SELEX--a (r)evolutionary method to generate high-affinity nucleic acid ligands

Droplet digital PCR-based single aptamer selection

Aptamers are potent alternatives to antibodies in applications including diagnostics and disease treatment. These synthetic molecules are generated from sequences identified through specific targets within an aptamer pool of random sequences, approximately 10^15 in size, via the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) process. Nevertheless, SELEX encompasses repetitive, time/money-consuming and stochastic methodologies. In this study, we introduce a method for the direct acquisition of target aptamers in a single step, rapidly identifying the aptamers of interest. Single molecules of aptamers are first encapsulated into droplets and amplified therein, and the fluorescence in the droplets will be active upon binding between the aptamers with the target with good affinity. Subsequent identification and sorting of these fluorescing droplets enable the immediate acquisition of desired aptamers without the need for synthesizing them based on selected sequences. This digital selection process bypasses traditional sequencing, thereby reducing stochastic events and costs associated with repeated sequencing, as well as mitigating the uncertainties tied to the synthesis of aptamers. Our proof-of-concept findings suggest that this straightforward yet effective strategy can directly yield aptamers, thereby enhancing the exploration of aptamer biology and promoting the development of aptamer-based applications.

Aptamers as a New Frontier in Molecular Cancer Imaging Technologies

Molecular imaging has emerged as a transformative tool in cancer diagnosis, enabling the visualization of biological processes at the cellular and molecular levels. Aptamers, single-stranded oligonucleotides with high affinity and specificity for target molecules, have gained significant attention as versatile probes for molecular imaging due to their unique properties, including small size, ease of modification, low immunogenicity, and rapid tissue penetration. This review explores the integration of aptamers with various imaging agents to enhance cancer diagnosis and therapy. Aptamer-based imaging probes offer high sensitivity and real-time visualization of tumor markers. Aptamer-based fluorescence probes and aptamer-conjugated magnetic resonance imaging (MRI) probes, including gadolinium-based contrast agents, improve tumor targeting and imaging resolution. Additionally, aptamers have been utilized in single-photon emission computed tomography (SPECT) and positron emission tomography (PET) imaging to enhance the specificity of radiotracers for cancer detection. Furthermore, aptamer-targeted ultrasound and computed tomography (CT) imaging demonstrate the potential for noninvasive and precise tumor localization. By leveraging the unique advantages of aptamers, these imaging strategies not only improve diagnostic accuracy but also pave the way for image-guided cancer therapies. This review highlights the significant role of aptamers in advancing molecular imaging and their potential to revolutionize cancer diagnosis and treatment.

Analysis of quadruplex propensity of aptamer sequences

Aptamers are short DNA or RNA sequences that can fold into unique three-dimensional structures, enabling them to bind specifically to target molecules with high affinity, similar to antibodies. A distinctive feature of many aptamers is their ability to adopt a G-quadruplex (G4) fold, a four-stranded structure formed by guanine-rich sequences. While G4 formation has been proposed or demonstrated for some aptamers, we aimed to investigate how frequently quadruplex-prone motifs emerge from the SELEX process. To achieve this, we examined quadruplex candidate sequences from the UTexas Aptamer Database, which contains over 1400 aptamer sequences extracted from 400 publications spanning several decades. We analyzed the G4 and i-motif propensity of these sequences. While no likely i-motif forming candidates were found, nearly 1/4 of DNA aptamers and 1/6 of RNA aptamers were predicted to form G4 structures. Interestingly, many motifs capable of forming G4 structures were not previously reported or suspected. Out of 311 sequences containing a potential stable G4 motif, only 53 of them (17%) reported the word "quadruplex" in the corresponding article. We experimentally tested G4 formation for 30 aptamer sequences and were able to confirm G4 formation for all the sequences with a G4Hunter score of 1.31 or more. These observations suggest the need to reevaluate G4 propensity among aptamer sequences.

Multifaceted arsenal in SELEX nanomedicine

Aptamers, short oligonucleotide sequences that bind specifically to cellular proteins and receptors, are emerging as versatile tools in molecular nanomedicine. Unlike passive tumor targeting via the enhanced permeability and retention (EPR) effect, aptamers enable precise drug delivery, enhancing therapeutic efficacy while minimizing side effects. Developed through the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) process, aptamers offer compact size, robust structure, chemical versatility, and cost-effective synthesis. They serve as effective delivery vehicles for therapeutic molecules, including miRNA, siRNA, and small-molecule drugs, and function as antibody-like ligands for applications in cancer, diabetes, and autoimmune disorders. Since the approval of Macugen, the first aptamer targeting VEGF, aptamers have also shown promise as diagnostic sensors and theranostic agents. This review explores SELEX-derived aptamers in nanomedicine, focusing on their therapeutic and diagnostic roles, particularly in precision cancer therapies. It also addresses challenges such as degradation and clinical translation alongside prospects in vaccines, tissue engineering, and regenerative medicine.

Chemically reduced graphene oxide based assembly of Aptasensor for sensitive and probe-free detection of penicillin-G

The widespread use of antibiotics in livestock and poultry leads to antibiotic residues in food, posing public health risks. To ensure food safety, monitoring antibiotic levels in dairy and poultry is essential, especially for Penicillin-G (Pen-G), a frequently used β-lactam antibiotic. This study presents an electrochemical aptasensor for detecting Pen-G in food samples, using chemically reduced graphene oxide (crGO) conjugated with Pen-G-specific aptamer on electrode. The sensors construction was validated via various microscopy and spectroscopy techniques and its performance optimized by adjusting factors such as pH, scan rate, temperature, concentration of aptamer, and reaction time using differential pulse voltammetry (DPV) and cyclic voltammetry (CV). It achieved a detection limit of 1.24 pM, effectively distinguishing Pen-G from other antibiotics in real milk, meat, and egg samples, with stability for up to 3 weeks, making it a valuable tool for antibiotic monitoring in food products.

A critical review of sensors for detecting per- and polyfluoroalkyl substances: Focusing on diverse molecular probes

Per and Polyfluoroalkyl Substances (PFASs) pose a severe threat to the ecological environment and human health due to their persistence, bioaccumulation, and potential toxicity in the environment. Currently, the detection methods of PFASs generally rely on the combination of chromatographic techniques and mass spectrometry, which are typically suitable for laboratory testing. To meet the requirements of on-site detection, there is an urgent need to develop convenient and efficient detection methods. Sensors, as the preferred alternative, have been widely studied. In order to deeply investigate the mechanism of sensors in recognizing PFASs, this review, from the unique perspective of molecular probes, summarizes the construction and recognition mechanisms of four molecular probes: antibodies, aptamers, synthesized micromolecules, and synthesized polymers for PFASs. This review focuses on PFOA and PFOS as representative perfluoroalkyl substances and systematically investigates their properties and effects. It also analyzes the respective advantages, disadvantages, and applicable scenarios, and discusses the future development trends.

