Search Results (105)

Breast cancer continues to be a major challenge in global health, in part due to significant inequalities in access to costly diagnostic and therapeutic technologies based on antibodies. Their manufacturing requires complex and expensive bioproduction systems, resulting in limited availability of these tools—essential for early detection and targeted treatment—in many regions, particularly in Latin America. This gap has highlighted the need for cost-effective and scalable theranostic alternatives, increasing interest in aptamers. Obtained through SELEX technology, aptamers are synthetic DNA or RNA oligomers that fold into functional structures. Among their advantages are high affinity for their target, low immunogenicity, and chemical synthesis, which assures reproducible production. Aptamers have expanded the landscape of diagnostic platforms through the development of sensitive aptasensors, liquid biopsy strategies, and imaging systems based on nanomedicines. They also contribute to targeted therapy by recognizing cancer biomarkers selectively and enabling controlled drug delivery. This review presents a critical summary of advances in aptamer-based theranostics for breast cancer, addressing molecular mechanisms, structural folding, selective ligand binding, and nanomaterial interfacing. We also discuss applications in extracellular vesicle capture, cancer stem cell detection, and therapeutic conjugates, emphasizing their advantages and limitations relative to approaches based on antibodies. Overall, current advances show aptamers as emerging tools capable of democratizing precision oncology, particularly in regions where access to advanced technologies remains limited. Full article

Aptamers are synthetic nucleic acid ligands that have been proposed as alternatives to antibodies for targeting molecules and cells. In hematology, most reviews have organized aptamer literature around diseases or technological platforms. This framing has obscured how unevenly different blood cell types have been covered. In this review, we present developed aptamers organized by blood cell lineages. Specifically, we examine aptamers for B cells, T cells, natural killer cells, and red blood cells. This organization revealed a strong concentration on a small set of canonical surface markers and on malignant cell models. A parallel gap appeared in aptamers that distinguish differentiation stages or functional cell states. Within this framework, we evaluated reported applications, design strategies, and experimental use cases alongside persistent limitations in target selection and biological resolution. Our analysis highlighted both practical constraints and conceptual blind spots in current blood-cell-targeting aptamer research. Together, these observations defined a set of clear opportunities for expanding aptamer development toward more state-resolved, biologically informative, and clinically relevant targeting strategies. Full article

Understanding the functions of all genes and their biological mechanisms based on comprehensive genome regulation mechanisms is an important issue in life sciences. YnfL is an uncharacterized LysR family transcription factor in Escherichia coli. Genomic SELEX screening was performed to identify YnfL regulatory targets in the E. coli genome and reveal the function of YnfL. Nine loci on the E. coli genome were identified as regulatory targets of YnfL, and the target genes were involved in supplying DNA substrates and DNA repair. RT-qPCR analysis in vivo revealed that YnfL activates its target genes during the stationary phase. Tests for drug resistance that causes DNA damage revealed that ynfL deficiency increased abnormal cell filamentation and the appearance of anucleate cells in the presence of hydroxyurea. Furthermore, ynfL deficiency reduced cell survival under long-term nitrogen starvation conditions. In summary, we propose renaming ynfL to hydroxyurea sensitivity regulator (husR). These findings contribute to understanding DNA maintenance and long-term survival through transcriptional regulation. Full article

Virus inactivation exhibits varying disinfection kinetics due to structural or genomic differences. Standard post-disinfection assessment relies on observing cytopathic effects in inoculated cell cultures, which are limited by sensitivity, availability, cost, and turnaround time. This study explores nucleic acid aptamers as molecular sensors to differentiate between intact and post-disinfection virus particles. To discover aptamers, 12 cycles of an automated SELEX (Systematic Evolution of Ligands by Exponential Enrichment) experiment were performed using recombinant (r)-VP2 protein of canine parvovirus (CPV). Enrichment of single stranded (ss) DNA binders was evaluated by sequencing the enriched libraries. The most abundant sequences were tested for binding with coated rVP2 and CPV (intact and treated with heat and peracetic acid (PAA) disinfectant) followed by detection using PCR. Binding specificity was assessed using intact and heat-treated feline panleukopenia virus (FPV) and porcine parvovirus (PPV). Sequencing of the DNA libraries from selection cycle 6 and cycle 12 products showed individual sequence enrichment with maximum frequencies of 2.14% and 8.65%, respectively. The top three abundant sequences from each cycle confirmed rVP2 binding. In the case of CPV, only heat-treated and PAA-treated CPV showed binding to the candidate sequences. However, reduced binding to the CPV-specific antibody was observed for rVP2 and treated CPV compared to intact CPV. No apparent binding of the tested sequences was observed for FPV and PPV. Aptamers binding to denatured but not intact CPV demonstrate the potential to distinguish between the two states, providing a basis for developing a molecular assay to assess disinfection efficacy. Full article

