MethodsPub Date : 2025-11-01Epub Date: 2025-08-22DOI: 10.1016/j.ymeth.2025.08.006
Chaweewan Suwanvecho , Lenka Kujovská Krčmová , František Švec
{"title":"Volumetric dried blood spot microsampling: A sustainable, patient-friendly, and practical approach for retinol and α-tocopherol analysis in a clinical setting","authors":"Chaweewan Suwanvecho , Lenka Kujovská Krčmová , František Švec","doi":"10.1016/j.ymeth.2025.08.006","DOIUrl":"10.1016/j.ymeth.2025.08.006","url":null,"abstract":"<div><div>Dried blood spot (DBS) technique has gained significant attention due to the growth of decentralized diagnostics. This technique reduces the number of hospital visits for patients and the workload for personnel in specialized hospitals. This microsampling method provides an environmentally friendly (green) and patient-friendly alternative to conventional phlebotomy. Challenges related to sample heterogeneity in traditional DBS cards have been overcome by the volumetric DBS sampling using new types of commercially available devices. Due to the unstable nature of the analytes, commercial volumetric DBS devices allow blood sampling at primary care units in remote settings and facilitate transport it via temperature-controlled systems. Blood sample stability has improved from 24 h at 4–8 °C to 30 days at −80°C. DBS also requires over 1000 times less shipping and storage space than liquid blood. We optimized the DBS method to require only 10 µL of blood and achieve extraction efficiencies of over 90 % for retinol when the result from validated method is the reference value. However, α-tocopherol recovery varied from 53 to 75 % depending on the filter paper type used. Furthermore, we successfully developed a liquid–liquid extraction method for both analytes from whole blood, with over 90 % recovery. Our approaches eliminate the need for separate serum and erythrocyte extractions, simplify sample preparation, and reduce reagent use and energy consumption. Both devices enable reliable volumetric collection. Our approach makes micronutrient monitoring more accessible and enables sample collection in decentralized settings. This aligns with the objectives of green analytical chemistry and universal health coverage.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"243 ","pages":"Pages 40-48"},"PeriodicalIF":4.3,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144895038","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Identification of immunoregulatory peptides from gut microbiota modulating Epstein-Barr virus-induced gene 3 (EBI3) using a novel specific AlphaLISA™ assay","authors":"Sothea Touch , Maria Lucia Orsini Delgado , Parfait Evouna-Mengue , Lydie Surand , Souphalone Luangsay , Naeemunnisa Mohamed Anesary , Francesco Strozzi , Laurent Chêne , Antonietta Cultrone","doi":"10.1016/j.ymeth.2025.08.002","DOIUrl":"10.1016/j.ymeth.2025.08.002","url":null,"abstract":"<div><div>Gut microbiota-derived compounds are pivotal in modulating host immunity by regulating the functions of various key innate and adaptive immune cells. Epstein-Barr virus-induced gene 3 (EBI3) serves as the beta subunit shared by the heterodimeric cytokines interleukin (IL)-27 and IL-35. Both these cytokines have been documented to inhibit the development of T helper 2 (Th2) and T helper 17 (Th17) cells, while enhancing the function of regulatory T cells (Tregs). EBI3, itself, has also been shown to regulate cell-mediated immune responses. Despite their critical roles in maintaining immune homeostasis, there is a significant lack of robust, high-throughput-compatible assays to evaluate the secretion of IL-27, IL-35, or EBI3.</div><div>In this study, we detail the development of a novel amplified luminescent proximity homogeneous assay (AlphaLISA™) to quantify EBI3 secretion by tolerogenic dendritic cells. We utilized this assay to screen a library of 9739 small proteins derived from the human gut microbiota to identify compounds that could stimulate EBI3 secretion.</div><div>Our findings revealed the immunoregulatory potential of VAC18, an unknown protein from <em>Fusicatenibacter saccharivorans</em> (Clostridium<!--> <!-->cluster XIVa) which significantly induces the secretion of both EBI3 and IL-27. This is the first study to demonstrate the effect of gut microbiota derived peptides on the balanced secretion of EBI3 and IL-27.