Biorecognition-based electrochemical sensors for highly sensitive C-reactive protein detection: A review

Highly sensitive C-reactive protein (hsCRP) is a widely recognized biomarker for inflammation and cardiovascular diseases and plays a critical role in early diagnosis, risk assessment, and treatment monitoring. The development of sensitive and selective techniques for hsCRP detection is of paramount importance for clinical diagnostics. Electrochemical sensors have emerged as promising alternatives to traditional methods, offering rapid, cost-effective, and portable solutions for hsCRP analysis. This review comprehensively discusses advancements in biorecognition-based electrochemical sensors for hsCRP detection, focusing on label- and label-free approaches. This review highlights the sensor principles, designs, and performance, and emphasizes their advantages as well as limitations in various target applications. Recent studies have shown the potential of both label- and label-free-based sensors to achieve low detection limits and wide linear ranges comparable to traditional methods. In addition, we discuss the mechanisms, challenges, and future directions of biorecognition-based electrochemical sensors for hsCRP detection. This innovation can potentially revolutionize the diagnosis and treatment of cardiovascular and inflammatory diseases by enhancing the detection sensitivity and specificity. Ultimately, these advancements aim to improve patient outcomes by enabling earlier diagnosis, cost-effectiveness, and more precise monitoring, contributing to more effective management of cardiovascular health globally.

Aptamers as innovative tools for malaria diagnosis and treatment: advances and future perspectives

Malaria, caused by Plasmodium spp. parasites (P. vivax, P. falciparum, P. ovale, P. malariae, and P. knowlesi), remains a significant global health challenge, with 263 million cases and 567 000 deaths reported in 2023. Diagnosis in endemic regions relies on clinical symptoms, microscopy, and rapid diagnostic tests. Although widely used, microscopy suffers from variability in sensitivity due to operator expertise and low parasitemia. Rapid diagnostic tests, which are favored for their simplicity and speed, show high sensitivity for P. vivax but reduced accuracy (80%) for P. falciparum, which is attributed to deletions in histidine-rich protein 2/3 proteins caused by Pfhrp2/3 gene mutations. Innovative diagnostic and therapeutic technologies, such as aptamers, are gaining attention. Aptamers are single-stranded oligonucleotides that bind specifically to target molecules with high affinity. They have shown promise in disease diagnosis, therapeutics, and environmental monitoring. In malaria, aptamers are being explored as highly sensitive and specific diagnostic tools capable of detecting Plasmodium proteins across all infection stages. Additionally, they offer potential for novel therapeutic strategies, enhancing disease control and treatment options. These advancements highlight the use of aptamers as versatile and innovative approaches for addressing malaria and other infectious diseases. A comprehensive literature search was conducted in the PubMed, ScienceDirect, and SCOPUS databases via the keywords "Aptamers" AND "Malaria" AND "Aptamers" AND "Plasmodium." Additionally, patent searches were carried out in the LENS, WIPO, and LATIPAT databases via the same search terms. In total, 88 relevant articles were selected for this review, providing a comprehensive and evidence-based foundation to discuss emerging aptamer technologies for malaria diagnosis and treatment. The proteins commonly employed in rapid malaria diagnostic tests, such as histidine-rich protein 2, P. lactate dehydrogenase, and prostaglandin dehydrogenase, are highlighted. However, the identification of new targets, such as HMIGB1 and DRX1 (1-deoxy-d-xylulose-5-phosphate reductoisomerase), and the detection of whole cells have also been emphasized.

DNA aptamers targeting P. aeruginosa RNAP

We present the first DNA aptamers designed to target the RNA polymerase (RNAP) of Pseudomonas aeruginosa. Utilizing SELEX, we identified and examined aptamers, among which the R2 aptamer demonstrated high specificity and significant binding affinity for RNAP. R2 effectively captured RNAP, making it suitable for protein tandem purification and coating applications. These results have revealed that aptamers are valuable tools for investigating P. aeruginosa RNAP.

Selection of DNA Aptamers Against Parathyroid Hormone for Electrochemical Impedimetric Biosensor System Development

This work presents the pioneering development of an aptamer-based electrochemical biosensor for real-time monitoring of parathyroid hormone (PTH) levels, with a focus on intraoperative assessment during parathyroid surgery. It introduces, for the first time, the selection and characterization of aptamers targeting distinct segments of the PTH peptide. The study demonstrates the feasibility and efficacy of the biosensing platform through a precisely designed experimental framework, including SELEX-based aptamer selection, aptamer-peptide interaction analysis, and biosensor fabrication. The SELEX process yields aptamers with notable binding affinities to different fragments of PTH, with the PTH (53-84) aptamer showing particularly sensitive binding to the hormone's C terminus, allowing for precise PTH analysis. Electrochemical characterization reveals significant changes in electrochemical impedance spectroscopy (EIS) signals upon exposure to varying PTH concentrations, highlighting the sensor's sensitivity and selectivity. The increase in charge transfer resistance (Rct) values with rising PTH concentrations underscores the biosensor's capability to detect PTH-induced structural changes, validating its potential for accurate measurement. The biosensor shows remarkable selectivity in the presence of common interferents in serum samples, ensuring precise PTH detection. Stability assessments over a 45-day storage period demonstrate the biosensor's robustness and long-term reliability, affirming its practical suitability. In summary, the developed aptamer-based biosensor represents a promising tool for sensitive and selective PTH detection, with potential applications in biomedical research and clinical diagnostics, particularly for intraoperative PTH analysis during parathyroidectomy. Continued research and optimization efforts hold promise for enhancing its performance and expanding its utility in diverse healthcare settings.

Manganese-Loaded pH-Responsive DNA Hydrogels Enable Tg-Guided Thyroid Tumor Targeted Magnetic Resonance Imaging

The diagnosis of metastatic and recurrent occult thyroid cancer presents a significant challenge. This study introduces a DNA-Mn hydrogel (M-TDH) that specifically targets thyroglobulin (Tg). This nanogel is loaded with paramagnetic Mn2+ for facilitating magnetic resonance (MR) imaging. As a cofactor of DNA polymerase, Mn2+ promotes the extension of long-strand DNA and forms Mn2PPi nuclei with PPi4- in the system. The synthesis of M-TDH is achieved through Mn2PPi nucleation and growth with long-strand DNA acting as the structural framework. The X-scaffold functions as a junction point, thereby enhancing structural stability. The Tg aptamer sequence is incorporated into M-TDH, ensuring specific targeting of thyroid cancer cells. Furthermore, M-TDH demonstrates an extended residence time at the thyroid tumor site, thus increasing the duration of enhanced MR imaging. Overall, this study introduces an aptamer-based, thyroid tumor-targeted DNA nanogel for MR imaging diagnostic applications, with the potential to advance a multifunctional magnetic nanosystem toward clinical application.

