Modelling aptamers with nucleic acid mimics (NAM): From sequence to three-dimensional docking

Aptamers capable of simultaneously identifying multiple targets and corresponding applications in medical diagnosis-A review

Aptamers, a unique class of nucleic acid sequences recognized for their specific binding capabilities, have found widespread application in biomedical field. While traditional aptamers are typically designed to target a single molecule recognition, recent attention has been directed towards multifunctional aptamers capable of simultaneously identifying multiple targets. In this review, the latest advancements in multifunctional aptamers and their applications in medical diagnosis are presented for the first time. This review focuses on the following essential aspects, including methods employed for developing multifunctional aptamers, detailed characteristics of these aptamers, practical applications across diverse diagnostic scenarios, and in-depth discussions on critical aspects of their design and utility. To conclude, future perspectives are provided to drive further development and broader application of multifunctional aptamers in the biomedical domain.

Deciphering aptamer-protein interactions for bovine sperm sorting through in silico and in vitro studies

BACKGROUND

In recent years, aptamers have emerged as versatile molecular tools with promising applications in various fields, including diagnostics and therapeutics. In livestock reproduction, their application holds promise for improving the sorting and identification of X and Y chromosome-bearing sperm cells, which is essential for increasing productivity in the dairy and beef industries.

METHOD

This study utilized seven rounds of Cell-SELEX using bovine X and Y sperm cells to isolate specific aptamers that target these cells. A comprehensive in-silico analysis was conducted to evaluate the binding interactions between the selected aptamer sequences and the differentially expressed plasma membrane proteins of X and Y sperm cells.

RESULT

The analysis identified the aptamer sequences APT1X, APT2X, and APT5X as having the most stable interactions with the X sperm surface proteins TLR8 (Toll-like receptor 8), CLRN3, and TLR7 (Toll-like receptor 7), respectively. APT2Y exhibited a relatively high affinity for the protein SCAMP1, a Y-sperm-specific protein. Aptamer‒protein interactions are characterized by hydrogen bonds and hydrophobic contacts. Notably, APT1X formed the greatest number of hydrogen bonds with the polar residues of TLR8, whereas TLR7-APT5X interactions exhibited the greatest number of hydrophobic contacts.

CONCLUSION

The use of in-silico analysis for evaluating the interaction between candidate aptamer sequences and differentially expressed X and Y bovine sperm proteins provides valuable insights. This approach might facilitate the sorting of bovine X and Y sperm cells, contributing to advancements in livestock reproduction strategies.

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.

Protein-nucleic acid complexes: Docking and binding affinity

Protein-nucleic interactions play essential roles in several biological processes, such as gene regulation, replication, transcription, repair and packaging. The knowledge of three-dimensional structures of protein-nucleic acid complexes and their binding affinities helps to understand these functions. In this review, we focus on two major aspects namely, (i) deciphering the three-dimensional structures of protein-nucleic acid complexes and (ii) predicting their binding affinities. The first part is devoted to the state-of-the-art methods for predicting the native structures and their performances including recent CASP targets. The second part is focused on different aspects of investigating the binding affinity of protein-nucleic acid complexes: (i) databases for thermodynamic parameters to understand the binding affinity, (ii) important features determining protein-nucleic acid binding affinity, (iii) predicting the binding affinity of protein-nucleic acid complexes using sequence and structure-based parameters and (iv) change in binding affinity upon mutation. It includes the latest developments in protein-nucleic acid docking algorithms and binding affinity predictions along with a list of computational resources for understanding protein-DNA and protein-RNA interactions.

High-throughput and computational techniques for aptamer design

INTRODUCTION

Aptamers refer to short ssDNA/RNA sequences that target small molecules, proteins, or cells. Aptamers have significantly advanced diagnostic applications, including biosensors for detecting specific biomarkers, state-of-the-art imaging, and point-of-care technology. Molecular computation helps identify aptamers with high-binding affinity, enabling high-throughput screening, predicting 3D structures, optimizing aptamers for improved stability, specificity, and complex target interactions.

