Selection and Characterization of DNA Aptamers for Constructing Aptamer-AuNPs Colorimetric Method for Detection of AFM1

Multi-group structure analysis and molecular docking of aptamers and small molecules: A case study of chloramphenicol

Aptamers, a kind of short nucleotide sequences with high specificity and affinity with targets, have attracted extensive attention in recent years. Molecular docking method (MDM) is the most common method to explore the binding mode and recognition mechanism of aptamers and small molecules, which generally use the target to dock with the highest scoring tertiary structural model of the aptamer, and the highest scoring result is used as the predicted model. However, this prediction results may miss out the true interaction pattern due to the fact that aptamers are not completely rigid and the natural aptamers conformations are not in a single state. Thus, evaluation of the binding pattern from two or more tertiary structural modes might be more accurate. The use of chloramphenicol (CAP) has been banned because it causes myelosuppression and aplastic anemia in humans. However, CAP is still abused and is often studied as a target for detection. Two CAP aptamers (Apt-11 and Apt-16) were used as cases in this study. All secondary structures of these two aptamers were predicted using the UNAFold Web Server tool, and then the corresponding tertiary structure models were built using the RNA Composer tool and Discovery Studio 4.5 Client software. The resulted six tertiary structure models were docked with CAP respectively. By optimizing the docking conditions, multiple groups of docking outcomes were obtained, including the tertiary structure, its binding free energy, and the binding site. The results suggested that there may be multiple binding sites in the same tertiary structure, and the binding energy of the same tertiary structure as well as the proportion of multiple binding sites vary greatly. In addition, it was found that Autodock4 works well in analyzing the binding mode between screened aptamers with its defined target, but cannot be used to identify that whether an aptamer could bind well with other molecule with big structural difference from the target. The CAP aptamer was tailored according to the molecular docking results, and the potential binding sites with CAP were verified by a colloidal gold colorimetry assay. In conclusion, we propose a method to explore the binding patterns between aptamer and its targets by using multiple optimized docking data from different tertiary structures of the aptamer, which provides a theoretical basis for the study of the binding mode of aptamers and targets, as well as the optimization and modification of aptamers.

Elucidating the molecular docking and binding dynamics of aptamers with spike proteins across SARS-CoV-2 variants of concern

DNA aptamers with high binding affinity against SARS-CoV-2 spike proteins have been selected and analyzed. To better understand the binding affinities between DNA aptamers and spike proteins (S-proteins) of relevant variants of concerns (VOCs), in silico and in vitro characterization are excellent approaches to implement. Here, we identified and generated DNA aptamer sequences targeting the S-protein of SARS-CoV-2 VOCs through systematic evolution of ligands by exponential enrichment (SELEX). In silico, prediction of aptamer binding was conducted, followed by a step-by-step workflow for secondary and tertiary aptamer structures determination, modeling, and molecular docking to target S-protein. The in silico strategy was limited to only providing predictions of possible outcomes based on scores, and ranking was complemented by characterization and analysis of identified DNA aptamers using a direct enzyme-linked oligonucleotides assay (ELONA), which showed dissociation constants (K d) within the 32 nM-193 nM range across the three significant VOCs. These three highly specific VOCs aptamers (Alpha Apt, Delta Apt, and Omicron Apt) can be further studied as potential candidates for both diagnostic and therapeutic applications.

Nucleic Acid Aptamers for Human Norovirus GII.4 and GII.17 Virus-Like Particles (VLPs) Exhibit Specific Binding and Inhibit VLPs from Entering Cells

Purpose

Human noroviruses (HuNoVs) are the main cause of non-bacterial acute gastroenteritis. Due to antigenic diversity, the discovery of ligands that can sensitively and specifically detect HuNoVs remains challenging. Limited by laboratory culture, no vaccines or drugs have been developed against HuNoVs. Here, we screened nucleic acid aptamers against the widespread HuNoV GII.4 and emerging HuNoV GII.17.

Methods

After ten rounds of sieving for HuNoV GII.4 and GII.17 virus-like particles (VLPs), eight ssDNA aptamers were generated and characterized for each genotype.

