The cellular positioning of lysosomes, especially their perinuclear accumulation, plays an essential role in regulating many biological processes. In this work, we developed a non-genetic approach to drive lysosomes to the perinuclear region by displaying a nucleus-targeting DNA nanodevice on their outer surface. Our experimental results demonstrated that this nanodevice efficiently anchored onto the outer leaflet of lysosomal membrane, and then effectively promoted perinuclear clustering of lysosomes. Further analysis revealed that this repositioning significantly enhanced autophagic flux and altered the expression of autophagy-associated genes. Our study provides a versatile platform for elucidating the functional consequences of lysosomal positioning and its regulatory mechanisms in cellular physiology.

Nucleic acid therapeutics are rapidly emerging as a transformative drug paradigm, offering precise and programmable regulation of gene expression across a broad spectrum of diseases. This review summarizes recent advances in key platforms—including antisense oligonucleotides, siRNA, miRNA, mRNA, and aptamers—emphasizing their unique mechanisms of action and therapeutic potential. We systematically outline critical contributions of chemical modification and delivery engineering, including backbone and sugar modifications, site-specific design, N-acetylgalactosamine (GalNAc) conjugation, and lipid nanoparticles, which collectively enhance stability, target specificity, and clinical applicability. Finally, we discuss persistent challenges such as immune activation, large-scale manufacturing, and long-term safety, and provide perspectives on future directions involving CRISPR-based gene editing, synthetic biology, nanotechnology, smart delivery systems, and combination therapies, aiming to offer strategic insights for the development and clinical translation of nucleic acid drugs.

DNA aptamers that bind small molecules with high affinity have revolutionized the fields of biosensing and bioimaging. Recently, a DNA aptamer named 1301b has been identified as the most potent DNA aptamer for the binding of adenosine triphosphate (ATP) with a dissociation constant (KD) of ~2.7 µM. However, the structural basis and recognition mechanism remain unclear, hindering further development of this DNA aptamer. In this study, we first design a shortened DNA aptamer namely 1301b_v1 that retains a good affinity for ATP and then determine the tertiary structure of 1:1 1301b_v1-ATP binding complex using solution NMR spectroscopy. The overall complex structure shows an "L" shape architecture with the binding pocket formed by two internal loops. The ATP intercalates into the binding pocket through forming hydrogen bond with G14 and stacking with T8·A28 and G9. We also reveal an adaptive binding mechanism where the DNA aptamer switches from a semifolded state to a stable tertiary structure upon ATP binding. Based on the structure-function relationship, we introduce 2'-O-methyl modification to residues in the central junction and obtain a DNA aptamer named 9/10/16OMe with a KD of ~0.7 µM for the binding of ATP. These results underscore the ability of DNA molecules to form intricate three-dimensional folds with sophisticated functionality, opening up avenues for designing novel DNA-based molecular tools.

Aptamers, developed through SELEX (systematic evolution of ligands by exponential enrichment), are generally short oligonucleotide molecules with remarkable specificity and binding affinity to diverse biological targets. These molecules have shown promise across such fields as biosensing, molecular diagnostics, and bioimaging. However, while conventional aptamer selection strategies predominantly emphasize binding affinity, they overlook the broader spectrum of potential biological functionalities. This oversight results in aptamers that frequently exhibit limited capacity for direct biological regulation. This inherent limitation in the selection process significantly constrains both the widespread application of aptamers across diverse fields and their therapeutic potential as direct drug candidates. Functional SELEX represents an advancement by refining selection library construction and selection processes to create F-aptamers that integrate precise molecular recognition with specific biological activities. F-aptamers hold transformative potential as therapeutic agents, diagnostic tools, and molecular regulators, marking a significant step forward in biomedical applications. This minireview critically assesses recent developments in F-aptamer SELEX strategies, addressing challenges, and exploring opportunities for future research in this dynamic field.

Cardiac troponin I (cTnI) is a critical biomarker for the diagnosis of acute myocardial infarction (AMI), but conventional detection methods are often time-consuming and require specialized laboratory equipment. To meet the need for rapid and feasible detection, there is an urgent demand for methods that are fast, specific, and easy to use. In this study, two aptamers (Tro4 and Tro6), which specifically bind to different epitopes of cTnI, were employed to construct a dual-aptamer sandwich system on a lateral flow assay (LFA) strip. The test strip can deliver results within 10 min and shows a detection limit of 11.70 ng·mL−1. It also exhibited excellent stability after storage at room temperature for up to four months. The assay demonstrated high analytical accuracy, as evidenced by recovery rates from spiked serum samples ranging from 95.11% to 103.17%. These results suggest that the proposed aptamer-based LFA is highly suitable for rapid screening of cTnI, especially in point-of-care settings and resource-limited environments. From a diagnostic perspective, this method holds great promise for improving the timely detection and management of AMI and other myocardial injuries.

