Design and Prediction of Aptamers Assisted by In Silico Methods

Computational Frontiers in Aptamer-Based Nanomedicine for Precision Therapeutics: A Comprehensive Review

In the rapidly evolving landscape of nanomedicine, aptamers have emerged as powerful molecular tools, demonstrating immense potential in targeted therapeutics, diagnostics, and drug delivery systems. This paper explores the computational features of aptamers in nanomedicine, highlighting their advantages over antibodies, including selectivity, low immunogenicity, and a simple production process. A comprehensive overview of the aptamer development process, specifically the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) process, sheds light on the intricate methodologies behind aptamer selection. The historical evolution of aptamers and their diverse applications in nanomedicine are discussed, emphasizing their pivotal role in targeted drug delivery, precision medicine and therapeutics. Furthermore, we explore the integration of artificial intelligence (AI), machine learning (ML), Internet of Things (IoT), Internet of Medical Things (IoMT), and nanotechnology in aptameric development, illustrating how these cutting-edge technologies are revolutionizing the selection and optimization of aptamers for tailored biomedical applications. This paper also discusses challenges in computational methods for advancing aptamers, including reliable prediction models, extensive data analysis, and multiomics data incorporation. It also addresses ethical concerns and restrictions related to AI and IoT use in aptamer research. The paper examines progress in computer simulations for nanomedicine. By elucidating the importance of aptamers, understanding their superiority over antibodies, and exploring the historical context and challenges, this review serves as a valuable resource for researchers and practitioners aiming to harness the full potential of aptamers in the rapidly evolving field of nanomedicine.

Disposable electrochemical biosensors for the detection of bacteria in the light of antimicrobial resistance

Persistent and inappropriate use of antibiotics is causing rife antimicrobial resistance (AMR) worldwide. Common bacterial infections are thus becoming increasingly difficult to treat without the use of last resort antibiotics. This has necessitated a situation where it is imperative to confirm the infection to be bacterial, before treating it with antimicrobial speculatively. Conventional methods of bacteria detection are either culture based which take anywhere between 24 and 96 hor require sophisticated molecular analysis equipment with libraries and trained operators. These are difficult propositions for resource limited community healthcare setups of developing or less developed countries. Customized, inexpensive, point-of-care (PoC) biosensors are thus being researched and developed for rapid detection of bacterial pathogens. The development and optimization of disposable sensor substrates is the first and crucial step in development of such PoC systems. The substrates should facilitate easy charge transfer, a high surface to volume ratio, be tailorable by the various bio-conjugation chemistries, preserve the integrity of the biorecognition element, yet be inexpensive. Such sensor substrates thus need to be thoroughly investigated. Further, if such systems were made disposable, they would attain immunity to biofouling. This article discusses a few potential disposable electrochemical sensor substrates deployed for detection of bacteria for environmental and healthcare applications. The technologies have significant potential in helping reduce bacterial infections and checking AMR. This could help save lives of people succumbing to bacterial infections, as well as improve the overall quality of lives of people in low- and middle-income countries.

Designing molecules: directing stem cell differentiation

Stem cells have been widely applied in regenerative and therapeutic medicine for their unique regenerative properties. Although much research has shown their potential, it remains tricky in directing stem cell differentiation. The advancement of genetic and therapeutic technologies, however, has facilitated this issue through development of design molecules. These molecules are designed to overcome the drawbacks previously faced, such as unexpected differentiation outcomes and insufficient migration of endogenous or exogenous MSCs. Here, we introduced aptamer, bacteriophage, and biological vectors as design molecules and described their characteristics. The methods of designing/developing discussed include various Systematic Evolution of Ligands by Exponential Enrichment (SELEX) procedures, in silico approaches, and non-SELEX methods for aptamers, and genetic engineering methods such as homologous recombination, Bacteriophage Recombineering of Electroporated DNA (BRED), Bacteriophage Recombineering with Infectious Particles (BRIP), and genome rebooting for bacteriophage. For biological vectors, methods such as alternate splicing, multiple promoters, internal ribosomal entry site, CRISPR-Cas9 system and Cre recombinase mediated recombination were used to design viral vectors, while non-viral vectors like exosomes are generated through parental cell-based direct engineering. Besides that, we also discussed the pros and cons, and applications of each design molecule in directing stem cell differentiation to illustrate their great potential in stem cells research. Finally, we highlighted some safety and efficacy concerns to be considered for future studies.