Results

Four of the eight aptamers generated for GII.4 VLP had dissociation constants (Kd) less than 100 nM, and all aptamers for GII.17 VLP had Kd less than 10 nM. All aptamers bound to their targets in VLP concentration-dependent manner. Two aptamers (AP4-2 and AP17-4) were selected for enzyme-linked aptamer sorbent assay (ELASA) and further analysis. Binding affinity was enhanced as the concentration of both aptamer and VLPs increased. The specificity of the aptamers was verified by ELASA and dot blotting. AP4-2 and AP17-4 were able to differentiate HuNoV from other diarrhea-causing pathogens or unrelated proteins (P < 0.0001). VLP/porcine gastric mucin (PGM) binding blockade assays revealed that AP4-2 and AP17-4 blocked the binding of HuNoV VLPs to PGM. VLP internalization inhibition assays showed that at a concentration of 0.5 µM, both AP4-2 and AP17-4 effectively inhibited attachment and internalization of HuNoV VLPs into 293T cell (P < 0.05). Cell viability assays confirmed that aptamers did not induce cellular toxicity.

Conclusion

AP4-2 and AP17-4 showed strong affinity and specificity for their target VLPs and represent promising candidates for HuNoV capture and detection. This is the first study to demonstrate that aptamers can effectively inhibit HuNoV VLPs from binding to or entering cells, thus providing a new concept for the treatment of HuNoVs.

A Double-Stranded Aptamer for Highly Sensitive Fluorescent Detection of Glutathione S-Transferases

Aptamer-based biosensors have been widely constructed and applied to detect diverse targets. Glutathione S-transferase (GST), a pivotal phase II metabolic enzyme, plays a critical role in biotransformation in vivo, and aberrant GST expression is associated with various health risks. Herein, aptamers targeting GST were systematically selected from a randomized single-stranded DNA (ssDNA) library of 79 nucleotides (nt) using a biotinylated GST-immobilized streptavidin agarose (SA) bead SELEX technology. Following rigorous screening across eight rounds, four aptamers with strikingly similar secondary structures emerged. Among these, Seq3 exhibited the highest affinity towards GST and was selected for further optimization. A semi-rational post-SELEX truncation strategy was then employed based on base composition analysis, secondary structure analysis and affinity assessment. This strategy enabled the systematic removal of redundant nucleotides in Seq3 without compromising its affinity, ultimately yielding a truncated aptamer, Seq3-3, which retains its specificity with a compact 39nt length. Building upon Seq3-3, a double-stranded fluorescent aptamer probe was ingeniously designed for the in vitro detection of GST. The detection mechanism hinges on the competitive displacement of the complementary chain from the probe, mediated by the target protein, leading to the separation of the antisense oligonucleotide from the double-stranded complex. This process triggers the restoration of the fluorescence signal, enabling sensitive detection, and the probe exhibits excellent response within a linear range of GST activity ranging from 0 to 1500 U/L. The results show that not only an efficient strategy for screening robust and practicable aptamers but also an ultrahighly sensitive detection platform for GST was established.

Process, advances, and perspectives of graphene oxide-SELEX for the development of aptamer molecular probes: A comprehensive review

BACKGROUND

Aptamers are screened via the systematic evolution of ligands by exponential enrichment (SELEX) and are widely used in molecular diagnostics and targeted therapies. The development of efficient and convenient SELEX technology has facilitated rapid access to high-performance aptamers, thereby advancing the aptamer industry. Graphene oxide (GO) serves as an immobilization matrix for libraries in GO-SELEX, making it suitable for screening aptamers against diverse targets.

RESULTS

This review summarizes the detailed steps involved in GO-SELEX, including monitoring methods, various sublibrary acquisition methods, and practical applications from its inception to the present day. In addition, the potential of GO-SELEX in the development of broad-spectrum aptamers is explored, and its current limitations for future development are emphasized. This review effectively promotes the application of the GO-SELEX technique by providing valuable insights and assisting researchers interested in conducting related studies.

SIGNIFICANCE AND NOVELTY

To date, no review on the topic of GO-SELEX has been published, making it challenging for researchers to initiate studies in this area. We believe that this review will broaden the SELEX options available to researchers, ensuring that they can meet the growing demand for molecular probes in the scientific domain.

Recent Advances in Design and Application of Nanomaterials-Based Colorimetric Biosensors for Agri-food Safety Analysis

A colorimetric sensor detects an analyte by utilizing the optical properties of the sensor unit, such as absorption or reflection, to generate a structural color that serves as the output signal to detect an analyte. Detecting the refractive index of an analyte by recording the color change of the sensor structure on its surface has several advantages, including simple operation, low cost, suitability for onsite analysis, and real-time detection. Colorimetric sensors have drawn much attention owing to their rapidity, simplicity, high sensitivity and selectivity. This Review discusses the use of colorimetric sensors in the food industry, including their applications for detecting food contaminants. The Review also provides insight into the scope of future research in this area.