A system for in vitro selection of fully 2'-modified RNA aptamers

SFM4-3, KOD DGLNK, and Therminator polymerase are investigated for their compatibility with SELection with Modified Aptamers (SELMA), an aptamer discovery method that enables incorporation of large nucleobase modifications such as glycans. We demonstrated that with suitable modifications to the primer design and protocol, these enzymes are compatible with SELMA, enabling 2'-fluoro or 2'-methoxy ribose modifications at all positions. In the case of 2'-fluoro modifications, Therminator exhibits cleaner incorporation of an alkyne-modified nucleobase for click chemistry.

Functional Aptamers In Vitro Evolution for Protein-Protein Interaction Blockage

As aptamer development progresses, their applications have expanded significantly beyond high affinity to include functional capabilities. Currently, the identification of functional aptamers relies on traditional SELEX techniques, followed by functional validation and computer-assisted redesign of high-affinity aptamers. However, high affinity does not guarantee optimal functionality, making the search for functional aptamers from binding pools time-consuming and labor-intensive. Addressing this challenge, we introduce functional aptamers in vitro evolution (FAIVE), a novel screening method that links sequence functionality to fluorescence intensity. We demonstrated the effectiveness of FAIVE by obtaining modified DNA aptamers capable of disrupting the interaction between the SARS-CoV-2 spike receptor-binding domain (RBD) and hACE2, targeting protein-protein interaction inhibition. Furthermore, we investigated the criteria for validating the quality of the bead library generated for selection by modeling the emulsion PCR process, providing theoretical insights for future applications. The concept of incorporating fluorescent signal reporting of aptamer functionality into the aptamer selection process holds the potential to facilitate the identification of aptamers with diverse functionalities and is readily adaptable to various research contexts.

The application of aptamers in the repair of bone, nerve, and vascular tissues

Aptamers represent a distinct category of short nucleotide sequences or peptide molecules characterized by their ability to bind to specific targets with high precision. These molecules are predominantly synthesized through SELEX (Systematic Evolution of Ligands by Exponential Enrichment) technology. Recent findings indicate that aptamers may have significant applications in regenerative medicine, particularly in the domain of tissue repair. In comparison to other bioactive agents, aptamers exhibit superior specificity and affinity, are more readily accessible, and can be chemically modified, thereby presenting a promising avenue for the functionalization of tissue engineering materials in tissue repair applications. This review delineates the properties of aptamers and examines the methodologies and advancements related to aptamer-functionalized hydrogels, nanoparticles, and electrospun materials. It categorizes the four primary functions of aptamers in tissue repair, namely regeneration, delivery systems, anti-inflammatory actions, and pro-coagulation effects. Furthermore, the review explores the utilization of aptamer-functionalized tissue engineering materials in the repair of bone, nerve, and vascular tissues, highlighting the mechanisms by which aptamers facilitate tissue growth and repair through regenerative properties and their role in transporting substances that promote repair. Lastly, the review addresses the future prospects and challenges associated with the application of aptamers in tissue repair, offering novel insights and directions for further research and application in this domain.

Development of a specific biosensor for sesquiterpene based on SELEX and directed evolution platforms

Biosensors are essential in synthetic biology, particularly for detecting compounds without distinct visual markers. In this study, a riboswitch biosensor specifically responsive to a sesquiterpene - amorpha-4,11-diene was developed for the first time. Through SELEX-SMB, a high-affinity aptamer library comprising 81,520 sequences was generated. Subsequent screening via the TBG-directed evolution platform identified riboswitch5, which downregulates downstream gene expression in response to amorpha-4,11-diene within a concentration range of 10-100 mg/L, achieving a log₂Foldchange of -0.51 at 100 mg/L. Structural predictions, combined with molecular docking and molecular dynamics simulations, revealed that ligand binding induced conformational changes that stabilize the riboswitch and enhance its repressive effect. This biosensor represents a powerful tool for the detection and regulation of small molecules, with broad applications in strain engineering, pathway regulation, and metabolic optimization in synthetic biology.

Targeted Covalent Modification Strategies for Drugging the Undruggable Targets

The term "undruggable" refers to proteins or other biological targets that have been historically challenging to target with conventional drugs or therapeutic strategies because of their structural, functional, or dynamic properties. Drugging such undruggable targets is essential to develop new therapies for diseases where current treatment options are limited or nonexistent. Thus, investigating methods to achieve such drugging is an important challenge in medicinal chemistry. Among the numerous methodologies for drug discovery, covalent modification of therapeutic targets has emerged as a transformative strategy. The covalent attachment of diverse functional molecules to targets provides a powerful platform for creating highly potent drugs and chemical tools as well the ability to provide valuable information on the structures and dynamics of undruggable targets. In this review, we summarize recent examples of chemical methods for the covalent modification of proteins and other biomolecules for the development of new therapeutics and to overcome drug discovery challenges and highlight how such methods contribute toward the drugging of undruggable targets. In particular, we focus on the use of covalent chemistry methods for the development of covalent drugs, target identification, drug screening, artificial modulation of post-translational modifications, cancer specific chemotherapies, and nucleic acid-based therapeutics.

Application of PS2M Aptamer as Receptor Layer for Electrochemical Detection of Lead Ions

Since lead can cause severe effects on living organisms' health and life, the regular monitoring of Pb levels in water and soil is of particular significance. Recently, it was shown that lead ions can also be detected using affinity-based biosensors, namely, using aptamers as recognition elements. In most cases, thrombin binding aptamer (TBA) was utilized; however, there are more examples of DNA aptamers which could also serve that purpose. Herein, we present studies on the electrochemical detection of lead ions using PS2M aptamer, which contains several guanine nucleotides, as the receptor element. Firstly, the method of aptamer-based layer fabrication was optimized along with the choice of a redox active indicator, which was a source of current signal. The experiments revealed the possibility of lead ion detection from 50 to 600 nM, which covers the range below and above the maximum accepted limit stated by US EPA (72 nM). Moreover, the sensing layer exhibited high selectivity towards lead ions and was successfully applied both for the analysis of tap water spiked with Pb2+ ions and as a miniaturized sensor. Finally, stability and regeneration studies on the aptamer-based receptor layer were executed to confirm the utility of the elaborated tool.

Ultra-Sensitive Aptamer-Based Diagnostic Systems for Rapid Detection of All SARS-CoV-2 Variants

The emergence of numerous SARS-CoV-2 variants, characterized by mutations in the viral RNA genome and target proteins, has presented challenges for accurate COVID-19 diagnosis. To address this, we developed universal aptamer probes capable of binding to the spike proteins of SARS-CoV-2 variants, including highly mutated strains like Omicron. These aptamers were identified through protein-based SELEX using spike proteins from three key variants (D614G-substituted Wuhan-Hu-1, Delta, and Omicron) and virus-based SELEX, known as viro-SELEX. Leveraging these universal aptamers, we created a highly sensitive lateral flow assay (LFA) and an ultra-sensitive molecular diagnostic platform that integrates a novel rapid PCR technique, enabling fast and reliable detection across all SARS-CoV-2 variants.