AREA COVERED

Aptamers are versatile in the development of specific and sensitive diagnostics. However, there needs to be more understanding of the precise workflow that integrates sequence, structure, and interaction with the target. In this review, the author discusses how significant progress has been made in aptamer discovery using bioinformatics for sequence analysis, docking to model interactions, and MD simulations to account for dynamicity and predict free-energy. Furthermore, the author discusses how quantum chemical calculations are critical for modelling electronic structures and assignin spectroscopic signals.

EXPERT OPINION

Incorporating machine learning into the aptamer discovery brings a transformative advancement. With NGS datasets, SELEX, and experimental structures, the implementation of newer workflows yields aptamers with improved binding affinity. Leveraging transfer learning to models using experimental structures and aptamer sequences expands the aptamer design space significantly. As ML continues to evolve, it is poised to become central in accelerating aptamer discovery for biomedical applications in the next 5 years.

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.

Molecular Modeling Methods in the Development of Affine and Specific Protein-Binding Agents

High-affinity and specific agents are widely applied in various areas, including diagnostics, scientific research, and disease therapy (as drugs and drug delivery systems). It takes significant time to develop them. For this reason, development of high-affinity agents extensively utilizes computer methods at various stages for the analysis and modeling of these molecules. The review describes the main affinity and specific agents, such as monoclonal antibodies and their fragments, antibody mimetics, aptamers, and molecularly imprinted polymers. The methods of their obtaining as well as their main advantages and disadvantages are briefly described, with special attention focused on the molecular modeling methods used for their analysis and development.

Unveiling the characteristics of D4 and R4 aptamers for their future use in prostate cancer clinical practice

The DNA and RNA aptamers D4 and R4, respectively, emerged from the modification of PC-3 cell-binding aptamer A4. Our objective was to characterize the aptamers in silico and in vitro and begin to identify their target molecules. We represented their structures using computational algorithms; evaluated their binding to several prostate cell lines and their effects on the viability and migration of these cells; and determined their dissociation constant by flow cytometry. We analyzed circulating prostate tumor cells from patients using D4, R4, anti-CD133 and anti-CD44. Finally, the target proteins of both aptamers were precipitated and identified by mass spectrometry to simulate their in silico docking. The aptamers presented similar structures and bound to prostate tumor cells without modifying the cellular parameters studied, but with different affinities. The ligand cells for both aptamers were CD44+, indicating that they could identify cells in the mesenchymal stage of the metastatic process. The possible target proteins NXPE1, ADAM30, and MUC6 need to be further studied to better understand their interaction with the aptamers. These results support the development of new assays to determine the clinical applications of D4 and R4 aptamers in prostate cancer.

Nucleic acid-based wearable and implantable electrochemical sensors

The rapid advancements in nucleic acid-based electrochemical sensors for implantable and wearable applications have marked a significant leap forward in the domain of personal healthcare over the last decade. This technology promises to revolutionize personalized healthcare by facilitating the early diagnosis of diseases, monitoring of disease progression, and tailoring of individual treatment plans. This review navigates through the latest developments in this field, focusing on the strategies for nucleic acid sensing that enable real-time and continuous biomarker analysis directly in various biofluids, such as blood, interstitial fluid, sweat, and saliva. The review delves into various nucleic acid sensing strategies, emphasizing the innovative designs of biorecognition elements and signal transduction mechanisms that enable implantable and wearable applications. Special perspective is given to enhance nucleic acid-based sensor selectivity and sensitivity, which are crucial for the accurate detection of low-level biomarkers. The integration of such sensors into implantable and wearable platforms, including microneedle arrays and flexible electronic systems, actualizes their use in on-body devices for health monitoring. We also tackle the technical challenges encountered in the development of these sensors, such as ensuring long-term stability, managing the complexity of biofluid dynamics, and fulfilling the need for real-time, continuous, and reagentless detection. In conclusion, the review highlights the importance of these sensors in the future of medical engineering, offering insights into design considerations and future research directions to overcome existing limitations and fully realize the potential of nucleic acid-based electrochemical sensors for healthcare applications.