Aptamer-Protein Interactions: From Regulation to Biomolecular Detection

Serving as the basis of cell life, interactions between nucleic acids and proteins play essential roles in fundamental cellular processes. Aptamers are unique single-stranded oligonucleotides generated by in vitro evolution methods, possessing the ability to interact with proteins specifically. Altering the structure of aptamers will largely modulate their interactions with proteins and further affect related cellular behaviors. Recently, with the in-depth research of aptamer-protein interactions, the analytical assays based on their interactions have been widely developed and become a powerful tool for biomolecular detection. There are some insightful reviews on aptamers applied in protein detection, while few systematic discussions are from the perspective of regulating aptamer-protein interactions. Herein, we comprehensively introduce the methods for regulating aptamer-protein interactions and elaborate on the detection techniques for analyzing aptamer-protein interactions. Additionally, this review provides a broad summary of analytical assays based on the regulation of aptamer-protein interactions for detecting biomolecules. Finally, we present our perspectives regarding the opportunities and challenges of analytical assays for biological analysis, aiming to provide guidance for disease mechanism research and drug discovery.

Aptamer-modified chitosan-capped mesoporous silica nanoparticles for co-delivery of cytarabine and daunorubicin in leukemia

In this study, surface modified mesoporous silica nanoparticles (MSNs) were prepared for the targeted delivery of the anticancer agents, daunorubicin (DNR) and cytarabine (CTR), against K562 leukemia cancer cell lines. The MSNs were surface-modified with pH-sensitive chitosan (CS) to prevent the burst release of anticancer agents at the physiological pH of 7.4 and to enable a higher drug release at lower pH and higher concentration of glutathione. Finally, the MSNs were surface modified with KK1B10 aptamer (Apt) to enhance their uptake by K562 cells through ligand-receptor interactions. The MSNs were characterized using different methods and both in vitro and in vivo experiments were utilized to demonstrate their suitability as targeted anticancer agents. The resultant MSNs exhibited an average particle size of 295 nm, a surface area of 39.06 m2/g, and a cumulative pore volume of 0.09 cm3/g. Surface modification of MSNs with chitosan (CS) resulted in a more regulated and acceptable continuous release rate of DNR. The drug release rate was significantly higher at pH 5 media enriched with glutathione, compared to pH 7.4. Furthermore, MSNs coated with CS and conjugated with aptamer (MSN-DNR + CTR@CS-Apt) exhibited a lower IC50 value of 2.34 µg/ml, compared to MSNs without aptamer conjugation, which displayed an IC50 value of 12.27 µg/ml. The results of the cell cycle analysis indicated that the administration of MSN-DNR + CTR@CS-Apt led to a significant increase in the population of apoptotic cells in the sub-G1 phase. Additionally, the treatment arrested the remaining cells in various other phases of the cell cycle. Furthermore, the interactions between Apt-receptors were found to enhance the uptake of MSNs by cancer cells. The results of in vivo studies demonstrated that the administration of MSN-DNR + CTR@CS-Apt led to a significant reduction in the expression levels of CD71 and CD235a markers, as compared to MSN-DNR + CTR@CS (p < 0.001). In conclusion, the surface modified MSNs prepared in this study showed lower IC50 against cancer cell lines and higher anticancer activity in animal models.

A self-assembled DNA double-crossover-based fluorescent aptasensor for highly sensitivity and selectivity in the simultaneous detection of aflatoxin M1 and aflatoxin B1