Non-Invasive Point-of-Care Detection of Methamphetamine and Cocaine via Aptamer-Based Lateral Flow Test

Drug abuse is a major public problem in the workplace, traffic, and forensic issues, which requires a standardized test device to monitor on-site drug use. For field testing, the most important requirements are portability, sensitivity, non-invasiveness, and quick results. Motivated by this problem, a point of care (POC) test based on lateral flow assay (LFA) was developed for the detection of cocaine (COC) and methamphetamine (MET) in saliva which has been selected as the matrix for this study due to its rapid and non-invasive collection process. In the design strategy of an LFA test, the use of gold nanoparticles (AuNPs) with strong optical properties has been combined with the advantages of selecting aptamers under in vitro conditions, making it a highly specific and stable recognition probe for the detection of small molecules in saliva. The developed aptamer-based LFA in a competitive format, was able to detect COC and MET in synthetic saliva at concentrations as low as 5.0 ng/mL. After analytical performance studies, the test system also detected COC and MET in real patient samples, which was verified by chromatographic methods.

SequenceCraft: machine learning-based resource for exploratory analysis of RNA-cleaving deoxyribozymes

BACKGROUND

Deoxyribozymes or DNAzymes represent artificial short DNA sequences bearing many catalytic properties. In particular, DNAzymes able to cleave RNA sequences have a huge potential in gene therapy and sequence-specific analytic detection of disease markers. This activity is provided by catalytic cores able to perform site-specific hydrolysis of the phosphodiester bond of an RNA substrate. However, the vast majority of existing DNAzyme catalytic cores have low efficacy in in vivo experiments, whereas SELEX based on in vitro screening offers long and expensive selection cycle with the average success rate of ~ 30%, moreover not allowing the direct selection of chemically modified DNAzymes, which were previously shown to demonstrate higher activity in vivo. Therefore, there is a huge need in in silico approach for exploratory analysis of RNA-cleaving DNAzyme cores to drastically ease the discovery of novel catalytic cores with superior activities.

RESULTS

In this work, we develop a machine learning based open-source platform SequenceCraft allowing experimental scientists to perform DNAzyme exploratory analysis via quantitative observed rate constant (kobs) estimation as well as statistical and clustering data analysis. This became possible with the development of a unique curated database of > 350 RNA-cleaving catalytic cores, property-based sequence representations allowing to work with both conventional and chemically modified nucleotides, and optimized kobs predicting algorithm achieving Q2 > 0.9 on experimental data published to date.

CONCLUSIONS

This work represents a significant advancement in DNAzyme research, providing a tool for more efficient discovery of RNA-cleaving DNAzymes. The SequenceCraft platform offers an in silico alternative to traditional experimental approaches, potentially accelerating the development of DNAzymes.

Aptasensors application for cow's milk allergens detection and early warning: Progress, challenge, and perspective

Cow's milk allergy (CMA) is considered one of the most prevalent food allergies and a public health concern. Modern medical research shows that the effective way to prevent allergic reactions is to prevent allergic patients from consuming allergenic substances. Therefore, the development of rapid and accurate detection technology for milk allergens detection and early warning is critical to safeguarding those with a cow milk allergy. As the oligonucleotide sequences with high specificity and selectivity, aptamers frequently assemble with transduction elements forming multifarious aptasensors for quantitative detection owing to their high-affinity binding to the target. Current aptasensors in the field of cow's milk allergen detection in recent years are explored in this review. This review takes a look back at a few common assays, including ELISA and PCR, before presenting a clear overview of the aptamer and threshold doses. It delves into a detailed discussion of the current aptamer-based detection techniques and related theories for milk allergen identification. Last but not least, we conclude with a discussion and outlook of the advancements made in allergen detection with aptamers. We sincerely hope that there will be more extensive applications for aptasensors in the future contributing to reducing the possibility of patients suffering from adverse reactions.

Selection of DNA aptamers against Chikungunya virus Envelope 2 Protein and their application in sandwich ELASA

Chikungunya fever, caused by Chikungunya virus (CHIKV) exhibits clinical features that mimic that of other arbovirus infections such as dengue. CHIKV Envelope 2 (E2) protein, an antigenic epitope of CHIKV, has been identified as an ideal marker for diagnostics. The current CHIKV antigen detection tests are largely based on antibodies but are beleaguered by issues such as sensitivity to high temperature, expensive and prone to batch-to-batch variations. Aptamers are suitable alternatives to antibodies as they are cheaper and have no batch-to-batch variations compared to antibodies. In this study, DNA aptamer selection against CHIKV E2 proteins was performed using two different randomized ssDNA libraries. Chik-2 (96-mer) and Chik-3 (76-mer) were isolated from these two libraries and were identified as the potential aptamers against CHIKV E2 protein. The binding affinity of Chik-2 and Chik-3 against CHIKV E2 protein was estimated at 177.5 ± 32.69 nM and 30.01 ± 3.60 nM, respectively. A sandwich ELASA was developed, and this assay showed a detection limit of 2.17 x 103 PFU/mL. The sensitivity and specificity of the assay were 80 % and 100 %, respectively. The assay showed no cross-reactivity with dengue-positive samples, demonstrating the enormous diagnostic potential of these aptamers for the detection of CHIKV.

Recent advances in aptamer discovery, modification and improving performance

Aptamers are nucleic acid (Ribonucleic acid (RNA) and single strand deoxyribonucleic acid (ssDNA)) with a length of approximately 25-80 bases that can bind to particular target molecules, similar to monoclonal antibodies. Due to their many benefits, which include a long shelf life, minimal batch-to-batch variations, extremely low immunogenicity, the possibility of chemical modifications for improved stability, an extended serum half-life, and targeted delivery, they are receiving a lot of attention in a variety of clinical applications. The development of high-affinity modification approaches has attracted significant attention in aptamer applications. Stable three-dimensional aptamers that have undergone chemical modification can engage firmly with target proteins through improved non-covalent binding, potentially leading to hundreds of affinity improvements. This review demonstrates how cutting-edge methodologies for aptamer discovery are being developed to consistently and effectively construct high-performing aptamers that need less money and resources yet have a high chance of success. Also, High-affinity aptamer modification techniques were discussed.