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"242 ","pages":"Pages 148-158"},"PeriodicalIF":4.3,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144779431","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A photoactivatable chemical lipidomics approach for local sphingolipid metabolic analysis","authors":"Xiaoxue Wang , Zhiyi Zhang , Shuwei Tian , Suihan Feng","doi":"10.1016/j.ymeth.2025.07.002","DOIUrl":"10.1016/j.ymeth.2025.07.002","url":null,"abstract":"<div><div>In eukaryotic cells, lipid metabolism is tightly regulated depending on the subcellular localization, which is essential for maintaining lipid homeostasis. However, understanding compartmentalized lipid metabolism remains challenging due to limited availability of suitable techniques. In this study, we present a chemical lipidomics approach that combines photoactivatable probes with high resolution mass spectrometry and stable-isotope labelling to analyze lipid dynamics at subcellular resolution. We applied this method to analyze the metabolism of 1-deoxysphingolipid (DoxSL), a non-canonical lipid species linked to various metabolic diseases and neuropathy, whose metabolism remains largely unexplored. Using the photoactivatable probes, we selectively delivered 1-deoxysphinganine, a key DoxSL intermediate, to mitochondria upon photo-illumination and subsequently analyzed its local metabolic products over time. Our data show that most 1-deoxysphinganine delivered to mitochondria is rapidly converted into 1-deoxyceramides, while only a small fraction forms oxidized products. Further lipidomic analysis revealed that 1-deoxyceramides are transported to the extracellular space and that DoxSL is also present in mouse and human serum samples. In summary, we developed novel probes to track lipid dynamics with high spatiotemporal resolution in a non-invasive manner and provided new insights into sphingolipid metabolism.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"242 ","pages":"Pages 62-71"},"PeriodicalIF":4.2,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144581287","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
MethodsPub Date : 2025-10-01Epub Date: 2025-07-15DOI: 10.1016/j.ymeth.2025.07.005
Wensi Li , Zhichao Tang , Xiang Zhu , Beijuan Wang , Xiuqin Zhang , Ze Ji , Suhang Cheng
{"title":"Ultrasensitive detection of MMP-2 via T7 RNA polymerase and CRISPR/Cas13a-Enhanced electrochemiluminescence biosensor for COPD diagnosis","authors":"Wensi Li , Zhichao Tang , Xiang Zhu , Beijuan Wang , Xiuqin Zhang , Ze Ji , Suhang Cheng","doi":"10.1016/j.ymeth.2025.07.005","DOIUrl":"10.1016/j.ymeth.2025.07.005","url":null,"abstract":"<div><div>In this work, an electrochemiluminescence (ECL) biosensor integrating T7 RNA polymerase amplification and CRISPR/Cas13a-mediated signal enhancement was developed for the ultrasensitive detection of matrix metalloproteinase-2 (MMP-2), a key biomarker associated with chronic inflammatory diseases such as COPD. A peptide nucleic acid (PNA) probe was designed to respond specifically to MMP-2 cleavage, enabling the release of DNA templates for subsequent T7 RNA polymerase-driven transcription amplification. The generated RNA triggers the collateral cleavage activity of CRISPR/Cas13a, resulting in a significant amplification of the ECL signal. The biosensor’s surface was constructed using a AuNPs/Ti<sub>3</sub>C<sub>2</sub>Tx/Ru(II)-PEI nanocomposite, which enhanced signal transduction and stability. Under optimized conditions, the proposed biosensor achieved a detection limit as low as 62.05 fM, demonstrating superior sensitivity compared to conventional methods, as summarized in <span><span>Table 1</span></span>. The platform also exhibited excellent specificity and anti-interference capability, ensuring reliable detection of MMP-2 in complex biological samples. This study provides a simple yet highly efficient strategy for enzymatic biomarker detection, offering great potential for clinical applications in early disease diagnosis and monitoring.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"242 ","pages":"Pages 80-88"},"PeriodicalIF":4.2,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144658091","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Bio-impedance spectroscopy-based classification of mental acuity in university students via machine-learning and deep-learning approaches","authors":"Kusum Tara , Sadman Sakib , Md Hasibul Islam , Shadhon Chandra Mohonta , Md.Shamim Anower , Takenao Sugi","doi":"10.1016/j.ymeth.2025.07.009","DOIUrl":"10.1016/j.ymeth.2025.07.009","url":null,"abstract":"<div><div>Mental acuity detection is crucial for identifying cognitive impairments linked to body composition imbalances and ensuring overall mental and physical fitness. This study