Search Results (333)

Aptamers are single-stranded DNA or RNA oligonucleotides screened by systematic evolution of ligands by exponential enrichment (SELEX) methods, which are widely used in food analysis. Aptamers have the advantages of low molecular weight, ease of preparation, simplicity of chemical modification, and structural stability. Aptamers generated by SELEX are typically 80–100 bases in length, and the affinity of the aptamer can be improved by sequence optimization. Methods of aptamer optimization commonly include truncation, mutation, and chemical modification, and molecular docking, molecular dynamics, circular dichroism, and isothermal titration to assess often the binding performance of the aptamer to the target. Optimized aptamers usually enhance the affinity of the aptamer for the target and increase its sensitivity in the detection of pesticides, heavy metals, fungal toxins, pathogenic bacteria, and other objects. This paper focuses on truncation, mutation, chemical modification, the introduction of rare nucleotides, and computer-aided design. It provides an overview of non-immobilized optimization metrics. Full article

The HIV-1 aspartic protease is an effective target for the treatment of HIV/AIDS. Current therapy utilizes a selection of nine protease inhibitors (PIs) in combination with other classes of antiretroviral drugs. Although PIs were originally developed based on the knowledge of the HIV-1 subtype B protease, the existence of other HIV-1 subtypes and the effects of drug resistance on currently available PIs have become a major challenge in the treatment of HIV/AIDS. Specifically, the HIV-1 subtype C accounts for more than half of the global HIV infections. Considering the importance and relevance of the subtype C virus, in this timely review we discuss the effect of polymorphisms in the HIV-1 subtype C protease on drug resistance, flap flexibility, and hinge region dynamics. We discuss novel paradigms of protease inhibition that attempt to overcome the limitations of currently available inhibitors which fall short considering genetic diversity and resistance mutations. Full article

Background/Objectives: After many years of research and the successful development of therapeutic products by a few industrial actors, the COVID-19 vaccines brought messenger RNAs, as well as other nucleic acid modalities, such as antisense oligonucleotides, small interfering RNA, and aptamers, into the spotlight, eliciting renewed interest from both academia and industry. However, owing to their structure, relative “fragility”, and the (usually) intracellular site of action, the delivery of these therapeutics has frequently proven to be a key limitation, especially when considering endosomal escape, which still needs to be overcome. Methods: By compiling delivery-related data on approved and late clinical-phase ribonucleic acid therapeutics, this review aims to assess the delivery strategies that have proven to be successful or are emerging, as well as areas where more research is needed. Results: In very specific cases, some strategies appeared to be quite effective, such as the N-acetylgalactosamine moiety in the case of liver delivery. Surprisingly, it also appears that for some modalities, efforts in molecular design have led to more “drug-like” properties, enablingthe administration of naked nucleic acids, without any form of encapsulation. This appears to be especially true when local administration, i.e., by injection, is possible, as this provides de facto targeting and a high local concentration, which can compensate for the small proportion of nucleic acids that reach the cytoplasm. Conclusions: Nucleic acid-based therapeutics have come a long way in terms of their physicochemical properties. However, due to their inherent limitations, targeting appears to be crucial for their efficacy, even more so than for traditional pharmaceutical modalities. Full article

Sepsis remains a global health emergency, demanding timely and accurate diagnostics to reduce morbidity and mortality. This review critically assesses the recent progress (2020–2025) in the development of electrochemical aptamer-based biosensors for sepsis detection. These biosensors combine aptamers’ high specificity and modifiability with the sensitivity and miniaturization potential of electrochemical platforms. The analysis highlights notable advances in detecting key sepsis biomarkers, such as C-reactive protein (CRP), procalcitonin (PCT), interleukins (e.g., interleukin-6 (IL-6), tumor necrosis factor-alpha (TNF-α)), lipopolysaccharides (LPSs), and microRNAs using diverse sensor configurations, including a field-effect transistor (FET), impedance spectroscopy, voltammetry, and hybrid nanomaterial-based systems. A comparative evaluation reveals promising analytical performance in terms of the limit of detection (LOD), rapid response time, and point-of-care (POC) potential. However, critical limitations remain, including variability in validation protocols, limited testing in real clinical matrices, and challenges in achieving multiplexed detection. This review underscores translational barriers and recommends future directions focused on clinical validation, integration with portable diagnostics, and interdisciplinary collaboration. By consolidating current developments and gaps, this work provides a foundation for guiding next-generation biosensor innovations aimed at effective sepsis diagnosis and monitoring. Full article