Selection of trophoblast cell surface antigen 2-targeted aptamer for the development of cytotoxic aptamer-drug conjugate

Trophoblast cell surface antigen 2 expressed in several malignant cancers promotes tumor growth and metastasis via several signal transduction pathways. Trop2 is reputed as a prospective biomarker and therapeutic target. Trophoblast cell surface antigen 2-targeted agents, including antibodies, antibody conjugates and therapeutic combinations, could be utilized to fight cancers. To develop an effective drug targeting strategy, we resorted to a new trophoblast cell surface antigen 2-targeted anticancer treatment through aptamer conjugated with chemotherapeutic drug. This study identified trophoblast cell surface antigen 2-specific ssDNA aptamers using engineered trophoblast cell surface antigen 2 overexpression cells for cell-SELEX. The obtained ssDNA aptamer bound to trophoblast cell surface antigen 2 overexpressed cells with nanomolar affinity and was specific for several tumor cell types which express trophoblast cell surface antigen 2 abundantly. Significant cytotoxicity against HT29 cell by the conjugate of trophoblast cell surface antigen 2 aptamer and Emtansine was observed while resulting negligible therapeutic effect on human normal intestinal epithelial cell line HIEC in vitro, indicating that the conjugate shows potential as a promising therapeutic agent. Furthermore, the isolated aptamer demonstrated the ability for the targeted delivery, resulting excellent therapeutic effectiveness of aptamer-drug conjugate for xenograft tumor model of mice with human colorectal cancer.

Comprehensive analysis of computational approaches in plant transcription factors binding regions discovery

Transcription factors (TFs) are regulatory proteins which bind to a specific DNA region known as the transcription factor binding regions (TFBRs) to regulate the rate of transcription process. The identification of TFBRs has been made possible by a number of experimental and computational techniques established during the past few years. The process of TFBR identification involves peak identification in the binding data, followed by the identification of motif characteristics. Using the same binding data attempts have been made to raise computational models to identify such binding regions which could save time and resources spent for binding experiments. These computational approaches depend a lot on what way they learn and how. These existing computational approaches are skewed heavily around human TFBRs discovery, while plants have drastically different genomic setup for regulation which these approaches have grossly ignored. Here, we provide a comprehensive study of the current state of the matters in plant specific TF discovery algorithms. While doing so, we encountered several software tools' issues rendering the tools not useable to researches. We fixed them and have also provided the corrected scripts for such tools. We expect this study to serve as a guide for better understanding of software tools' approaches for plant specific TFBRs discovery and the care to be taken while applying them, especially during cross-species applications. The corrected scripts of these software tools are made available at https://github.com/SCBB-LAB/Comparative-analysis-of-plant-TFBS-software.

A Novel Approach for Colorimetric Detection of Glyphosate in Food Based on a Split Aptamer Nanostructure and DNAzyme Activity

Glyphosate has become the most widely used herbicide worldwide in recent years. There are many concerns about toxicity and mutagenicity from long-term use of glyphosate in humans and animals. Therefore, the methods that can help in easy and quick detection of this chemical compound in food and water are critical. In this work, a biosensor was fabricated by combining the enzymatic properties of a specific DNA G-quadruplex and selectivity of a split aptamer to detect glyphosate in foods and water in a quick and simple colorimetric manner. The color change in this method is based on the oxidation of TMB by the G-quadruplex enzyme and the function of aptamer to trap glyphosate, which is visible to the naked eye in the presence and absence of the herbicide. The biosensor showed its high performance in various real samples of water and foods and provided a detection limit of 1.37 nM (R² = 0.9899) with a linear response range of 100 to 400 nM of glyphosate. This biosensor can provide an innovative, cheap and fast approach for the detection and monitoring of glyphosate in various foods and water.

Advances in nucleic acid aptamer-based detection of respiratory virus and bacteria: a mini review

Respiratory pathogens infecting the human respiratory system are characterized by their diversity, high infectivity, rapid transmission, and acute onset. Traditional detection methods are time-consuming, have low sensitivity, and lack specificity, failing to meet the needs of rapid clinical diagnosis. Nucleic acid aptamers, as an emerging and innovative detection technology, offer novel solutions with high specificity, affinity, and broad target applicability, making them particularly promising for respiratory pathogen detection. This review highlights the progress in the research and application of nucleic acid aptamers for detecting respiratory pathogens, discussing their selection, application, potential in clinical diagnosis, and future development. Notably, these aptamers can significantly enhance the sensitivity and specificity of detection when combined with detection techniques such as fluorescence, colorimetry and electrochemistry. This review offers new insights into how aptamers can address the limitations of traditional diagnostic methods and advance clinical diagnostics. It also highlights key challenges and future research directions for the clinical application of nucleic acid aptamers.

Electrochemical aptasensor for sensitive detection of staphylococcal enterotoxin type A in milk and fruit juice

An aptamer-based electrochemical sensor for the sensitive detection of staphylococcal enterotoxin type A (SEA) is presented. The truncated aptamer AptSEA1.4 used in this work was screened using computational techniques, which reduced the cost of the SELEX screening process. The aptamer-SEA interactions were confirmed by employing circular dichroism (CD) and fluorescence spectroscopy. Afterwards, for developing an electrochemical aptasensor, a fabricated GNR/FTO aptasensor was prepared and characterized using scanning electron microscopy-energy-dispersive X-ray analysis (SEM-EDX), atomic force microscopy (AFM), cyclic voltammetry (CV), and square wave voltammetry (SWV). A detailed investigation of aptamer and SEA interaction in the presence of various experimental conditions was also conducted through SWV and electrochemical impedance spectroscopy (EIS). The aptamer exhibits a strong affinity for SEA, with a dissociation constant (Kd) of 19.93 nM. The aptasensor is sensitive, with a lower limit of detection of 12.44 pg mL-1. It has good stability, repeatability, and specificity and has displayed highly specific and sensitive detection SEA in spiked packaged mixed fruit juice and milk, with a recovery of 95-110%. The aptasensor has high promise for detecting SEA in other food items.

Rho-dependent transcriptional switches regulate the bacterial response to cold shock

Binding of the bacterial Rho helicase to nascent transcripts triggers Rho-dependent transcription termination (RDTT) in response to cellular signals that modulate mRNA structure and accessibility of Rho utilization (Rut) sites. Despite the impact of temperature on RNA structure, RDTT was never linked to the bacterial response to temperature shifts. We show that Rho is a central player in the cold-shock response (CSR), challenging the current view that CSR is primarily a posttranscriptional program. We identify Rut sites in 5'-untranslated regions of key CSR genes/operons (cspA, cspB, cspG, and nsrR-rnr-yjfHI) that trigger premature RDTT at 37°C but not at 15°C. High concentrations of RNA chaperone CspA or nucleotide changes in the cspA mRNA leader reduce RDTT efficiency, revealing how RNA restructuring directs Rho to activate CSR genes during the cold shock and to silence them during cold acclimation. These findings establish a paradigm for how RNA thermosensors can modulate gene expression.