Objective:The combination of DOX and 5-Fu is an important chemotherapeutic regimen but lacks targeting to solid tumor sites. Precise drug delivery via folate-modified nanomaterials is an important measure to improve efficacy and reduce toxicity. Methods:CaCO3 nanoparticles served as the carrier for loading DOX and 5-Fu, followed by encapsulation with folic acid-modified polydopamine (PDA) to form a smart dual drug-carrying nanosystem called FA-DCFP. The nanoparticles (NPs) were characterized and the release kinetics and anti-tumor effectiveness of FA-DCFP were studied in vitro and in vivo. Results:The prepared nanoparticles had an average particle size of 188.79±0.93nm and exhibited pH-sensitive drug release. Cellular experiments demonstrated that the synergistic effect of tumor cell calcium overload and chemotherapy resulted in tumor cell death. Small animal in vivo imaging showed that FA-DCFP was well enriched in the tumour region. In vivo experiments demonstrated that FA-DCFP exhibited significant inhibition of tumour growth, attenuation of toxic side effects, and good biosafety compared to other groups. Conclusion:An intelligent-responsive nano-dual drug delivery system was developed to enhance the therapeutic effectiveness of tumors through calcium overload synergistic chemotherapy, offering a novel approach to tumor treatment.

Interleukin-12 (IL-12) is a robust proinflammatory cytokine that activates immune cells, such as T cells and natural killer cells, to induce antitumor immunity. However, the clinical application of recombinant IL-12 has been limited by systemic immune-related adverse events (irAEs) and rapid degradation. To address these challenges, we employed mRNA technology to encode a tumor-activated IL-12 "lock" fusion protein that offers both therapeutic efficacy and systemic safety. Lock-IL-12 mRNA encodes a sequence consisting of the IL-12 receptor-binding domain, a matrix metalloproteinase-2 (MMP-2)-cleavable linker, and two IL-12 subunits. Systemic delivery of the mRNA via lipid nanoparticles (LNPs) enables widespread systemically expression of Lock-IL-12 protein in the locked state, and maintaining an inactive state during circulation. Upon reaching the MMP-2-rich tumor microenvironment (TME), the fusion protein undergoes cleavage, activating IL-12 to initiate a powerful antitumor immune response. This strategy represents a promising approach for cytokine-based tumor therapy, combining efficient delivery with minimal systemic toxicity.

The analysis of small extracellular vesicles (sEVs) has shown clinical significance in early cancer diagnostics and considerable potential in prognostic assessment and therapeutic monitoring, offering possibilities for precise clinical intervention. Despite recent diagnostic progress based on blood-derived sEVs, the inability to specifically profile multiple parameters of sEVs proteins has hampered advancement in clinical applications. Herein, we report an approach to profile colorectal cancer (CRC)-derived sEVs by using multiaptamer-triggered rolling circle amplification (RCA) cascades. In practice, in the presence of target sEVs, the complementary strands are released from the duplexes of the structure-switching aptamer. Then, the RCA cascade occurs but only when the specific DNA strand pair is presented. As a result, the noncanonical DNA assemblies are generated whose size reaches micrometers that can be directly analyzed by conventional flow cytometry, thereby facilitating facile clinical diagnostics. In this study, the developed diagnostic method is verified on cell-derived sEVs, followed by achieving modeling based on clinical samples. The final diagnostic results from the clinical cohort indicate promising diagnostic efficacy for CRC-derived sEVs with 92% sensitivity, 86.7% specificity, and 90% overall accuracy, highlighting the substantial potential of sEVs as biomarkers for CRC diagnosis and significantly advancing the development of clinical tools for early disease diagnosis.

Pancreatic cancer remains one of the most lethal malignancies, with conventional treatment options providing limited efficacy. Recent advancements in immunotherapy have offered new hope, yet the unique tumor microenvironment (TME) of pancreatic cancer poses significant challenges to its successful application. This review explores the transformative impact of single-cell technology on the understanding and treatment of pancreatic cancer. By enabling high-resolution analysis of cellular heterogeneity within the TME, single-cell approaches have elucidated the complex interplay between various immune and tumor cell populations. These insights have led to the identification of predictive biomarkers and the development of innovative, personalized immunotherapeutic strategies. The review discusses the role of single-cell technology in dissecting the intricate immune landscape of pancreatic cancer, highlighting the discovery of T cell exhaustion profiles and macrophage polarization states that influence treatment response. Moreover, it outlines the potential of single-cell data in guiding the selection of immunotherapy drugs and optimizing treatment plans. The review also addresses the challenges and prospects of translating these single-cell-based innovations into clinical practice, emphasizing the need for interdisciplinary research and the integration of artificial intelligence to overcome current limitations. Ultimately, the review underscores the promise of single-cell technology in driving therapeutic strategy innovation and improving patient outcomes in the battle against pancreatic cancer.