Enhanced sensitivity in electrochemical detection of ochratoxin A within food samples using ferrocene- and aptamer-tethered gold nanoparticles on disposable electrodes

Ensuring food security is crucial for public health, and the presence of mycotoxins, produced by fungi in improperly stored processed or unprocessed food, poses a significant threat. This research introduces a novel approach - a disposable aptasensing platform designed for the detection of ochratoxin A (OTA). The platform employs gold-nanostructured screen-printed carbon electrodes functionalized with a ferrocene derivative, serving as an integrated faradaic transducing system, and an anti-OTA aptamer as a bioreceptor site. Detection relies on the ferrocene electrochemical signal changes induced by the aptamer folding in the presence of the target molecule. Remarkably sensitive, the platform detects OTA within the range of 0.5 to 70 ng mL-1 and a detection limit of 11 pg mL-1. This limit is approximately 200 times below the levels stipulated by the European Commission for agricultural commodities. Notably, the sensing device exhibits efficacy in detecting OTA in complex media, such as roasted coffee beans and wine, without the need for sample pretreatment, yielding accurate recoveries. Furthermore, while label-free electrochemical aptasensors have proliferated, this study addresses a gap in understanding the binding mechanisms of some aptasensors. To enhance the experimental findings, a theoretical study was conducted to underscore the specificity of the anti-OTA aptamer as a donor for OTA detection. The molecular docking technique was employed to unveil the key binding region of the aptamer, providing valuable insights into the aptasensor specificity.

The Development and Characterisation of ssDNA Aptamers via a Modified Cell-SELEX Methodology for the Detection of Human Red Blood Cells

Blood is one of the most commonly found biological fluids at crime scenes, with the detection and identification of blood holding a high degree of evidential value. It can provide not only information about the nature of the crime but can also lead to identification via DNA profiling. Presumptive tests for blood are usually sensitive but not specific, so small amounts of the substrate can be detected, but false-positive results are often encountered, which can be misleading. Novel methods for the detection of red blood cells based on aptamer-target interactions may be able to overcome these issues. Aptamers are single-stranded DNA or RNA sequences capable of undergoing selective antigen association due to three-dimensional structure formation. The use of aptamers as a target-specific moiety poses several advantages and has the potential to replace antibodies within immunoassays. Aptamers are cheaper to produce, display no batch-to-batch variation and can allow for a wide range of chemical modifications. They can help limit cross-reactivity, which is a hindrance to current forensic testing methods. Within this study, a modified Systematic Evolution of Ligands by Exponential Enrichment (SELEX) process was used to generate aptamers against whole red blood cells. Obtained aptamer pools were analysed via massively parallel sequencing to identify viable sequences that demonstrate a high affinity for the target. Using bioinformatics platforms, aptamer candidates were identified via their enrichment profiles. Binding characterisation was also conducted on two selected aptamer candidates via fluorescent microscopy and qPCR to visualise and quantify aptamer binding. The potential for these aptamers is broad as they can be utilised within a range of bioassays for not only forensic applications but also other analytical science and medical applications. Potential future work includes the incorporation of developed aptamers into a biosensing platform that can be used at crime scenes for the real-time detection of human blood.