Despite various methods for detecting and treating SARS-CoV-2, affordable and easily applicable solutions are still needed. Aptamers can potentially fill this gap. Here, we establish a workflow to identify aptamers that bind to the spike proteins of SARS-CoV-2, a process applicable to other targets as well. The spike protein is crucial for the virus’s entry into host cells. The aptamer development process for the spike protein’s receptor binding domain (RBD) begins with splitting the SARS-CoV-2’s genome into 40 nucleotide-long sequences, predicting their two-dimensional structure, and sorting based on the free energy. Selected oligomers undergo three-dimensional structure prediction and docking onto the viral spike protein’s RBD. Six RNA oligomers were identified as top candidates based on the RNA docking with the SARS-CoV-2 wild-type (WT) (Wuhan-Hu-1 strain) and Omicron variant BA.1 RBD and molecular dynamics simulations. Three oligomers also demonstrated strong predicted binding affinity with other SARS-CoV-2 variants, including BA.2, XBB.1.5, and EG.5, based on the protein–aptamer docking followed by stability evaluation using the MD simulations. The aptamer with the best fit for the spike protein RBD was later validated using biolayer interferometry. The process has resulted in identifying a single aptamer from a library of 29,000 RNA oligomers, which exhibited affinity in the submicromolar range and the potential to develop into a viral screen or therapeutic. Full article

Aptamers are synthetic nucleic acids or peptides that exhibit high specificity and affinity for target molecules such as small molecules, proteins, or cells. Due to their ability to bind precisely to these targets, aptamers have found widespread use in bioanalytical and diagnostic applications. Rolling circle amplification (RCA) is an amplification technique that utilizes DNA or RNA templates, where circular primers are extended by polymerases to generate multiple repeated sequences, enabling highly sensitive detection of target molecules. The integration of aptamers with RCA offers significant advantages, enhancing both the specificity and sensitivity of detection while ensuring a fast and straightforward process. This synergy has already been widely applied across various fields, including fluorescence, microfluidics, visualization, and electrochemical technologies. Examples include molecular probe development, rapid detection of disease biomarkers, and environmental monitoring. Looking ahead, the aptamer-RCA platform holds great promise for advancing early disease diagnosis, precision medicine, and the development of nanosensors, driving innovation and new applications in these fields. Full article

Oligonucleotides (ODNs) such as siRNA, saRNA, and miRNA regulate gene expression through a variety of molecular mechanisms and show unique potential in the treatment of genetic diseases and rare diseases, but their clinical application is still limited by the efficiency of the delivery system, especially the problem of the insufficient targeting of extrahepatic tissues. As homologous nucleic acid molecules, aptamers have become a key tool to improve the targeted delivery of ODNs. Aptamer–ODN chimeras can not only bind to multiple proteins on the cell surface with high specificity and selectivity, but they can also internalize into cells. Furthermore, they outperform traditional delivery systems in terms of cost-effectiveness and chemical modification flexibility. This review systematically summarizes the origin and progress of aptamer–ODN chimera therapy, discusses some innovative design strategies, and proposes views on the future direction of aptamer-ODN chimeras. Full article