Nucleic acid aptamers are single-stranded DNA or RNA molecules that can bind to a target with high specificity and affinity, as screened by the Systematic Evolution of Ligands by Exponential Enrichment (SELEX). In recent years, SELEX technologies have been significantly advanced for the screening of aptamers for a variety of target molecules, cells, and even bacteria and viruses. By integrating recent advances of emerging technologies with SELEX, novel screening technologies for nucleic acid aptamers have emerged with improved screening efficiency, reduced production costs and enhanced aptamer performance for a wide range of applications in medical diagnostics, drug delivery, and environmental monitoring. Aptasensors utilize aptamers to detect a wide range of analytes, allowing for the accurate identification and determination of small molecules, proteins, and even whole cells with remarkable specificity and sensitivity. Further optimization of the aptasensor can be achieved by aptamer truncation, which not only maintains the high specificity and affinity of the aptamer binding with the target analytes, but also reduces the manufacturing cost. Predictive models also demonstrate the powerful capability of determination of the minimal functional sequences by simulation of aptamer–target interaction processes, thus effectively shortening the aptamer screening procedure and reducing the production costs. This paper summarizes the research progress of protein-targeted aptamer screening in recent years, introduces several typical aptasensors at present, discusses the optimization methods of aptasensors by combining efficient SELEX with advanced predictive algorithms or post-SELEX processes, as well as the challenges and opportunities faced by aptasensors. Full article

Access to safe water remains a vital public health challenge, especially in low- and middle-income countries like Colombia, where untreated sources lead to severe diarrheal diseases in children under five. Escherichia coli (E. coli), a key indicator of fecal contamination, is often detected using culture-based methods that are time-consuming and rely on specialized infrastructure. To overcome these limitations, we developed an aptamer-based isolation system targeting environmental E. coli. Aptamers were obtained using a Cell-SELEX protocol, and after six enrichment rounds, two candidates—APT-EC-1 and its truncated version APT-EC-MUT—were synthesized and attached to carboxyl-functionalized magnetic nanoparticles (MNP-COOH). Both complexes demonstrated a strong binding affinity and high specificity, successfully isolating E. coli from environmental and ATCC reference strains in the laboratory. Sensitivity tests detected E. coli at dilutions up to 1:10,000, showing reliable performance. In early in-field testing with environmental water samples, APT-EC-1 consistently identified E. coli colonies, while APT-EC-MUT struggled with low bacterial levels, illustrating performance differences. These findings demonstrate the promise of aptamer-functionalized MNPs as the basis for quick, affordable, and portable biosensors for water quality testing, especially in resource-scarce areas. Future efforts will add colorimetric or electrochemical readouts to allow real-time, on-site detection of fecal contamination. Full article

The prevalence of food allergies has been steadily increasing in recent years. β-lactoglobulin (β-LG), the main allergenic protein of milk and dairy allergies, is more commonly observed in infants and children. In this study, a β-LG-specific aptamer was selected using the combinatorial chemistry process known as systematic evolution of ligands by exponential enrichment (SELEX), and a quartz crystal microbalance with dissipation monitoring (QCM-D)-based aptasensor was developed using a novel surface functionalization technique, which mimics an artificial cell membrane on the QCM-D sensor surface, creating a physiologically relevant environment for the binding of the target to the sensor. Through SELEX combined with next-generation sequencing (NGS), the aptamer Apt 356 was identified. Its binding to β-LG was confirmed via dot blot analysis. The selected Apt 356 was then used for the development of a QCM-D-based sensor. To fabricate the sensor, the quartz surface was functionalized with a supported lipid bilayer (SLB). The β-LG-specific aptamer was immobilized onto this SLB. The results demonstrated that the QCM-D system allows real-time observation and evaluation of the binding of β-LG. While there have been some studies on aptasensors for the β-LG protein, to the best of our knowledge, this is the first QCM-D-based aptasensor developed specifically for β-LG protein detection. Full article

Pseudomonas aeruginosa is a clinically significant pathogen with high antibiotic resistance, necessitating rapid and reliable diagnostic methods. In this study, we developed a whole-cell aptamer selection method for P. aeruginosa using an Eppendorf-tube-based SELEX system, where bacterial cells were directly incubated with an ssDNA library. This configuration enhanced the recovery of bound aptamers and overcame the cell quantity limitations often encountered in microtiter-plate-based SELEX. After 10 selection rounds, six aptamer candidates were obtained and evaluated for affinity. Molecular docking analysis revealed that aptamer T1 possessed the highest target selectivity. To demonstrate diagnostic applicability, aptamer T1 was integrated into a hybrid lateral flow immunoassay (LFIA), replacing the conventional detection antibody. In this format, the AuNP–aptamer complex bound to the target bacteria and was captured by a specific antibody immobilized on the test line. The LFIA achieved a visual detection limit of 2.34 × 10² CFU/mL within 15 min, showing high specificity and suitability for point-of-care applications. This study presents the first demonstration of an aptamer–antibody hybrid LFIA for bacterial detection and highlights the potential of aptamers as low-cost, rapidly synthesized recognition elements adaptable for the detection of other infectious agents. Full article

