThT.2-2, which could specifically bind to the tumor cell SMMC-7721 and activate the fluorescence of thioflavin T (ThT). A Helper strand was introduced to hybridize with BFSA-b, and then BFSA-a and BFSA-b were separated if the target cell was absent. Only when the target cell is present can BFSA-a approach and hybridize with BFSA-b due to the 'induced-fit effect', which made the Helper strand dissociate. Then ThT bound to BFSA and the fluorescence of ThT was activated. The results indicated that this fluorescence assay had a good linear response to the target cells in the range of 250-20 000 cells in 100 μL binding buffer; the lowest cell number actually detected was 125 cells in 100 μL buffer. This assay also displayed excellent selectivity and was successfully applied to detect target cells in 20% human serum samples. The design of bifunctional split aptamers realized no-washing, label-free, low-cost, one-step detection of tumor cells, which could generate detectable fluorescence signals just by mixing nucleic acid aptamers and fluorescent reporter molecules with target cells. Such a design of aptamer probes also has the potential to construct stimuli-responsive controlled drug delivery systems.

Chimeric Aptamers-Based and MoS2 Nanosheet-Enhanced Label-Free Fluorescence Polarization Strategy for Adenosine Triphosphate Detection

Adenosine triphosphate (ATP) as a primary energy source plays a unique role in the regulation of all cellular events. The necessity to detect ATP requires sensitive and accurate quantitative analytical strategies. Herein, we present our study of developing a MoS₂ nanosheet-enhanced aptasensor for fluorescence polarization-based ATP detection. A bifunctional DNA strand was designed to consist of chimeric aptamers that recognize and capture ATP and berberine, a fluorescence enhancer. In the absence of ATP, the DNA strand bound to berberine will be hydrolyzed when Exonuclease I (Exo I) is introduced, releasing berberine as a result. In contrast, when ATP is present, ATP aptamer folds into a G-quadruplex structure; thus, the complex can resist degradation by Exo I to maintain berberine for fluorescent detection purpose. In addition, to magnify the fluorescence polarization (FP) signal, MoS₂ nanosheets were also adopted in the system. This nanosheets-enhanced FP strategy is simple and facile which does not require traditional dye-labeled DNA strands and complex operation steps. The developed fluorescence polarization aptasensor showed high sensitivity for the quantification of ATP with a detection limit of 34.4 nM, performing well both in buffer solution and in biological samples.

Aptamer-functionalized Fe3 O4 magnetic nanoparticles as a solid-phase extraction adsorbent for the selective extraction of berberine from Cortex phellodendri

The extraction adsorbent was fabricated by immobilizing the highly specific recognition and binding of aptamer onto the surface of Fe₃ O₄ magnetic nanoparticles, which not only acted as recognition elements to recognize and capture the target molecule berberine from the extract of Cortex phellodendri, but also could favor the rapid separation and purification of the bound berberine by using an external magnet. The developed solid-phase extraction method in this work was useful for the selective extraction and determination of berberine in Cortex phellodendri extracts. Various conditions such as the amount of aptamer-functionalized Fe₃ O₄ magnetic nanoparticles, extraction time, temperature, pH value, Mg²⁺ concentration, elution time and solvent were optimized for the solid-phase extraction of berberine. Under optimal conditions, the purity of berberine extracted from Cortex phellodendri was as high as 98.7% compared with that of 4.85% in the extract, indicating that aptamer-functionalized Fe₃ O₄ magnetic nanoparticles-based solid-phase extraction method was very effective for berberine enrichment and separation from a complex herb extract. The applicability and reliability of the developed solid-phase extraction method were demonstrated by separating berberine from nine different concentrations of one Cortex phellodendri extract. The relative recoveries of the spiked solutions of all the samples were between 95.4 and 111.3%, with relative standard deviations ranging between 0.57 and 1.85%.