On-site sensing for aflatoxicosis poisoning via ultraviolet excitable aptasensor based on fluorinated ethylene propylene strip: a promising forensic tool

The environmental contamination by extremophile Aspergillus species, i.e., Aflatoxin B1, is hardly controllable in Southeast Asia and Sub-Saharan Africa, which lack handling resources and controlled storage facilities. Acute aflatoxicosis poisoning from aflatoxin-prone dietary staples could cause acute hepatic necrosis, acute liver failure, and death. Here, as the cheaper, more straightforward, and facile on-site diagnostic kit is needed, we report an ultraviolet-excitable optical aptasensor based on a fluorinated ethylene propylene film strip. Molecular dynamics on the aptamer.AFB1 complex revealed that the AFB1 to the aptamer increases the overall structural stability, suggesting that the aptamer design is suitable for the intended application. Under various influencing factors, the proposed label-free strategy offers a fast 20-min on-site fabrication simplicity and 19-day shelf-life. The one-pot incubation provides an alternative to catalytic detection and exhibited 4 times reusability. The recovery of crude brown sugar, processed peanuts, and long-grain rice were 102.74 ± 0.41 (n = 3), 86.90 ± 3.38 (n = 3), and 98.50 ± 0.42 (n = 3), comparable to High-Performance Liquid Chromatography-Photodiode Array Detector results. This study is novel owing to the peculiar UV-active spectrum fingerprint and the convenient use of hydrophobic film strips that could promote breakthrough innovations and new frontiers for on-site/forensic detection of environmental pollutants.

DNA aptamer-functionalized PDA nanoparticles: from colloidal chemistry to biosensor applications

Polydopamine nanoparticles (PDA NPs) are widely utilized in the field of biomedical science for surface functionalization because of their unique characteristics, such as simple and low-cost preparation methods, good adhesive properties, and ability to incorporate amine and oxygen-rich chemical groups. However, challenges in the application of PDA NPs as surface coatings on electrode surfaces and in conjugation with biomolecules for electrochemical sensors still exist. In this work, we aimed to develop an electrochemical interface based on PDA NPs conjugated with a DNA aptamer for the detection of glycated albumin (GA) and to study DNA aptamers on the surfaces of PDA NPs to understand the aptamer-PDA surface interactions using molecular dynamics (MD) simulation. PDA NPs were synthesized by the oxidation of dopamine in Tris buffer at pH 10.5, conjugated with DNA aptamers specific to GA at different concentrations (0.05, 0.5, and 5 μM), and deposited on screen-printed carbon electrodes (SPCEs). The charge transfer resistance of the PDA NP-coated SPCEs decreased, indicating that the PDA NP composite is a conductive bioorganic material. Transmission electron microscopy (TEM) and scanning electron microscopy (SEM) confirmed that the PDA NPs were spherical, and dynamic light scattering (DLS), Fourier transform infrared spectroscopy (FTIR), and Raman spectroscopy data indicated the successful conjugation of the aptamers on the PDA NPs. The as-prepared electrochemical interface was employed for the detection of GA. The detection limit was 0.17 μg/mL. For MD simulation, anti-GA aptamer through the 5'terminal end in a single-stranded DNA-aptamer structure and NH2 linker showed a stable structure with its axis perpendicular to the PDA surface. These findings provide insights into improved biosensor design and have demonstrated the potential for employing electrochemical PDA NP interfaces in point-of-care applications.