introduces a deep-learning neural network (NN) model with MobileNetV2 deep learning architecture to classify mental acuity levels of university students—excellent, good, and average—using bioelectrical impedance spectroscopy (BIS)-based body composition and bio-impedance measurements. Body composition and bio-impedance features such as basal metabolic rate (BMR), body cell mass (BCM), total body water (TBW), bioelectrical impedance (BI), and phase angle (PA) were utilized as inputs for a feature-based random forest (RF) machine-learning model, achieving an accuracy of 88.26% and an F1-score of 84.89%. However, an image-based NN model with MobileNetV2 deep learning architecture, leveraging 2D impedance spectrum images, outperformed RF model, achieving exceptional accuracy of 98.39% and an F1-score of 97.83%. Additionally, the Nyquist diagram showed that excellent mental acuity had the smallest semicircle, average mental acuity had the largest, and good mental acuity level was intermediate. Similarly, feature analysis revealed that excellent mental acuity level corresponded to high BMR, BCM, TBW, and PA with low BI, while average mental acuity level had the opposite trend, while good mental acuity levels fell in between. The reliability and performance of the NN model in detecting mental acuity using 2D impedance spectrum analysis highlights its potential for this task. These results emphasize the value of deep-learning approaches in integrating BIS data for accurate mental acuity assessment and their broader implications for monitoring cognitive health.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"242 ","pages":"Pages 89-96"},"PeriodicalIF":4.2,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144711965","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
MethodsPub Date : 2025-10-01Epub Date: 2025-08-05DOI: 10.1016/j.ymeth.2025.07.011
Weiguang Gao , Qi Wang , Weili Gong , Lan Zheng , Qingai Liu , Lihe Zhang , Yaohong Ma
{"title":"Recent advances in biosensors: structure, principles, classification, and application in bio-manufacturing","authors":"Weiguang Gao , Qi Wang , Weili Gong , Lan Zheng , Qingai Liu , Lihe Zhang , Yaohong Ma","doi":"10.1016/j.ymeth.2025.07.011","DOIUrl":"10.1016/j.ymeth.2025.07.011","url":null,"abstract":"<div><div>Bio-manufacturing, as a frontier field of the new round of global scientific and technological revolution and industrial change, is becoming a core driving force for the future development of the bioeconomy. However, the bio-manufacturing process itself contains complex metabolic mechanisms and fine process control, which undoubtedly increases its technical difficulty. Especially at a time when the field of intelligent bio-manufacturing is developing rapidly, more stringent requirements have been placed on the ability to sense key biochemical information during the bio-manufacturing process. Biosensors based on biomolecular recognition provide powerful technical support for real time monitoring and precise control of key biochemical information that can rapidly sense the production process, and their applications have made remarkable progress. This article reviews the structure, classification, and working principle of biosensors and discusses their applications in bio-manufacturing, such as real-time monitoring of key biochemical parameters, intracellular and extracellular metabolite concentrations, and high-throughput screening for precise control and optimization of bioprocesses. The article also analyses the challenges facing biosensors, including the need for stability and reliability enhancements, and future directions. Researchers are developing new biometric components and sensor materials with advanced signal conversion techniques, while microelectronics and nanotechnology are driving the miniaturization and integration of sensors. These advances are expected to make biosensors more useful in microbial fermentation and biotechnology.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"242 ","pages":"Pages 123-142"},"PeriodicalIF":4.3,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144768180","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
MethodsPub Date : 2025-10-01Epub Date: 2025-06-16DOI: 10.1016/j.ymeth.2025.06.005
Bakr Ahmed Taha , Ghassan M. Sulaiman , Ali J. Addie , Khalil A.A. Khalil , Elsadig M. Ahmed , Vishal Chaudhary , Norhana Arsad