Recent progress of SELEX methods for screening nucleic acid aptamers

Nucleic acid aptamers are oligonucleotide sequences screened by an in vitro methodology called Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Known as "chemical antibodies", aptamers can achieve specific recognition towards the targets through conformational changes with high affinity, and possess multiple attractive features including, but not limited to, easy and inexpensive to prepare by chemical synthesis, relatively stable and low batch-to-batch variability, easy modification and signal amplification, and low immunogenicity. Now, aptamers are attracting researchers' attentions from more than 25 disciplines, and have showed great potential for application and economic benefits in disease diagnosis, environmental detection, food security, drug delivery and discovery. Although some aptamers exist naturally as the ligand-binding elements of riboswitches, SELEX is a recognized method for aptamers screening. After thirty-two years of development, a series of SELEX methods have been investigated and developed, as well as have shown unique advantages to improve sequence performances or to explore screening mechanisms. This review would mainly focus on the novel or improved SELEX methods that are available in the past five years. Firstly, we present a clear overview of the aptamer's history, features, and SELEX development. Then, we highlight the specific examples to emphasize the recent progress of SELEX methods in terms of carrier materials, technical improvements, real sample-improved screening, post-SELEX and other methods, as well as their respects of screening strategies, implementation features, screening parameters. Finally, we discuss the remaining challenges that have the potential to hinder the success of SELEX and aptamers in practical applications, and provide the suggestions and future directions for developing more convenient, efficient, and stable SELEX methods in the future.

Computational generation and characterization of IsdA-binding aptamers with single-molecule FRET analysis

Staphylococcus aureus is a major foodborne bacterial pathogen. Early detection of S. aureus is crucial to prevent infections and ensure food quality. The iron-regulated surface determinant protein A (IsdA) of S. aureus is a unique surface protein necessary for sourcing vital iron from host cells for the survival and colonization of the bacteria. The function, structure, and location of the IsdA protein make it an important protein for biosensing applications relating to the pathogen. Here, we report an in-silico approach to develop and validate high-affinity binding aptamers for the IsdA protein detection using custom-designed in-silico tools and single-molecule Fluorescence Resonance Energy Transfer (smFRET) measurements. We utilized in-silico oligonucleotide screening methods and metadynamics-based methods to generate 10 aptamer candidates and characterized them based on the Dissociation Free Energy (DFE) of the IsdA-aptamer complexes. Three of the aptamer candidates were shortlisted for smFRET experimental analysis of binding properties. Limits of detection in the low picomolar range were observed for the aptamers, and the results correlated well with the DFE calculations, indicating the potential of the in-silico approach to support aptamer discovery. This study showcases a computational SELEX method in combination with single-molecule binding studies deciphering effective aptamers against S. aureus IsdA, protein. The established approach demonstrates the ability to expedite aptamer discovery that has the potential to cut costs and predict binding efficacy. The application can be extended to designing aptamers for various protein targets, enhancing molecular recognition, and facilitating the development of high-affinity aptamers for multiple uses.

In vitro selection of aptamers and their applications

The introduction of the in-vitro evolution method known as SELEX (Systematic Evolution of Ligands by Exponential enrichment) more than 30 years ago led to the conception of versatile synthetic receptors known as aptamers. Offering many benefits such as low cost, high stability and flexibility, aptamers have sparked innovation in molecular diagnostics, enabled advances in synthetic biology and have facilitated new therapeutic approaches. The SELEX method itself is inherently adaptable and offers near limitless possibilities in yielding functional nucleic acid ligands. This Primer serves to provide guidance on experimental design and highlight new growth areas for this impactful technology.

Electrochemiluminescence of Semiconductor Quantum Dots and Its Biosensing Applications: A Comprehensive Review

Electrochemiluminescence (ECL) is the chemiluminescence triggered by electrochemical reactions. Due to the unique excitation mode and inherent low background, ECL has been a powerful analytical technique to be widely used in biosensing and imaging. As an emerging ECL luminophore, semiconductor quantum dots (QDs) have apparent advantages over traditional molecular luminophores in terms of luminescence efficiency and signal modulation ability. Therefore, the development of an efficient ECL system with QDs as luminophores is of great significance to improve the sensitivity and detection flux of ECL biosensors. In this review, we give a comprehensive summary of recent advances in ECL using semiconductor QDs as luminophores. The luminescence process and ECL mechanism of semiconductor QDs with various coreactants are discussed first. Specifically, the influence of surface defects on ECL performance of semiconductor QDs is emphasized and several typical ECL enhancement strategies are summarized. Then, the applications of semiconductor QDs in ECL biosensing are overviewed, including immunoassay, nucleic acid analysis and the detection of small molecules. Finally, the challenges and prospects of semiconductor QDs as ECL luminophores in biosensing are featured.