Multiplexed In Vivo Screening Using Barcoded Aptamer Technology to Identify Oligonucleotide-Based Targeting Reagents

Recent FDA approvals of mRNA vaccines, short-interfering RNAs, and antisense oligonucleotides highlight the success of oligonucleotides as therapeutics. Aptamers are excellent affinity reagents that can selectively label protein biomarkers, but their clinical application has lagged. When formulating a given aptamer for in vivo use, molecular design details can determine biostability and biodistribution; therefore, extensive postselection manipulation is often required for each new design to identify clinically useful reagents harboring improved pharmacokinetic properties. Few methods are available to comprehensively screen such aptamers, especially in vivo, constituting a significant bottleneck in the field. In this study, we introduce barcoded aptamer technology (BApT) for multiplexed screening of predefined aptamer formulations in vitro and in vivo. We demonstrate this technology by simultaneously investigating 20 aptamer formulations, each harboring different molecular designs, for targeting Non-Small Cell Lung Cancer cells and tumors. Screening in vitro identified a 45 kDa bispecific formulation as the best cancer cell targeting reagent, whereas screening in vivo identified a 30 kDa monomeric formulation as the best tumor-specific targeting reagent. The multiplexed analysis pipeline also identified biodistribution phenotypes shared among formulations with similar molecular architectures. The BApT approach we describe here has the potential for broad application to fields where oligonucleotide-based targeting reagents are desired.

Emerging Approaches for Mitigating Biofilm-Formation-Associated Infections in Farm, Wild, and Companion Animals

The importance of addressing the problem of biofilms in farm, wild, and companion animals lies in their pervasive impact on animal health and welfare. Biofilms, as resilient communities of microorganisms, pose a persistent challenge in causing infections and complicating treatment strategies. Recognizing and understanding the importance of mitigating biofilm formation is critical to ensuring the welfare of animals in a variety of settings, from farms to the wild and companion animals. Effectively addressing this issue not only improves the overall health of individual animals, but also contributes to the broader goals of sustainable agriculture, wildlife conservation, and responsible pet ownership. This review examines the current understanding of biofilm formation in animal diseases and elucidates the complex processes involved. Recognizing the limitations of traditional antibiotic treatments, mechanisms of resistance associated with biofilms are explored. The focus is on alternative therapeutic strategies to control biofilm, with illuminating case studies providing valuable context and practical insights. In conclusion, the review highlights the importance of exploring emerging approaches to mitigate biofilm formation in animals. It consolidates existing knowledge, highlights gaps in understanding, and encourages further research to address this critical facet of animal health. The comprehensive perspective provided by this review serves as a foundation for future investigations and interventions to improve the management of biofilm-associated infections in diverse animal populations.

Virtual screening and site-directed mutagenesis-derived aptamers for precise Salmonella typhimurium prediction: emphasizing OmpD targeting and G-quadruplex stability

The efficient detection of the foodborne pathogen Salmonella typhimurium has historically been hampered by the constraints of traditional methods, characterized by protracted culture periods and intricate DNA extraction processes for PCR. To address this, our research innovatively focuses on the crucial and relatively uncharted virulence factor, the Outer Membrane Protein D (OmpD) in Salmonella typhimurium. By harmoniously integrating the power of virtual screening and site-directed mutagenesis, we unveiled aptamers exhibiting marked specificity for OmpD. Among these, aptamer 7ZQS stands out with its heightened binding affinity. Capitalizing on this foundation, we further engineered a repertoire of mutant aptamers, wherein APT6 distinguished itself, reflecting unmatched stability and specificity. Our rigorous validation, underpinned by cutting-edge bioinformatics tools, amplifies the prowess of APT6 in discerning and binding OmpD across an array of Salmonella typhimurium strains. This study illuminates a transformative approach to the prompt and accurate detection of Salmonella typhimurium, potentially redefining boundaries in applied analytical chemistry and bolstering diagnostic precision across diverse research and clinical domains.