Realizing the simultaneous speedy detection of multiple mycotoxins in contaminated food and feed is of great practical importance in the domain of food manufacturing and security. Herein, a fluorescent aptamer sensor based on self-assembled DNA double-crossover was developed and used for effective simultaneous quantitative detection of aflatoxins M₁ and B₁ by fluorescence resonance energy transfer (FRET). Fluorescent dye-modified aflatoxin M₁ and B₁ aptamers are selected as recognition elements and signal probes, and DNA double crosses are consistently locked by the aflatoxin aptamers, which results in a "turn-off" of the fluorescent signal. In the presence of AFM₁ and AFB₁, the aptamer sequences are more inclined to form Apt-AFM₁ and Apt-AFB₁ complexes, and the fluorescent probes are released from the DNA double-crossing platform, leading to an enhanced fluorescent signal (Cy3: 568 nm; Cy5: 660 nm). Under the optimal conditions, the signal response of the constructed fluorescent aptamer sensor showed good linearity with the logarithm of AFM₁ and AFB₁ concentrations, with detection limits of 6.24 pg/mL and 9.0 pg/mL, and a wide linear range of 0.01-200 ng/mL and 0.01-150 ng/mL, respectively. In addition, the effect of potential interfering substances in real samples was analyzed, and the aptasensor presented a good interference immunity. Moreover, by modifying and designing aptamer probes, the sensor can be applied to high-throughput simultaneous screening of other analytes, providing a new approach for the development of fluorescent aptamer sensors.

AFB1 colorimetric aptamer sensor for the detection of AFB1 in ten different kinds of miscellaneous beans based on gold nanoparticles and smartphone imaging

A simple, rapid, low-cost, sensitive, intuitive, visual, label-free, colorimetric smartphone-assisted assay was developed for the measurement of aflatoxin B1 in miscellaneous beans. Ten different kinds of miscellaneous beans were treated and measured by modified QuEChERS(Quick、Easy、Cheap、Effective、Rugged、Safe) method with aflatoxin B1 nucleic acid aptamer as a recognition element and gold nanoparticles as indicators. Several factors influencing its sensitivity were investigated, including consumes and NaCl concentrations, as well as incubation time and specificity. The results showed a good linear relationship between concentrations of 0.2-8.0 ng/g under optimal conditions. With a detection limit of 0.08 ng/g, the linear regression equation was Y = 0.024X + 0.4615 (R = 0.9989). Sensor specificity is good. The content of aflatoxin B1 in bean samples was determined successfully. The recovery of aflatoxin B1 ranged from 87.18% to 110.24%. The whole thing took 15 min. This smartphone-assisted colorimetric aptamer sensor can be used to detect aflatoxin B1 in beans.

Recent advances in colorimetric sensors based on nanozymes with peroxidase-like activity

Nanozymes have been widely used to construct colorimetric sensors due to their advantages of cost-effectiveness, high stability, good biocompatibility, and ease of modification. The emergence of nanozymes greatly enhanced the detection sensitivity and stability of the colorimetric sensing platform. Recent significant research has focused on designing various sensors based on nanozymes with peroxidase-like activity for colorimetric analysis. However, with the deepening of research, nanozymes with peroxidase-like activity has also exposed some problems, such as weak affinity and low catalytic activity. In view of the above issues, existing investigations have shown that the catalytic properties of nanozymes can be improved by adding surface modification and changing the structure of nanomaterials. In this review, we summarize the recent trends and advances of colorimetric sensors based on several typical nanozymes with peroxidase-like activities, including noble metals, metal oxides, metal sulfides/metal selenides, and carbon and metal-organic frameworks (MOF). Finally, the current challenges and prospects of colorimetric sensors based on nanozymes with peroxidase-like activity are summarized and discussed to provide a reference for researchers in related fields.

Polymeric membranes functionalized with nanomaterials (MP@NMs): A review of advances in pesticide removal

The excessive contamination of drinking water sources by pesticides has a pernicious impact on human health and the environment since only 0.1% of pesticides is utilized effectively to control the and the rest is deposited in the environment. Filtration by polymeric membranes has become a promising technique to deal with this problem; however, the scientific community, in the need to find better pesticide retention results, has begun to meddle in the functionalization of polymeric membranes. Given the great variety of membrane, polymer, and nanomaterial synthesis methods present in the market, the possibilities of obtaining membranes that adjust to different variables and characteristics related to a certain pesticide are relatively extensive, so it is expected that this technology will represent one of the main pesticide removal strategies in the future. In this direction, this review focused on, - the main characteristics of the nanomaterials and their impact on pristine polymeric membranes; - the removal performance of functionalized membranes; and - the main mechanisms by which membranes can retain pesticides. Based on these insights, the functionalized polymeric membranes can be considered as a promising technology in the removal of pesticides since the removal performance of this technology against pesticide showed a significant increase. Obtaining membranes that adjust to different variables and characteristics related to a certain pesticide are relatively extensive, so it is expected that functionalized membrane technology will represent one of the main pesticide removal strategies in the future.