{"title":"Multifunctional nanophotonic photoacoustic biosensors: a new era in molecular imaging–guided deep-tissue cancer monitoring","authors":"Bakr Ahmed Taha , Ghassan M. Sulaiman , Ali J. Addie , Khalil A.A. Khalil , Elsadig M. Ahmed , Vishal Chaudhary , Norhana Arsad","doi":"10.1016/j.ymeth.2025.06.005","DOIUrl":"10.1016/j.ymeth.2025.06.005","url":null,"abstract":"<div><div>Monitoring cancer therapy is difficult because of restricted imaging depth, inadequate molecular specificity, and delayed response evaluation. Moreover, conventional imaging techniques fail to provide high-resolution, real-time views of the dynamic tumor microenvironment during therapy. Among emerging technologies, nanophotonic photoacoustic biosensors have gained prominence as multifunctional platforms that enable real-time, non-invasive imaging and dynamic monitoring of cancer therapy. This review discusses advances in nanophotonic engineering, including plasmonic nanostructures, NIR-II fluorophore-integrated systems, SERS-active materials, fiber-optic probes, and hybrid nanosystems, all tailored to enhance molecular targeting and signal specificity. In addition, biomimetic and biologically inspired nanosystems with enhanced tissue penetration and reduced autofluorescence in the NIR-II spectrum can be specifically highlighted. The key aspects of clinical translation are examined including biosafety, molecular specificity, and scalability. Furthermore, further explore the convergence of these biosensors with artificial intelligence and Internet of Things (IoT) frameworks to support adaptive, patient-specific decision-making in oncology. As a result of these multifunctional systems that combine nanophotonics, machine learning, and molecular diagnostics, oncology could shift towards precision-guided treatment. Finally, it proposes strategic avenues for clinical adoption, placing PAS at the vanguard of the next generation of cancer diagnostics.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"242 ","pages":"Pages 1-23"},"PeriodicalIF":4.2,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144293159","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
MethodsPub Date : 2025-10-01Epub Date: 2025-08-06DOI: 10.1016/j.ymeth.2025.08.001
Yifei Zhang, Junfang Li, Yu Zhang, Yi Qu
{"title":"A newly developed ferroptosis-related gene signature for forecasting prognosis in uveal melanoma.","authors":"Yifei Zhang, Junfang Li, Yu Zhang, Yi Qu","doi":"10.1016/j.ymeth.2025.08.001","DOIUrl":"10.1016/j.ymeth.2025.08.001","url":null,"abstract":"<p><strong>Background: </strong>Uveal melanoma is the most common primary intraocular malignancy in adults, characterized by significant inter-patient heterogeneity and poor long-term prognosis. Ferroptosis, an iron-dependent form of regulated cell death, has emerged as a promising avenue for cancer therapy, yet its role in UVM remains insufficiently explored.</p><p><strong>Methods: </strong>We systematically screened ferroptosis-related genes (FRGs) associated with UVM prognosis by integrating univariate Cox regression, LASSO regression, and Random Forest algorithms. A prognostic signature was constructed and validated using data from The Cancer Genome Atlas and Gene Expression Omnibus cohorts. We further evaluated the model's association with clinicopathological features, tumor immune microenvironment, and drug sensitivity. In vitro experiments were conducted to validate the functional role of SIRT3, the most pivotal gene in the signature.</p><p><strong>Results: </strong>A robust FRG-based prognostic model comprising SIRT3, RRM2, and PANX2 was developed and successfully stratified patients into high- and low-risk groups with significantly different survival outcomes. Multivariate Cox regression confirmed the risk score as an independent prognostic factor. High-risk patients exhibited immunosuppressive microenvironmental features, including elevated regulatory T cells and macrophage infiltration, as well as lower predicted response to immune checkpoint blockade. Drug sensitivity analysis identified ten compounds with lower predicted IC50 values in the high-risk group, suggesting potential therapeutic relevance. Functional assays demonstrated that SIRT3 knockdown promoted UVM cell proliferation and migration, while attenuating susceptibility to ferroptosis, highlighting its tumor-suppressive role.</p><p><strong>Conclusion: </strong>This study presents a novel FRG signature with strong prognostic and immunological implications in UVM. The model offers a promising tool for risk stratification and may assist in guiding ferroptosis- and immunotherapy-based precision treatment. Our findings also suggest that SIRT3 acts as a ferroptosis sensitizer in UVM, representing a potential therapeutic target warranting further investigation.</p>","PeriodicalId":390,"journal":{"name":"Methods","volume":" ","pages":"187-199"},"PeriodicalIF":4.3,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144787991","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