Highly-efficient selection of aptamers for detecting various HPV subtypes in clinical samples

Nucleic acid aptamers are of great potentials in diagnostic and therapeutic applications because of their unique molecular recognition capabilities. However, satisfactory aptamers with high affinity and specificity are still in short supply. Herein, we have developed new selection methods allowing the free interactions between the targets and potential aptamers in solution. In our selection system, the protein targets (biotinylated randomly or site-specifically) were first incubated with the random DNA library, followed by the pull-down with the streptavidin magnetic beads or biolayer-interferometry (BLI) sensors. By comparing the two biotinylation strategies (random or site-specific) and two states of the targets (free or immobilized), we have found that the combination of the site-specific biotinylation and free-target strategies was most successful. Based on these highly-efficient selection strategies, HPV L1 aptamers were obtained. By designing the sandwich aptasensor assisted with RCA and CRISPR/Cas12a, we have diagnosed various HPV subtypes in clinical samples, such as easily-collected urine samples. In summary, our new strategy can allow efficient selection of aptamers with high affinity and specificity for clinical applications.

Modified nucleic acid aptamers: development, characterization, and biological applications

Aptamers are single-stranded oligonucleotides that bind to their targets via specific structural interactions. To improve the properties and performance of aptamers, modified nucleotides are incorporated during or after a selection process such as systematic evolution of ligands by exponential enrichment (SELEX). We summarize the latest modified nucleotides and strategies used in modified (mod)-SELEX and post-SELEX to develop modified aptamers, highlight the methods used to characterize aptamer-target interactions, and present recent progress in modified aptamers that recognize different targets. We discuss the challenges and perspectives in further advancing the methodologies and toolsets to accelerate the discovery of modified aptamers, improve the throughput of aptamer-target characterization, and expand the functional diversity and complexity of modified aptamers.

Fluorescent nanostructured carbon dot-aptasensor for chlorpyrifos detection: Elucidating the interaction mechanism for an environmentally hazardous pollutant

Chlorpyrifos (CPF) is a commonly used insecticide found in many water sources and is related to several health and environmental effects. Biosensors based on aptamers (single-stranded nucleic acid oligonucleotides) are promising alternatives to achieve the detection of CPF and other pesticides in natural waters. However, several challenges need to be addressed to promote the real application of functional aptasensing devices. In this work, an ssDNA aptamer (S1) is combined with carbon quantum dots (CD) and graphene oxide (GO) to produce a stable fluorescent aptasensor characterized through spectrophotometric and electrophoretic techniques. For a deeper understanding of the system, the mechanism of molecular interaction was studied through docking modeling using free bioinformatic tools like HDOCK, showing that the stem-loops and the higher guanine (G) content are crucial for better interaction. The model also suggests the possibility of generating a truncated aptamer to improve the binding affinity. The biosensor was evaluated for CPF detection, showing a low LOD of 0.01 μg L-1 and good specificity in tap water, even compared to other organophosphates pesticides (OPs) like profenofos. Finally, the recovery of the proposed aptasensor was evaluated in some natural water using spiked samples and compared with UPLC MS-MS chromatography as the gold standard, showing a good recovery above 2.85 nM and evidencing the need of protecting ssDNA aptamers from an erratic interaction with the aromatic groups of dissolved organic matter (humic substances). This work paves the way for a better aptasensors design and the on-site implementation of novel devices for environmental monitoring.

Aptamer-Based Point-of-Care Devices: Emerging Technologies and Integration of Computational Methods

Recent innovations in point-of-care (POC) diagnostic technologies have paved a critical road for the improved application of biomedicine through the deployment of accurate and affordable programs into resource-scarce settings. The utilization of antibodies as a bio-recognition element in POC devices is currently limited due to obstacles associated with cost and production, impeding its widespread adoption. One promising alternative, on the other hand, is aptamer integration, i.e., short sequences of single-stranded DNA and RNA structures. The advantageous properties of these molecules are as follows: small molecular size, amenability to chemical modification, low- or nonimmunogenic characteristics, and their reproducibility within a short generation time. The utilization of these aforementioned features is critical in developing sensitive and portable POC systems. Furthermore, the deficiencies related to past experimental efforts to improve biosensor schematics, including the design of biorecognition elements, can be tackled with the integration of computational tools. These complementary tools enable the prediction of the reliability and functionality of the molecular structure of aptamers. In this review, we have overviewed the usage of aptamers in the development of novel and portable POC devices, in addition to highlighting the insights that simulations and other computational methods can provide into the use of aptamer modeling for POC integration.