Multiplexed sequential imaging in living cells with orthogonal fluorogenic RNA aptamer/dye pairs

Detecting multiple targets in living cells is important in cell biology. However, multiplexed fluorescence imaging beyond two-to-three targets remains a technical challenge. Herein, we introduce a multiplexed imaging strategy, 'sequential Fluorogenic RNA Imaging-Enabled Sensor' (seqFRIES), which enables live-cell target detection via sequential rounds of imaging-and-stripping. In seqFRIES, multiple orthogonal fluorogenic RNA aptamers are genetically encoded inside cells, and then the corresponding cell membrane permeable dye molecules are added, imaged, and rapidly removed in consecutive detection cycles. As a proof-of-concept, we have identified in this study four fluorogenic RNA aptamer/dye pairs that can be used for highly orthogonal and multiplexed imaging in living bacterial and mammalian cells. After further optimizing the cellular fluorescence activation and deactivation kinetics of these RNA/dye pairs, the whole four-color semi-quantitative seqFRIES process can be completed in ∼20 min. Meanwhile, seqFRIES-mediated simultaneous detection of critical signalling molecules and mRNA targets was also achieved within individual living cells. We expect our validation of this new seqFRIES concept here will facilitate the further development and potential broad usage of these orthogonal fluorogenic RNA/dye pairs for multiplexed and dynamic live-cell imaging and cell biology studies.

Enhanced SELEX Platforms for Aptamer Selection with Improved Characteristics: A Review

This review delves into the advancements in molecular recognition through enhanced SELEX (Systematic Evolution of Ligands by Exponential Enrichment) platforms and post-aptamer modifications. Aptamers, with their superior specificity and affinity compared to antibodies, are central to this discussion. Despite the advantages of the SELEX process-encompassing stages like ssDNA library preparation, incubation, separation, and PCR amplification-it faces challenges, such as nuclease susceptibility. To address these issues and propel aptamer technology forward, we examine next-generation SELEX platforms, including microfluidic-based SELEX, capillary electrophoresis SELEX, cell-based aptamer selection, counter-SELEX, in vivo SELEX, and high-throughput sequencing SELEX, highlighting their respective merits and innovations. Furthermore, this article underscores the significance of post-aptamer modifications, particularly chemical strategies that enhance aptamer stability, reduce renal filtration, and expand their target range, thereby broadening their utility in diagnostics, therapeutics, and nanotechnology. By synthesizing these advanced SELEX platforms and modifications, this review illuminates the dynamic progress in aptamer research and outlines the ongoing efforts to surmount existing challenges and enhance their clinical applicability, charting a path for future breakthroughs in this evolving field.

Selection of antibody-binding covalent aptamers

Aptamers are oligonucleotides with antibody-like binding function, selected from large combinatorial libraries. In this study, we modified a DNA aptamer library with N-hydroxysuccinimide esters, enabling covalent conjugation with cognate proteins. We selected for the ability to bind to mouse monoclonal antibodies, resulting in the isolation of two distinct covalent binding motifs. The covalent aptamers are specific for the Fc region of mouse monoclonal IgG1 and are cross-reactive with mouse IgG2a and other IgGs. Investigation into the covalent conjugation of the aptamers revealed a dependence on micromolar concentrations of Cu2+ ions which can be explained by residual catalyst remaining after modification of the aptamer library. The aptamers were successfully used as adapters in the formation of antibody-oligonucleotide conjugates (AOCs) for use in detection of HIV protein p24 and super-resolution imaging of actin. This work introduces a new method for the site-specific modification of native monoclonal antibodies and may be useful in applications requiring AOCs or other antibody conjugates.

Functionalized DNA Origami-Enabled Detection of Biomarkers

Biomarkers are crucial physiological and pathological indicators in the host. Over the years, numerous detection methods have been developed for biomarkers, given their significant potential in various biological and biomedical applications. Among these, the detection system based on functionalized DNA origami has emerged as a promising approach due to its precise control over sensing modules, enabling sensitive, specific, and programmable biomarker detection. We summarize the advancements in biomarker detection using functionalized DNA origami, focusing on strategies for DNA origami functionalization, mechanisms of biomarker recognition, and applications in disease diagnosis and monitoring. These applications are organized into sections based on the type of biomarkers - nucleic acids, proteins, small molecules, and ions - and concludes with a discussion on the advantages and challenges associated with using functionalized DNA origami systems for biomarker detection.

Bridging biological samples to functional nucleic acid biosensor applications: current enzymatic-based strategies for single-stranded DNA generation

The escalating threat of emerging diseases, often stemming from contaminants and lethal pathogens, has precipitated a heightened demand for sophisticated diagnostic tools. Within this landscape, the functional nucleic acid (FNA) biosensor, harnessing the power of single-stranded DNA (ssDNA), has emerged as a preeminent choice for target analyte detection. However, the dependence on ssDNA has raised difficulties in realizing it in biological samples. Therefore, the production of high-quality ssDNA from biological samples is critical. This review aims to discuss strategies for generating ssDNA from biological samples for integration into biosensors. Several innovative strategies for ssDNA generation have been deployed, encompassing techniques, such as asymmetric PCR, Exonuclease-PCR, isothermal amplification, biotin-streptavidin PCR, transcription-reverse transcription, ssDNA overhang generation, and urea denaturation PAGE. These approaches have been seamlessly integrated with biosensors for biological sample analysis, ushering in a new era of disease detection and monitoring. This amalgamation of ssDNA generation techniques with biosensing applications holds significant promise, not only in improving the speed and accuracy of diagnostic processes but also in fortifying the global response to deadly diseases, thereby underlining the pivotal role of cutting-edge biotechnology in public health and disease prevention.

A High-Avidity, Thermostable, and Low-Cost Synthetic Capture for Ultrasensitive Detection and Quantification of Viral Antigens and Aerosols

Lateral flow assays (LFAs) are currently the most popular point-of-care diagnostics, rapidly transforming disease diagnosis from expensive doctor checkups and laboratory-based tests to potential on-the-shelf commodities. Yet, their sensitive element, a monoclonal antibody, is expensive to formulate, and their long-term storage depends on refrigeration technology that cannot be met in resource-limited areas. In this work, LCB1 affibodies (antibody mimetic miniproteins) were conjugated to bovine serum albumin (BSA) to afford a high-avidity synthetic capture (LCB1-BSA) capable of detecting the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein and virus like particles (VLPs). Substituting the monoclonal antibody 2B04 for LCB1-BSA (stable up to 60 °C) significantly improved the thermal stability, shelf life, and affordability of plasmonic-fluor-based LFAs (p-LFAs). Furthermore, this substitution significantly improved the sensitivity of p-LFAs toward the spike protein and VLPs with precise quantitative ability over 2 and 3 orders of magnitude, respectively. LCB1-BSA sensors could detect VLPs at 100-fold lower concentrations, and this improvement, combined with their robust nature, enabled us to develop an aerosol sampling technology to detect aerosolized viral particles. Synthetic captures like LCB1-BSA can increase the ultrasensitivity, availability, sustainability, and long-term accuracy of LFAs while also decreasing their manufacturing costs.

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.

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.