RNA aptamer-mediated gene therapy of prostate cancer: lessons from the past and future directions

INTRODUCTION

Prostate cancer (PCa) is one of the most prevalent cancers in the world, and the fifth cause of death from cancer in men. Among the non-surgical treatments for PCa, gene therapy strategies are in the early stages of development and recent clinical trials have provided new insights suggesting promising future.

AREAS COVERED

Recently, the creation of targeted gene delivery systems, based on specific PCa cell surface markers, has been viewed as a viable therapeutic approach. Prostate-specific membrane antigen (PSMA) is vastly expressed in nearly all prostate malignancies, and the intensity of expression increases with tumor aggressiveness, androgen independence, and metastasis. RNA aptamers are short and single-stranded oligonucleotides, which selectively bind to a specific ligand on the surface of the cells, which makes them fascinating small molecules for target delivery of therapeutics. PSMA-selective RNA aptamers represent great potential for developing targeted-gene delivery tools for PCa.

EXPERT OPINION

This review provides a thorough horizon for the researchers interested in developing targeted gene delivery systems for PCa via PSMA RNA aptamers. In addition, we provided general information about different prospects of RNA aptamers including discovery approaches, stability, safety, and pharmacokinetics.

Structural RNA components supervise the sequential DNA cleavage in R2 retrotransposon

Retroelements are the widespread jumping elements considered as major drivers for genome evolution, which can also be repurposed as gene-editing tools. Here, we determine the cryo-EM structures of eukaryotic R2 retrotransposon with ribosomal DNA target and regulatory RNAs. Combined with biochemical and sequencing analysis, we reveal two essential DNA regions, Drr and Dcr, required for recognition and cleavage. The association of 3' regulatory RNA with R2 protein accelerates the first-strand cleavage, blocks the second-strand cleavage, and initiates the reverse transcription starting from the 3'-tail. Removing 3' regulatory RNA by reverse transcription allows the association of 5' regulatory RNA and initiates the second-strand cleavage. Taken together, our work explains the DNA recognition and RNA supervised sequential retrotransposition mechanisms by R2 machinery, providing insights into the retrotransposon and application reprogramming.

Use of S2.2/DOX Magnetic Nanoliposomes in MR Molecule Imaging and Targeted Thermochemotherapy for Breast Cancer In Vitro

OBJECTIVE

To prepare S2.2/DOX magnetic nanoliposomes by combining the potential benefits of MNPs in MRI and the targeted performance of nano-drugs as an innovative method for integrated diagnosis and treatment of breast cancer (BC).

METHODS

We created a S2.2-PEG-MZF/DOX molecular probe by using a lipid material to encapsulate PEG-MZF-NPs and doxorubicin (DOX), and a S2.2 aptamer to target MUC1 to conjugate with PEG-MZF/DOX nanoliposomes. The potential of probe for cell-specific targeting and magnetic resonance (MR) molecular imaging was evaluated by MR scanner and Prussian blue staining. Additionally, we explored the feasibility by using nanoliposome magnetic induction heating to interfere with MCF-7 (MUC1+) BC cells under the influence of an alternating magnetic field (AMF).

RESULTS

PEG-MZF-NPs were biologically safe. The T2 relaxation rate of PEG-MZF-NPs was found to inhibit T2 signal in a concentration-dependent manner, and the T2 signal of the S2.2-PEG-MZF molecular probe in MCF-7 cells was significantly lower than that in PEG-MZF-NPs group. Moreover, the T2 signal reduction was more pronounced in MCF-7 cells than in the hepatoma cell line HepG2 (MUC1-), suggesting a strong MRI potential of the S2.2-PEG-MZF molecular probe. The S2.2-PEG-MZF/DOX nanoliposome was able to achieve the desired temperature range for tumor hyperthermia (42-44 °C) in vitro. The S2.2-PEG-MZF/DOX nanoliposome accompanied by magnetic fluid hyperthermia (MFH) could inhibit proliferation and invasion and induce apoptosis of MCF-7 cells. The effects of this approach were significantly higher than those observed in the other groups.

CONCLUSION

We successfully developed a novel technique for BC diagnosis and treatment using thermochemotherapy under the guidance of MR molecular imaging. This approach holds great potential for improving the management of this devastating disease in the future.