The 17-3 RNA aptamer recognizes DMHBI and induces its fluorescence. We showed that the 17-3 RNA aptamer predominantly induced emission of the phenolate form of DMHBI. We also demonstrated that the active structure of the minimal form of the 17-3 aptamer possessed three stem elements and two large loop elements, which we named Karashi and its sequence-optimized variant, Jigarashi, respectively. Chemical modification experiments suggested that the two loop regions formed tertiary interactions and/or non-Watson–Crick base pairs, and no remarkable structural alterations occurred upon DMHBI binding. AlphaFold3 also predicted a tertiary structure of the ligand-free form of Jigarashi RNA, which was consistent with the results of chemical modification experiments. Full article

In addition to classic small-molecule drugs and modern protein-based biologics, an intriguing class of medicines is the therapeutic oligonucleotides. Most approved drugs in this category are antisense oligomers or those acting via RNA interference, both of which use base hybridization. Aptamers, also known as chemical antibodies form a smaller, yet equally interesting group of oligonucleotides that can recognize a wide range of molecular targets. Despite their high potential, only two aptamers have been approved to date, pegaptanib (MacugenTM) and avacincaptad pegol (IzervayTM), both for the treatment of age-related macular degeneration (AMD). Targeting vascular endothelial growth factor (VEGF), which plays an important role in the pathogenesis of many eye diseases, pegaptanib emerged as the first anti-VEGF agent and was used in various indications, further inspiring the development of other anti-VEGF therapies. In this review, we summarize the history of the first approved aptamer medicine, pegaptanib. We describe its chemistry and track its development from the earliest stages to the preclinical phase, clinical trials, and eventual regulatory approval. Additionally, we evaluate its position among other therapeutic agents and provide a comprehensive overview of pegaptanib’s efficacy, safety, and cost-effectiveness, comparing these aspects with those of monoclonal antibodies with similar indications, bevacizumab and ranibizumab. Full article

Nano-luciferase binary technology (NanoBiT)-based pseudoviral sensors are innovative tools for monitoring viral infection dynamics. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects host cells via its trimeric surface spike protein, which binds to the human angiotensin-converting enzyme II (hACE2) receptor. This interaction is crucial for viral entry and serves as a key target for therapeutic interventions against coronavirus disease 2019 (COVID-19). Aptamers, short single-stranded DNA (ssDNA) or RNA molecules, are highly specific, high-affinity biorecognition elements for detecting infective pathogens. Despite their potential, optimizing viral infection assays using traditional protein–protein interaction (PPI) methods often face challenges in optimizing viral infection assays. In this study, we selected and evaluated aptamers for their ability to interact with viral proteins, enabling the dynamic visualization of infection progression. The NanoBiT-based pseudoviral sensor demonstrated a rapid increase in luminescence within 3 h, offering a real-time measure of viral infection. A comparison of detection technologies, including green fluorescent protein (GFP), luciferase, and NanoBiT technologies for detecting PPI between the pseudoviral spike protein and hACE2, highlighted NanoBiT’s superior sensitivity and performance, particularly in aptamer selection. This bioluminescent system provides a robust, sensitive, and early-stage quantitative approach to studying viral infection dynamics. Full article

Efficient bacterial lysis and RNA purification are essential for molecular diagnostics and biosensing applications. This study presents a piezoelectric platform integrated with gold-plated RNA capture pins (RCPs) functionalized with synthetic oligonucleotides to extract and enrich E. coli 16S ribosomal RNA (rRNA). The 3D-printed device enables selective bacterial capture using E. coli-specific aptamers and incorporates a piezoelectric transducer operating at 60 kHz to facilitate bacterial cell wall disruption. The platform demonstrated high specificity for E. coli over B. cereus, confirming aptamer selectivity. E. coli viability assessment demonstrated that positioning the piezoelectric plate in contact with the bacterial suspension significantly improved the bacterial lysis, reducing viability to 33.68% after 15 min. RNA quantification confirmed an increase in total RNA released by lysed E. coli, resulting in 10,913 ng after 15 min, compared to 4310 ng obtained via conventional sonication. RCP-extracted RNA has a threefold enrichment of 16S rRNA relative to 23S rRNA. RT-qPCR analysis indicated that the RCPs recovered, on average, 2.3 ng of 16S RNA per RCP from bacterial suspensions and 0.1 ng from aptamer-functionalized surfaces. This integrated system offers a rapid, selective, and label-free approach for bacterial lysis, RNA extraction, and enrichment for specific types of RNA with potential applications in clinical diagnostics and microbial biosensing. Full article

