Optimization of an aptamer against Prorocentrum minimum - A common harmful algae by truncation and G-quadruplex-forming mutation

Experimentally verified flexible molecular docking and dynamic simulation of aptamer with intracellular proteins based on direct DNA 3D structure prediction

Despite the rising spotlight on biotargeting aptamers, their mechanism of regulating cellular functions remained elusive due to lack of systematic method to investigate their intracellular behavior. This study systematically established a complete workflow including DNA secondary and 3D structure prediction, flexibilization, docking, experimental validation, and molecular dynamic (MD) simulation. RNAfold was demonstrated to provide more accurate ssDNA secondary structure predictions and compatibility for flexible docking. Feasibility of a novel direct prediction tool of DNA 3D structure, 3dDNA, has first been proven with similar reliability and better data stability in flexible docking compared to indirect prediction by RNAComposer. Flexible docking by AutoDock Vina exhibited higher reliability, while rigid docking was less reliable. Docking results were influenced by secondary and 3D structures, but the proteins' inherent affinity to nucleic acids was the key determinant. Aptamer bound to proteins with non-specificity (KD > 100 nM) and affinities (Rmax) exponentially correlated to flexible docking scores, necessitating further MD validation and identification of binding sites. Via the established workflow, binding sites of stem cell-recruiting aptamer Apt-19s on its known target (ALPL) was identified, Sec24B was first screened as its potential intracellular targets, providing theoretical guidance and feasible methodology for future exploration of aptamer biotargeting mechanisms.

A Chromatography Test Strip of Exonuclease III-Amplified Aptamer for Rapid Identification of Prorocentrum minimum

Recently, the scale and frequency of harmful algae blooms (HABs) have gradually increased, posing a serious threat to human health, marine ecosystems and economic development. For early warning, a method is required that can quickly detect and monitor microalgae. It is proposed to use aptamer targeted to Prorocentrum minimum, along with exonuclease III (Exo III), gold nanoparticles, target single-stranded DNA and hairpin structure probe to construct a new method, i.e. aptamer-lateral flow dipstick (LFD) based on Exo III-assisted signal amplification assay (ALBEA). The key conditions, including signal amplification and LFD detection, are optimized. Under the optimal conditions, the detection limit of ALBEA was 1.25 cells mL-1. The cross-reactivity test showed no positive result except for P. minimum, indicating that the method is highly specific. The anti-interference test confirmed that the technique was not affected by the presence of other microalgae. The tested results of P. minimum cultured under different nutrient conditions and different growth stages demonstrated that the method is not affected by the cell state. Furthermore, the test results of simulated natural water samples further validated the practicality of the ALBEA. In conclusion, the established ALBEA offers a sensitive, specific and user-friendly tool, which can be used for the rapid detection of P. minimum and also provides a reference for the detection of other microalgae.

Selection and characterization of ssDNA aptamer targeting Macrobrachium rosenbergii nodavirus capsid protein: A potential capture agent in gold-nanoparticle-based aptasensor for viral protein detection

The giant freshwater prawn holds a significant position as a valuable crustacean species cultivated in the aquaculture industry, particularly well-known and demanded among the Southeast Asian countries. Aquaculture production of this species has been impacted by Macrobrachium rosenbergii nodavirus (MrNV) infection, which particularly affects the larvae and post-larvae stages of the prawn. The infection has been recorded to cause mortality rates of up to 100% among the affected prawns. A simple, fast, and easy to deploy on-site detection or diagnostic method is crucial for early detection of MrNV to control the disease outbreak. In the present study, novel single-stranded DNA aptamers targeting the MrNV capsid protein were identified using the systematic evolution of ligands by exponential enrichment (SELEX) approach. The aptamer was then conjugated with the citrate-capped gold nanoparticles (AuNPs), and the sensitivity of this AuNP-based aptasensor for the detection of MrNV capsid protein was evaluated. Findings revealed that the aptamer candidate, APT-MrNV-CP-1 was enriched throughout the SELEX cycle 4, 9, and 12 with the sequence percentage of 1.76%, 9.09%, and 12.42%, respectively. The conjugation of APT-MrNV-CP-1 with citrate-capped AuNPs exhibited the highest sensitivity in detecting the MrNV capsid protein, where the presence of 62.5 nM of the viral capsid protein led to a significant agglomeration of the AuNPs. This study demonstrated the practicality of an AuNP-based aptasensor for disease diagnosis, particularly for detecting MrNV infection in giant freshwater prawns.

A detection method for Prorocentrum minimum by an aptamer-gold nanoparticles based colorimetric assay

Here, to give early waring for harmful algal blooms caused by Prorocentrum minimum, we reported a simple and rapid colorimetric assay that is named aptamer-gold nanoparticles (GNPs) based colorimetric assay (AGBCA). The GNPs maintain a dispersed state and have a strong characteristic absorption peak at 520 nm. With the addition of NaCl, the stability of the solution will be destroyed and the dispersed GNPs will aggregate. Therefore, the characteristic absorption peak of the GNPs solution will change from 520 nm to 670 nm. Aptamers can be adsorbed on the surface of GNPs, effectively preventing the aggregation of GNPs. In the presence of P. minimum, aptamers will specifically bind to P. minimum, causing the dissociation of the aptamers from GNPs. Consequently, the GNPs will aggregate in the NaCl solution, corresponding to a new absorption peak at 670 nm. A linear relationship between the absorbance ratio variation (ΔA₆₇₀/A₅₂₀) and the P. minimum concentration was observed in the concentration range of 1 × 10² - 1 × 10⁷ cells mL^-1, with a low detection limit of 8 cells mL^-1. The developed AGBCA is characterized by simplicity, strong specificity, and high sensitivity and is thus promising for the quantitative detection of P. minimum in natural samples.