Analysis of aptamer-target binding and molecular mechanisms by thermofluorimetric analysis and molecular dynamics simulation

Enhanced Detection of Enrofloxacin in Seawater Using a Newly Selected Aptamer on a Graphite Oxide-Based Biosensor

Developing aptasensors offers several advantages including sensitivity, selectivity, cost-effectiveness, and speed over traditional analytical techniques for antibiotic detection. We have successfully identified Enro_ap3, a 30-mer enrofloxacin-binding aptamer with micromolar binding affinity, through an optimized Capture-SELEX platform. Compared to other reported enrofloxacin-binding aptamers, this shorter aptamer not only streamlines the design process but also eliminates the common issue of strong nonspecific binding to the GO surface, thereby improving the overall detection capabilities of the biosensor (GO-Enro_ap3-FAM). This GO aptasensor demonstrated remarkable selectivity by effectively distinguishing enrofloxacin from different structurally diverse antibiotics. The sensor boasts a LOD of 32.15 μg/mL, 2.5 times more sensitive than the original 30-mer, with recoveries of 74%-92% and relative standard deviations of 6.3%-12.5% in seawater samples spiked with enrofloxacin. Furthermore, the GO aptasensor's detection capabilities were found to be on par with traditional LC-MS/MS techniques, exhibiting no significant differences in recovery rates even in complex matrices. The sensor's performance remained consistent across variations in salinity, acidity, and total organic carbon concentrations in seawater samples collected from different locations, underlining its robustness in diverse environmental conditions and its suitability for real-world seawater monitoring applications. Our findings highlight the importance of the aptamer's chain length and its binding affinity toward the target after immobilization on the GO substrate. These factors significantly impact the performance of GO aptasensors in seawater. Overall, the GO aptasensor provides a well-balanced approach, combining sensitivity, environmental adaptability, and practical usability for detecting pharmaceutical contaminants, such as antibiotics, in marine environments.

Multimodal nanoenzyme-linked aptamer assay for Salmonella typhimurium based on catalysis and photothermal effect of PB@Au

A composite nanomaterial of Prussian blue@gold nanoparticles (PB@Au) with catalytic and photothermal properties was proposed, which combined with anti-matrix interference aptamers to achieve robust specificity and sensitivity in the detection of Salmonella typhimurium (S. typhimurium). The detection probe, PB@Au-Aptamer (PB@Au-Apt), was designed to exhibit high specificity for the target and catalyze the signal generation to produce a color change, thereby enabling rapid detection. Additionally, the excellent photothermal performance of the PB@Au catalytic system was utilized for multimodal sensitive detection in the multimodal nanoenzyme-linked aptamer assay. Moreover, the utilization of both catalytic and photothermal dual-mode detection was mutually verified to enhance detection accuracy. Under optimal conditions, the detection of S. typhimurium in a sample can be completed in 2 h. The developed assay exhibited exceptional specificity in detecting S. typhimurium, with an impressive detection limit down to 23 CFU·mL-1. Furthermore, the assay exhibited excellent repeatability and stability. Real sample analyses have proven the high reliability and practicality of this assay, highlighting its significant potential for applications in food safety testing.

Label-free SELEX of aptamers for ultra-sensitive electrochemical aptasensor detection of amanitin in wild mushrooms

BACKGROUND

Mushroom poisoning poses a significant global health concern, with high morbidity and mortality rates. The primary lethal toxins responsible for this condition are alpha-amanitin (ɑ-AMA) and beta-amanitin (β-AMA). As a promising bio-recognition molecules in biosensors, aptamers, have been broadly used in the field of food detection. However, the current SELEX-based methods for screening aptamers for structurally similar small molecules were limited by the labelling or salt ion induction. In this study, we aimed to develop a novel label-free SELEX strategy for the screening of aptamers with high affinity and constructed new aptasensors for the detection of ɑ-AMA and β-AMA.

RESULTS

A novel label-free SELEX strategy based on the positively charged gold nanoparticles (AuNPs) was proposed to simultaneous screening of aptamers for ɑ-AMA and β-AMA. Only 18 rounds of SELEX were required to obtain new aptamers. The candidate aptamers were analyzed by colloidal gold assay, and the sequences of ɑ-30 and β-37 displayed great affinity with Kd values of 22.26 nM and 23.32 nM, respectively, without interference from botanical toxins. Notably, the truncated aptamers ɑ-30-2 (50 bp) and β-37-2 (57 bp) exhibited higher affinity than their original counterpart (79 bp). Subsequently, the selected aptamers were utilized to construct recognition probes for electrochemical aptasensors based on hairpin cyclic cleavage of substrates by Cu2+ dependent DNAzyme and Exo I-triggered recycling cascades. The detection platform showed excellent analytical performance with limits of detection as low as 4.57 pg/mL (ɑ-AMA) and 8.49 pg/mL (β-AMA). Moreover, the aptasensors exhibited superior performance in mushroom and urine samples.