Electrochemical detection of manganese ions using aptamer-based layers

Heavy metals are one of the major pollutants found in drinking water and their abnormal level may pose a threat to human's health and life. Manganese also belongs to heavy metals group, and it is generally used in production of batteries, fertilizers, and ceramics. Even though, Mn is necessary for proper development of central nervous system, its elevated concentration might lead to certain diseases such as epilepsies, cell death in focal cerebral ischemia as well as neurodegenerative diseases such as Huntington and Alzheimer. Hence, it is crucial to elaborate novel methods for manganese ions detection that could be applied for in situ analysis of water samples. Herein, we present the studies on the electrochemical detection of manganese ions using aptamer-modified electrodes. This is the first attempt of application of aptamer strands as receptor layers for electrochemical analysis of manganese ions and for that purpose gold disk electrodes served as transducers, which were further modified with disulfide - based aptamers and 6-mercapto-1-hexanol blocking agent. The electrochemical measurements concerned the choice of the conditions for formation of aptamer receptor layer as well as the type of redox indicator that served as the source of current signal. The studies referred to the definition of aptasensor working parameters including the verification of the possibility of manganese ion detection in cell culture media. It was shown that it was possible to detect Mn2+ ions within 25 nM-1 μM concentration and the proposed aptasensor exhibited high selectivity towards target analyte for which at least 2 - times higher response was recorded than for interfering ions. Moreover, the possibility of Mn2+ detection in real samples was depicted followed by stability and regeneration studies.

In vitro selection of DNA aptamers against staphylococcal enterotoxin A

Staphylococcal enterotoxin A (SEA) is the most frequently reported in staphylococcal food poisoning (SFP) outbreaks. Aptamers are single-stranded nucleic acids that are seen as promising alternatives to antibodies in several areas, including diagnostics. In this work, systematic evolution of ligands by exponential enrichment (SELEX) was used to select DNA aptamers against SEA. The SELEX protocol employed magnetic beads as an immobilization matrix for the target molecule and real-time quantitative PCR (qPCR) for monitoring and optimizing sequence enrichment. After 10 selection cycles, the ssDNA pool with the highest affinity was sequenced by next generation sequencing (NGS). Approximately 3 million aptamer candidates were identified, and the most representative cluster sequences were selected for further characterization. The aptamer with the highest affinity showed an experimental dissociation constant (KD) of 13.36 ± 18.62 nM. Increased temperature negatively affected the affinity of the aptamer for the target. Application of the selected aptamers in a lateral flow assay demonstrated their functionality in detecting samples containing 100 ng SEA, the minimum amount capable of causing food poisoning. Overall, the applicability of DNA aptamers in SEA recognition was demonstrated and characterized under different conditions, paving the way for the development of diagnostic tools.

A responsive disulfide bond switch aptamer prodrug exhibiting enhanced stability and anticancer efficacy

Aptamers have shown significant potential in treating diverse diseases. However, challenges such as stability and drug delivery limited their clinical application. In this paper, the development of AS1411 prodrug-type aptamers for tumor treatment was introduced. A Short oligonucleotide was introduced at the end of the AS1411 sequence with a disulfide bond as responsive switch. The results indicated that the aptamer prodrugs not only enhanced the stability of the aptamer against nuclease activity but also facilitated binding to serum albumin. Furthermore, in the reducing microenvironment of tumor cells, disulfide bonds triggered drug release, resulting in superior therapeutic effects in vitro and in vivo compared to original drugs. This paper proposes a novel approach for optimizing the structure of nucleic acid drugs, that promises to protect other oligonucleotides or secondary structures, thus opening up new possibilities for nucleic acid drug design.

An IoT-based aptasensor biochip for the diagnosis of periodontal disease

Severe periodontitis affects nearly 1 billion individuals worldwide, highlighting the need for early diagnosis. Here, an integrated system consisting of a microfluidic chip and a portable point-of-care (POC) diagnostic device is developed using a polymethyl methacrylate (PMMA) chip fabrication and a three-dimensional printing technique, which is automatically controlled by a custom-designed smartphone application to routinely assess the presence of a specific periodontitis biomarker, odontogenic ameloblast-associated protein (ODAM). A sandwich-type fluorescence aptasensor is developed on a microfluidic chip, utilizing aptamer pair (MB@OD64 and OD35@FAM) selectively binding to target ODAM. Then this microfluidic chip is integrated into an automated Internet of Things (IoT)-based POC device, where fluorescence intensity, as a signal, from the secondary aptamer binding to ODAM in a sandwich-type binding reaction on the microfluidic chip is measured by a complementary metal oxide semiconductor (CMOS) camera with a 488 nm light-emitting diode (LED) excitation source. Obtained signals are processed by a microprocessor and visualized on a wirelessly connected smartphone application. This integrated biosensor system allows the rapid and accurate detection of ODAM within 30 min with a remarkable limit of detection (LOD) of 0.011 nM under buffer conditions. Clinical application is demonstrated by successfully distinguishing between low-risk and high-risk individuals with 100 % specificity. A strong potential in the translation of this fluorescence-based microfluidic aptasensor integrated with an IoT-based POC system is expected to be employed for non-invasive, on-site, rapid, and accurate ODAM detection, facilitating periodontitis diagnosis.

Development of Better Aptamers: Structured Library Approaches, Selection Methods, and Chemical Modifications

Systematic evolution of ligands by exponential enrichment (SELEX) has been used to discover thousands of aptamers since its development in 1990. Aptamers are short single-stranded oligonucleotides capable of binding to targets with high specificity and selectivity through structural recognition. While aptamers offer advantages over other molecular recognition elements such as their ease of production, smaller size, extended shelf-life, and lower immunogenicity, they have yet to show significant success in real-world applications. By analyzing the importance of structured library designs, reviewing different SELEX methodologies, and the effects of chemical modifications, we provide a comprehensive overview on the production of aptamers for applications in drug delivery systems, therapeutics, diagnostics, and molecular imaging.

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.

Aptamers as an approach to targeted cancer therapy

Conventional cancer treatments can cause serious side effects because they are not specific to cancer cells and can damage healthy cells. Aptamers often are single-stranded oligonucleotides arranged in a unique architecture, allowing them to bind specifically to target sites. This feature makes them an ideal choice for targeted therapeutics. They are typically produced through the systematic evolution of ligands by exponential enrichment (SELEX) and undergo extensive pharmacological revision to modify their affinity, specificity, and therapeutic half-life. Aptamers can act as drugs themselves, directly inhibiting tumor cells. Alternatively, they can be used in targeted drug delivery systems to transport drugs directly to tumor cells, minimizing toxicity to healthy cells. In this review, we will discuss the latest and most advanced approaches to using aptamers for cancer treatment, particularly targeted therapy overcoming resistance to conventional therapies.

Molecular probes targeting HER2 PET/CT and their application in advanced breast cancer

PURPOSE

Human epidermal growth factor receptor 2 (HER2)-positive breast cancer cases are among the most aggressive breast tumor subtypes. Accurately assessing HER2 expression status is vital to determining whether patients will benefit from targeted anti-HER2 treatment. HER2-targeted positron emission tomography (PET/CT) is noninvasive, enabling the real-time evaluation of breast cancer patient HER2 status with accuracy.