In Silico Approaches for the Identification of Aptamer Binding Interactions to Leptospira spp. Cell Surface Proteins

Aptamers are nucleic acids that can bind with high affinity and specificity to a range of target molecules. However, their functionality relies on their secondary and tertiary structures such that the combination of nucleotides determines their three-dimensional conformation. In this study, the binding mechanisms of candidate aptamers and their interactions with selected target proteins found in the cell surface of Leptospira were predicted to select high-affinity aptamers. Four aptamers were evaluated through molecular modeling and docking using available software and web-based tools, following the workflow previously designed for in silico evaluation of DNA aptamers. The most predominant and highly conserved surface-exposed proteins among pathogenic Leptospira species were used as aptamer targets. The highest number of interactions was seen in aptamers AP5 and AP1. Hydrogen bonds, along with a few hydrophobic interactions, occur in most aptamer-protein complexes. Further analysis revealed serine, threonine, glutamine, and lysine as main protein residues. H-bond interactions occur mostly with polar amino acids, as reflected in the predicted interaction profiles of aptamer-protein complexes. In silico strategies allowed the identification of key residues crucial in aptamer-target interaction during aptamer screening. Such information can be used in aptamer modification for improved binding affinity and accuracy for diagnostics application.

An overview of structural approaches to study therapeutic RNAs

RNAs provide considerable opportunities as therapeutic agent to expand the plethora of classical therapeutic targets, from extracellular and surface proteins to intracellular nucleic acids and its regulators, in a wide range of diseases. RNA versatility can be exploited to recognize cell types, perform cell therapy, and develop new vaccine classes. Therapeutic RNAs (aptamers, antisense nucleotides, siRNA, miRNA, mRNA and CRISPR-Cas9) can modulate or induce protein expression, inhibit molecular interactions, achieve genome editing as well as exon-skipping. A common RNA thread, which makes it very promising for therapeutic applications, is its structure, flexibility, and binding specificity. Moreover, RNA displays peculiar structural plasticity compared to proteins as well as to DNA. Here we summarize the recent advances and applications of therapeutic RNAs, and the experimental and computational methods to analyze their structure, by biophysical techniques (liquid-state NMR, scattering, reactivity, and computational simulations), with a focus on dynamic and flexibility aspects and to binding analysis. This will provide insights on the currently available RNA therapeutic applications and on the best techniques to evaluate its dynamics and reactivity.

Prediction of Aptamer-Small-Molecule Interactions Using Metastable States from Multiple Independent Molecular Dynamics Simulations

Understanding aptamer-ligand interactions is necessary to rationally design aptamer-based systems. Commonly used in silico tools have proven to be accurate to predict RNA and DNA oligonucleotide tertiary structures. However, given the complexity of nucleic acids, the most thermodynamically stable conformation is not necessarily the one with the highest affinity for a specific ligand. Because many metastable states may coexist, it remains challenging to predict binding sites through molecular docking simulations using available computational pipelines. In this study, we used independent simulations to broaden the conformational diversity sampled from DNA initial models of distinct stability and assessed the binding affinity of selected metastable representative structures. In our results, utilizing multiple metastable conformations for molecular docking analysis helped identify structures favorable for ligand binding and accurately predict the binding sites. Our workflow was able to correctly identify the binding sites of the characterized adenosine monophosphate and l-argininamide aptamers. Additionally, we demonstrated that our pipeline can be used to aid the design of competition assays that are conducive to aptasensing strategies using an uncharacterized aflatoxin B1 aptamer. We foresee that this approach may help rationally design effective and truncated aptamer sequences interacting with protein biomarkers or small molecules of interest for drug design and sensor applications.