SIGNIFICANCE

This work developed a simple and efficient label-free SELEX method for screening new aptamers for ɑ-AMA and β-AMA, which employed the positively charged AuNPs as the screening medium, without the need for chemical labelling of libraries or induction of salt ions. Furthermore, two novel electrochemical aptasensors were developed based on our newly obtained aptamers, which offer the new biosensing tool for ultrasensitive detection of the AMA poisoning, showing great potential in practical applications.

In silico selection of aptamers against SARS-CoV-2

Aptamers are molecular recognition elements that have been extensively deployed in a wide array of applications ranging from diagnostics to therapeutics. Due to their unique properties as compared to antibodies, aptamers were also largely isolated during the COVID-19 pandemic for multiple purposes. Typically generated by conventional SELEX, the inherent drawbacks of the process including the time-consuming, cumbersome and resource-intensive nature catalysed the move to adopt in silico approaches to isolate aptamers. Impressive performances of these in silico-derived aptamers in their respective assays have been documented thus far, bearing testimony to the huge potential of the in silico approaches, akin to the traditional SELEX in isolating aptamers. In this study, we provide an overview of the in silico selection of aptamers against SARS-CoV-2 by providing insights into the basic steps involved, which comprise the selection of the initial single-stranded nucleic acids, determination of the secondary and tertiary structures and in silico approaches that include both rigid docking and molecular dynamics simulations. The different approaches involving aptamers against SARS-CoV-2 were illuminated and the need to verify these aptamers by experimental validation was also emphasized. Cognizant of the need to continuously improve aptamers, the strategies embraced thus far for post-in silico selection modifications were enumerated. Shedding light on the steps involved in the in silico selection can set the stage for further improvisation to augment the functionalities of the aptamers in the future.

Aptamer Screening: Current Methods and Future Trend towards Non-SELEX Approach

Aptamers are nucleic acid sequences that specifically bind with target molecules and are vital to applications such as biosensing, drug development, disease diagnostics, etc. The traditional selection procedure of aptamers is based on the Systematic Evolution of Ligands by an Exponential Enrichment (SELEX) process, which relies on repeating cycles of screening and amplification. With the rapid development of aptamer applications, RNA and XNA aptamers draw more attention than before. But their selection is troublesome due to the necessary reverse transcription and transcription process (RNA) or low efficiency and accuracy of enzymes for amplification (XNA). In light of this, we review the recent advances in aptamer selection methods and give an outlook on future development in a non-SELEX approach, which simplifies the procedure and reduces the experimental costs. We first provide an overview of the traditional SELEX methods mostly designed for screening DNA aptamers to introduce the common tools and methods. Then a section on the current screening methods for RNA and XNA is prepared to demonstrate the efforts put into screening these aptamers and the current difficulties. We further predict that the future trend of aptamer selection lies in non-SELEX methods that do not require nucleic acid amplification. We divide non-SELEX methods into an immobilized format and non-immobilized format and discuss how high-resolution partitioning methods could facilitate the further improvement of selection efficiency and accuracy.

Aptamer as a targeted approach towards treatment of breast cancer

Aptamers, a novel type of targeted ligand used in drug delivery, have quickly gained popularity due to their high target specificity and affinity. Different aptamer-mediated drug delivery systems, such as aptamer-drug conjugate (ApDC), aptamer-siRNA, and aptamer-functionalised nanoparticle systems, are currently being developed for the successful treatment of cancer based on the excellent properties of aptamers. These systems can decrease potential toxicity and enhance therapeutic efficacy by targeting the drug moiety. In this review, we provide an overview of recent developments in aptamer-mediated delivery systems for cancer therapy, specifically for breast cancer, and talk about the potential applications and current issues of novel aptamer-based techniques. This study in aptamer technology for breast cancer therapy highlights key aptamers targeting well-established biomarkers such as HER2, oestrogen receptor, and progesterone receptor. Additionally, we explore the potential of aptamers in overcoming various challenges such as drug resistance and improving the delivery of therapeutic agents. This review aims to provide a deeper understanding of the present aptamer-based targeted delivery applications through in-depth analysis to increase efficacy and create new therapeutic approaches that may ultimately lead to better treatment outcomes for cancer patients.

Strategies for targeted gene delivery using lipid nanoparticles and cell-derived nanovesicles

Gene therapy is a promising approach for the treatment of many diseases. However, the effective delivery of the cargo without degradation in vivo is one of the major hurdles. With the advent of lipid nanoparticles (LNPs) and cell-derived nanovesicles (CDNs), gene delivery holds a very promising future. The targeting of these nanosystems is a prerequisite for effective transfection with minimal side-effects. In this review, we highlight the emerging strategies utilized for the effective targeting of LNPs and CDNs, and we summarize the preparation methodologies for LNPs and CDNs. We have also highlighted the non-ligand targeting of LNPs toward certain organs based on their composition. It is highly expected that continuing the developments in the targeting approaches of LNPs and CDNs for the delivery system will further promote them in clinical translation.