MethodsPub Date : 2025-10-01Epub Date: 2025-07-07DOI: 10.1016/j.ymeth.2025.07.003
Stephen A. Bustin , Carl T. Wittwer
{"title":"Fragile methods, fractured trust: rethinking scientific responsibility","authors":"Stephen A. Bustin , Carl T. Wittwer","doi":"10.1016/j.ymeth.2025.07.003","DOIUrl":"10.1016/j.ymeth.2025.07.003","url":null,"abstract":"<div><div>Science has a credibility problem, and it is not just the fault of politicians, journalists, or conspiracy theorists. It begins within science itself. This review examines how flawed methods and selective reporting, combined with overly polished communications that prioritise image over clarity, have normalised bad practice in molecular biology, diagnostics, and related applied sciences. The quantitative real-time polymerase chain reaction (qPCR) offers a clear example: a conceptually simple, technically mature technology that is nonetheless routinely misused, despite published standards and repeated calls for methodological rigour over the past two decades. If qPCR is so often misapplied, what does that suggest about confidence in more complex, less transparent technologies? An additional problem lies in the way scientific findings are misreported or exaggerated. Such distortions have far-reaching consequences beyond individual studies. From the MMR-autism scare to COVID-19 testing and vaccine hesitancy, they have fuelled confusion, eroded public trust, and endangered public health. Consequently, when flawed or overstated findings shape public policy or clinical decisions, the damage undermines science’s role as a reliable source of knowledge and informed choice. Credibility must rest on transparent practice, ethical responsibility, and attention to both how results are produced and how they are communicated. Until scientists recognise that communication is not value-neutral, and that our public voice carries consequences far beyond the lab, public scepticism will be justified.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"242 ","pages":"Pages 54-61"},"PeriodicalIF":4.2,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144581286","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
MethodsPub Date : 2025-10-01Epub Date: 2025-07-16DOI: 10.1016/j.ymeth.2025.07.006
Omar Eladl
{"title":"Circularization enhances RNA aptamer binding and Stability: Evidence from in-cell NMR","authors":"Omar Eladl","doi":"10.1016/j.ymeth.2025.07.006","DOIUrl":"10.1016/j.ymeth.2025.07.006","url":null,"abstract":"<div><div>RNA aptamers are emerging as promising molecular probes due to their high specificity and low immunogenicity. However, their clinical potential is often limited by instability under physiological conditions, primarily due to exonucleolytic degradation and structural flexibility. To address these challenges in a model system, we designed a circular RNA aptamer targeting the HIV-1 Tat protein.</div><div>Enzymatic circularization of the aptamer was performed using T4 RNA ligase, and circularization was confirmed by mobility shift assays and RNase R digestion. Binding affinity was assessed via filter dot blot assay, while structural stability was evaluated using 1D imino proton NMR and CLEANEX-PM experiments. Intracellular stability was monitored using in-cell NMR following transfection into HeLa cells.</div><div>In our study, the circular aptamer showed approximately tenfold higher binding affinity compared to its linear counterpart, as determined by filter binding assay. NMR analysis indicated improved structural rigidity, preservation of native base pairing, and reduced solvent exchange. Notably, in-cell NMR revealed that the circular aptamer remained detectable up to 18 h post-transfection, whereas the linear aptamer degraded within a few hours.</div><div>In this system, circularization substantially improved the binding performance and intracellular persistence of the RNA aptamer. These findings demonstrate the feasibility of applying RNA circularization to enhance aptamer functionality in living cells and lay the groundwork for future therapeutic exploration.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"242 ","pages":"Pages 72-79"},"PeriodicalIF":4.2,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144655189","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}