Shaking off the forgetfulness towards the methodological power of inosine-mediated error-prone PCR (epPCR), this study reintroduces an often-underappreciated method as a considerably powerful approach for generating aptamer libraries from a single decameric ATCG-repeat-oligonucleotide. The aim was to demonstrate that this simple way of creating sequence diversity was suitable for delivering functional starting libraries for a set of ten whole-cell-SELEX (Systematic Evolution of Ligands by Exponential Enrichment) processes. This epPCR method uses inosine to introduce targeted mutations, avoiding the need for commercial oligo pools or large-scale synthesis. We applied this method to a “universal aptamer” and subjected the three resulting libraries to two rounds of selection against ten diverse targets including probiotic and pathogenic bacteria (Gram-negative and -positive) as well as human cell lines. The enriched aptamers exhibited new binding specificities, demonstrating that the approach supports functional selection. Much like dusting off an old tool and finding it perfectly suited for a modern task, this work shows that revisiting established techniques can address current challenges in aptamer development. Our main finding is that epPCR provides a robust, cost-effective strategy for generating starting libraries and lowers the barrier for initiating successful SELEX campaigns. Full article

Nucleic acid aptamers, selected through the Systematic Evolution of Ligands by Exponential Enrichment (SELEX), are short nucleic acid sequences that exhibit high affinity and specificity towards diverse targets. Over the past three decades, substantial advancements have been made in both the technology and applications of nucleic acid aptamers. This review provides an in-depth analysis of the historical development and defining characteristics of aptamers, highlighting recent technological innovations in SELEX, including Capillary Electrophoresis SELEX, Microfluidic SELEX, Cell-SELEX, and others. We explore the applications of aptamers in therapeutic and targeted drug delivery, emphasizing their advantages over traditional antibodies such as cost-effectiveness, ease of synthesis, and lower immunogenicity. Key challenges such as stability, specificity, and efficient delivery are discussed, with proposed strategies for improvement including advanced chemical modifications and integration with nanotechnology. By integrating advanced technologies, aptamers hold significant promise for enhancing precision medicine and personalized therapeutic interventions, offering new avenues for the treatment of complex diseases. Full article

Chronic and non-communicable diseases (NCDs) account for a large proportion of global disorders and mortality, posing significant burdens on healthcare systems. Early diagnosis and timely interference are critical for effective management and disease prevention. However, the traditional methods of diagnosis still suffer from high costs, time delays in processing, and infrastructure requirements that are usually unaffordable in resource-constrained settings. Aptamer-based biosensors have emerged as promising alternatives to offer enhanced specificity, stability, and cost-effectiveness for disease biomarker detection. The SELEX (Systematic Evolution of Ligands by Exponential Enrichment) methodology allows developing aptamers with high-affinity binding capabilities to a variety of targets, for instance proteins, cells, or even small molecules, hence rendering them suitable for NCD diagnosis. Aptasensors—recent developments in the electrochemical and optical dominion—offer much enhanced sensitivity, selectivity, and stability of detection across a diverse range of diseases from lung cancer and leukemia to diabetes and chronic respiratory disorders. This study provides a comprehensive review of progress in aptamer-based sensors, focusing on their role in point-of-care diagnostics and adaptability in a real-world environment with future directions in overcoming current limitations. Full article

Background/Objectives: Ricin’s high toxicity and potential as a bioweapon underscore the need for effective antidotes. Monoclonal antibodies, though effective, are limited by complex production. This study aimed to develop a graphene oxide-based aptamer nanoarray (ARMAN) for improved neutralization and protection against ricin. Methods: High-affinity aptamers targeting ricin’s RTA and RTB subunits were selected using SELEX technology and conjugated to graphene oxide (GO) via click chemistry. ARMAN’s characteristics, including morphology, stability, and biosecurity, were assessed. Its performance was evaluated in terms of affinity for ricin, neutralization capacity, and therapeutic effects in cellular assays and a mouse model of ricin poisoning. Results: ARMAN exhibited a uniform morphology with an average particle size of 217 nm and demonstrated significantly enhanced affinity for ricin compared to free aptamers. ARMAN showed rapid and effective neutralization ability, significantly increasing cell viability in BEAS-2B, GES-1, and HL7702 cell lines exposed to ricin. In vivo, ARMAN treatment led to a notable prolongation of survival in ricin-poisoned mice, highlighting its potential for both pre- and post-exposure treatment. These findings indicate that ARMAN not only neutralizes ricin effectively but also provides a therapeutic window for treatment. Conclusions: ARMAN’s superior binding affinity, serum stability, biocompatibility, and broad therapeutic efficacy make it a promising new antidote against ricin poisoning. This study’s findings represent significant progress in the development of rapid-response antidotes, with ARMAN offering a potential solution for both military and civilian emergency response scenarios. Full article