METHODS

We summarize the research progress of PET/CT targeting HER2 in breast cancer, focusing on PET/CT molecular probes targeting HER2 and their clinical application in the management of advanced breast cancer.

RESULTS

At present, a variety of different HER2 targeted molecular probes for PET/CT imaging have been developed, including nucleolin-labeled antibodies, antibody fragments, nanobodies, and peptides of various affinities, among others. HER2-targeted PET/CT can relatively accurately evaluate HER2 expression status in advanced breast cancer patients. It has good performance in the early detection of small HER2-positive lesions, evaluation of HER2 status in lesions that cannot be readily biopsied, evaluation of the heterogeneity of multiple metastases, identification of lesions with altered HER2 status, and evaluation of the efficacy of anti-HER2 drugs.

CONCLUSION

HER2-targeted PET/CT offers a promising noninvasive approach for real-time assessment of HER2 status，which can be guide targeted treatment for HER2-positive breast cancer patients. Future prospective clinical studies will be invaluable for fully evaluating the importance of HER2-targeted molecular imaging in the management of breast cancer.

A photoelectrochemical aptasensor based on double Z-scheme α-Fe2O3/MoS2/Bi2S3 ternary heterojunction for sensitive detection of circulating tumor cells

A novel photoelectrochemical (PEC) aptasensor based on a dual Z-scheme α-Fe2O3/MoS2/Bi2S3 ternary heterojunction for the ultrasensitive detection of circulating tumor cells (CTCs) was developed. The α-Fe2O3/MoS2/Bi2S3 nanocomposite was prepared via a step-by-step route, and the photoproduced electron/hole transfer path was speculated by conducting trapping experiments of reactive species. α-Fe2O3/MoS2/Bi2S3-modified electrodes exhibited greatly enhanced photocurrent under visible light due to the double Z-scheme charge transfer process, which met the requirement of the PEC sensor for detecting larger targets. After the aptamer was conjugated on the photoelectrode through chitosan (CS) and glutaraldehyde (GA), when MCF-7 cells were presented and captured, the photocurrent of the PEC biosensing system decreased due to steric hindrance. The current intensity had a linear relationship with the logarithm of MCF-7 cell concentration ranging from 10 to 1×105 cells mL-1, with a low detection limit of 3 cell mL-1 (S/N = 3). The dual Z-scheme α-Fe2O3/MoS2/Bi2S3 ternary heterojunction-modified PEC aptasensor exhibited high sensitivity and excellent specificity and stability. Additionally, MCF-7 cells in human serum were determined by this PEC aptasensor, exhibiting great potential as a promising tool for clinical detection.

Aptamer-Based fluorescent DNA biosensor in antibiotics detection

The inappropriate employment of antibiotics across diverse industries has engendered profound apprehensions concerning their cumulative presence within human bodies and food commodities. Consequently, many nations have instituted stringent measures limiting the admissible quantities of antibiotics in food items. Nonetheless, conventional techniques employed for antibiotic detection prove protracted and laborious, prompting a dire necessity for facile, expeditious, and uncomplicated detection methodologies. In this regard, aptamer-based fluorescent DNA biosensors (AFBs) have emerged as a sanguine panacea to surmount the limitations of traditional detection modalities. These ingenious biosensors harness the binding prowess of aptamers, singular strands of DNA/RNA, to selectively adhere to specific target antibiotics. Notably, the AFBs demonstrate unparalleled selectivity, affinity, and sensitivity in detecting antibiotics. This comprehensive review meticulously expounds upon the strides achieved in AFBs for antibiotic detection, particularly emphasizing the labeling modality and the innovative free-label approach. It also elucidates the design principles behind a diverse array of AFBs. Additionally, a succinct survey of signal amplification strategies deployed within these biosensors is provided. The central objective of this review is to apprise researchers from diverse disciplines of the contemporary trends in AFBs for antibiotic detection. By doing so, it aspires to instigate a concerted endeavor toward the development of heightened sensitivity and pioneering AFBs, thereby contributing to the perpetual advancement of antibiotic detection methodologies.

Chapter 9: Life as We Don't Know It

While Earth contains the only known example of life in the universe, it is possible that life elsewhere is fundamentally different from what we are familiar with. There is an increased recognition in the astrobiology community that the search for life should steer away from terran-specific biosignatures to those that are more inclusive to all life-forms. To start exploring the space of possibilities that life could occupy, we can try to dissociate life from the chemistry that composes it on Earth by envisioning how different life elsewhere could be in composition, lifestyle, medium, and form, and by exploring how the general principles that govern living systems on Earth might be found in different forms and environments across the Solar System. Exotic life-forms could exist on Mars or Venus, or icy moons like Europa and Enceladus, or even as a shadow biosphere on Earth. New perspectives on agnostic biosignature detection have also begun to emerge, allowing for a broader and more inclusive approach to seeking exotic life with unknown chemistry that is distinct from life as we know it on Earth.

Recent Advances in Biosensors for Diagnosis of Autoimmune Diseases

Over the last decade, autoimmune diseases (ADs) have undergone a significant increase because of genetic and/or environmental factors; therefore, their simple and fast diagnosis is of high importance. The conventional diagnostic techniques for ADs require tedious sample preparation, sophisticated instruments, a dedicated laboratory, and qualified personnel. For these reasons, biosensors could represent a useful alternative to these methods. Biosensors are considered to be promising tools that can be used in clinical analysis for an early diagnosis due to their high sensitivity, simplicity, low cost, possible miniaturization (POCT), and potential ability for real-time analysis. In this review, recently developed biosensors for the detection of autoimmune disease biomarkers are discussed. In the first part, we focus on the main AD biomarkers and the current methods of their detection. Then, we discuss the principles and different types of biosensors. Finally, we overview the characteristics of biosensors based on different bioreceptors reported in the literature.

Advancements in Brain Research: The In Vivo/In Vitro Electrochemical Detection of Neurochemicals

Neurochemicals, crucial for nervous system function, influence vital bodily processes and their fluctuations are linked to neurodegenerative diseases and mental health conditions. Monitoring these compounds is pivotal, yet the intricate nature of the central nervous system poses challenges. Researchers have devised methods, notably electrochemical sensing with micro-nanoscale electrodes, offering high-resolution monitoring despite low concentrations and rapid changes. Implantable sensors enable precise detection in brain tissues with minimal damage, while microdialysis-coupled platforms allow in vivo sampling and subsequent in vitro analysis, addressing the selectivity issues seen in other methods. While lacking temporal resolution, techniques like HPLC and CE complement electrochemical sensing's selectivity, particularly for structurally similar neurochemicals. This review covers essential neurochemicals and explores miniaturized electrochemical sensors for brain analysis, emphasizing microdialysis integration. It discusses the pros and cons of these techniques, forecasting electrochemical sensing's future in neuroscience research. Overall, this comprehensive review outlines the evolution, strengths, and potential applications of electrochemical sensing in the study of neurochemicals, offering insights into future advancements in the field.