Metabolic dysfunction-associated steatotic liver disease (MASLD) affects one-third of adults globally. Despite efforts to develop non-invasive diagnostic tools, liver biopsy remains the gold standard for diagnosing metabolic dysfunction-associated steatohepatitis (MASH) and assessing fibrosis. This study investigated RNA aptamer panels, selected using APTASHAPE technology, for non-invasive MASLD diagnosis and fibrosis stratification. Aptamer panels were selected in a cohort of individuals with MASLD (development cohort, n = 77) and tested in separate cohorts: one with MASLD (test cohort, n = 57) and one assessed for bariatric surgery (bariatric cohort, n = 62). A panel distinguishing MASLD without steatohepatitis from MASH accurately stratified individuals in the developmentcohort (AUC = 0.83) but failed in the test and bariatric cohorts. It did, however, distinguish healthy controls from individuals with MASLD, achieving an AUC of 0.72 in the test cohort. A panel for fibrosis stratification differentiated F0 from F3–4 fibrosis in the development cohort (AUC = 0.68) but not in other cohorts. Mass spectrometry identified five plasma proteins as potential targets of the discriminative aptamers, with complement factor H suggested as a novel MASLD biomarker. In conclusion, APTASHAPE shows promise as a non-invasive tool for diagnosing and staging MASLD and identifying associated plasma biomarkers. Full article

Enzymes play an essential role in many different industries; however, their operating conditions are limited due to the loss of enzyme activity in the presence of proteases and at temperatures significantly above physiological conditions. One way to improve the stability of these enzymes against high temperatures and proteases is to encapsulate them in protective shells or virus-like particles. This work presents a streamlined, three-step, cell-free protein synthesis (CFPS) procedure that enables rapid in vitro enzyme production, targeted encapsulation in protective virus-like particles (VLPs), and facile purification using a 6× His-tag fused to the VLP coat protein. This process is performed in under 12 h and overcomes several limitations of enzyme encapsulation, such as the control of packing density, speed, and complexity of the process. Here, we encapsulate the enzyme Candida antarctica lipase B in the VLP from the bacteriophage Qβ, while in the presence of a linking RNA aptamer. The encapsulated enzymes largely retained their activity in comparison to the free enzymes. Additionally, when subjected to 90 °C temperatures or 5 h incubation with proteases, the encapsulated enzymes maintained their activity, whereas the free enzymes lost their activity. In this work, we also demonstrate control over packing density by achieving packing densities of 4.7 and 6.5 enzymes per VLP based off the concentration of enzyme added to the encapsulation step. Full article

This study developed an artificial chimeric intron module with an RNA riboswitch and TetR aptamer that were integrated into essential gene exons. Doxycycline can modulate Pre-mRNA alternative splicing, modify the exon reading frame, and dynamically regulate gene expression. By shifting the aptamer 2 base pair within the switch, we unexpectedly obtained the “on-switch” CTM and “off-switch” C2ITetR>4A, which possess thoroughly contrasting regulatory functions. The CTM module can conditionally induce tumor cell apoptosis and regulate genes reversibly and sustainably following doxycycline induction. We integrated the C2ITetR>4A/CTM switches with the L7Ae/k-turn module to create an intron-spliced double-switched RNA cascade system. The system can both activate and inhibit the splicing mechanism utilizing the same ligand to minimize crosstalk among aptamer switching elements, control target gene leakage, and enhance the dynamic range of gene expression. We analyzed numerous factors affecting Pre-mRNA splicing to identify the optimal equilibrium point for switch regulation. This will enable precise predictions of dynamic regulatory efficiency and the rational design of genetic modules, thereby providing a valuable instrument for mammalian synthetic biology. Full article

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. Full article