Tumor cell-induced platelet aggregation (TCIPA) is a mechanism for the protection of tumor cells in the bloodstream and the promotion of tumor progression and metastases. The platelet C-type lectin-like receptor 2 (CLEC-2) can bind podoplanin (PDPN) on a cancer cell surface to facilitate TCIPA. Selective blockage of PDPN-mediated platelet–tumor cell interaction is a plausible strategy for inhibiting metastases. In this study, we aimed to screen for aptamers, which are the single-stranded DNA oligonucleotides that form a specific three-dimensional structure, bind to specific molecular targets with high affinity and specificity, bind to PDPN, and interfere with PDPN/CLEC-2 interactions. The systematic evolution of ligands by exponential enrichment (SELEX) was employed to enrich aptamers that recognize PDPN. The initial characterization of ssDNA pools enriched by SELEX revealed a PDPN aptamer designated as A1 displaying parallel-type G-quadruplexes and long stem-and-loop structures and binding PDPN with a material with a dissociation constant (K_d) of 1.3 ± 1.2 nM. The A1 aptamer recognized both the native and denatured form of PDPN. Notably, the A1 aptamer was able to quantitatively detect PDPN proteins in Western blot analysis. The A1 aptamer could interfere with the interaction between PDPN and CLEC-2 and inhibit PDPN-induced platelet aggregation in a concentration-dependent manner. These findings indicated that the A1 aptamer is a candidate for the development of biosensors in detecting the levels of PDPN expression. The action by A1 aptamer could result in the prevention of tumor cell metastases, and if so, could become an effective pharmacological agent in treating cancer patients. Full article

Pearl millet is a major cereal crop that feeds more than 90 million people worldwide in arid and semi-arid regions. The stalk phenotypes of Poaceous grasses are critical for their productivity and stress tolerance; however, the molecular mechanisms governing stalk development in pearl millet remain to be deciphered. In this study, we spatiotemporally measured 19 transcriptomes for stalk internodes of four different early developmental stages. Data analysis of the transcriptomes defined four developmental zones on the stalks and identified 12 specific gene sets with specific expression patterns across the zones. Using weighted gene co-expression network analysis (WGCNA), we found that two co-expression modules together with candidate genes were involved in stalk elongation and the thickening of pearl millet. Among the elongation-related candidate genes, we established by SELEX that a MYB-family transcription factor PMF7G02448 can bind to the promoters of three cell wall synthases genes (CesAs). In summary, these findings provide insights into stalk development and offer potential targets for future genetic improvement in pearl millet. Full article

EGFRvIII is expressed only in tumor cells and strongly in glioblastoma and is considered a promising target in cancer diagnosis and therapy. Aptamers are synthetic single-stranded oligonucleotides that bind to biochemical target molecules with high binding affinity and specificity. This study examined the potential of the ⁶⁸Ga-NOTA-EGFRvIII aptamer as a nuclear imaging probe for visualizing EGFRvIII-expressing glioblastoma by positron emission tomography (PET). EGFRvIII aptamer was selected using the SELEX technology, and flow cytometry and fluorescence microscopy verified the high binding affinity to EGFRvIII positive U87MG vIII 4.12 glioma cells but not to EGFRvIII negative U87MG cells. The EGFRvIII aptamer was conjugated with a chelator (1,4,7-triazanonane-1,4,7-triyl)triacetic acid (NOTA) for ⁶⁸Ga-labeling. The ⁶⁸Ga-NOTA-EGFRvIII aptamer was prepared using the preconcentration-based labeling method with a high radiolabeling yield at room temperature. Ex vivo biodistribution analyses confirmed the significantly higher tumor uptake of the ⁶⁸Ga-NOTA-EGFRvIII aptamer in EGFRvIII-expressing xenograft tumors than that in EGFRvIII negative tumors, confirming the specific tumor uptake of the ⁶⁸Ga-NOTA-EGFRvIII aptamer in vivo. PET imaging studies revealed a high retention rate of the ⁶⁸Ga-NOTA-EGFRvIII aptamer in U87MG vIII 4.12 tumors but only low uptake levels in U87-MG tumors, suggesting that the ⁶⁸Ga-NOTA-EGFRvIII aptamer may be used as a PET imaging agent for EGFRvIII-expressing glioblastoma. Full article