Purpose: This study aimed to establish a radiomics model based on DSA during TACE to predict transcatheter arterial chemoembolization in patients with PLC who have undergone TACE treatment. Methods: A retrospective cohort of 133 TACE patients split into training (79) and validation (54) sets extracted radiomics features from DSA images, followed by consistency assessment, feature dimension reduction, and computation of the radiomics score (Radscore). Radiomics models, clinical models, and combined radiomics and clinical models were established on the basis of the Radscore and independent clinical risk factors. Goodness-of-fit assessments were performed for all the models, and calibration and decision curves were used to evaluated their calibration ability and clinical utility. Results: After applying multiple feature reduction methods, 15 radiomics features were ultimately selected to calculate the Radscore. The mPFS in the low-risk group was significantly longer than that in the high-risk group (training: 15.7 vs. 5.5 months, P < 0.001; validation: 9.3 vs. 2.4 months, P = 0.0012). The combined model outperformed both radiomics and clinical models with higher AUCs, better AIC and BIC values, and a higher log-likelihood. Calibration curves and decision curves confirmed its superior predictive accuracy and clinical utility. Conclusion: The Radscore based on DSA radiomics features can be used to stratify patients into risk groups, and nomograms based on intraoperative DSA radiomics and clinical indicators during TACE constitute a novel strategy to predict PFS in PLC patients receiving TACE treatment.

The era of molecular medicine arose as we began to diagnose and treat diseases based on understanding how genes, proteins, and cells work, providing optimal therapeutic care through molecular profiling. Central to molecular medicine is molecular recognition, which is underpinned by techniques involving omics analysis, gene editing, and targeted agents. Recent advancements in these tools not only expand our understanding of biological processes but also aid in the development of diagnostic and treatment modalities at the molecular level, thus bridging the gap between medical research and clinical applications. This perspective traces the development of molecular tools, highlighting, along the way, their pivotal role in advancing molecular medicine for the global health of people.

Classically, a molecular element (ME) is a pure substance composed of two or more atoms of the same element. However, MEs, in the context of this review, can be any molecules as elements bonded together into the backbone of synthetic oligonucleotides (ONs) with designed sequences and functions, including natural A, T, C, G, U, and unnatural bases. The use of MEs can facilitate the synthesis of designer molecules and smart materials. In particular, we discuss the landmarks associated with DNA structure and related technologies, as well as the extensive application of ONs, the ideal type of molecules for intervention therapy aimed at correcting disease-causing genetic errors (indels). It is herein concluded that the discovery of ON therapeutics and the fabrication of designer molecules or nanostructures depend on the ME concept that we previously published. Accordingly, ME will be our focal point as we discuss related research directions and perspectives in making molecules and materials. This article is part of the theme issue ‘Reactivity and mechanism in chemical and synthetic biology’.

All Supplementary Tables in one file. Supplementary Table 1. Clinical data on the rNPC and pNPC for whole-exome and whole-genome sequencing. Supplementary Table 2.Clinical characteristics of rNPC and pNPC FFPE samples. Supplementary Table 3. The correspondence between sample ID in the manuscript and sample alias in the database (HRA000053) Supplementary Table 4. Summary of WES/WGS on 55rNPC and 44pNPC. Supplementary Table 5. Summary of mutation in 55 rNPC and 44 pNPC cases. Supplementary Table 6. Somatic SNVs and indels of coding regions in 55 rNPC and 44 pNPC cases. Supplementary table 7. Validation of somatic mutations in rNPC and pNPC. Supplementary Table 8. Summary of WES in 7 paired rNPC and pNPC samples. Supplementary table 9. Somatic SNVs and indels of coding regions in pired rNPC and pNPC cases. Supplementary Table 10. Overlapped somatic SNVs and indels of coding regions in 7 paired rNPC and pNPC cases. Supplementary table 11. Summary of CNVs and SVs in 55 rNPC and 44 pNPC cases. Supplementary Table 12. Summary of survival analyses by multivariate Cox proportional hazards model by overall survival. Supplementary Table 13. Summary of survival analyses by multivariate Cox proportional hazards model by loco-regional relapse-free survival.

A bioinspired "point-and-shoot" molecular strategy is described for engineering noncovalent aptamers via K+-induced reassembly of a split G-quadruplex sequence at the end of monomeric aptamers. This design compensates for insufficient cell recognition of monovalent aptamers in biological environments and minimizes structure-induced nonspecific cell binding, expending the aptamer toolbox available for complex systems.

Due to the advantages of its numerous modification sites, predictable structure, high thermal stability, and excellent biocompatibility, DNA is the ideal choice as a key component of biosensors. DNA biosensors offer significant advantages over existing bioanalytical techniques, addressing limitations in sensitivity, selectivity, and limit of detection. Consequently, they have attracted significant attention from researchers worldwide. Here, we exemplify four foundational categories of functional nucleic acids: aptamers, DNAzymes, i-motifs, and G-quadruplexes, from the perspective of the structure-driven functionality in constructing DNA biosensors. Furthermore, we provide a concise overview of the design and detection mechanisms employed in these DNA biosensors. Noteworthy advantages of DNA as a sensor component, including its programmable structure, reaction predictility, exceptional specificity, excellent sensitivity, and thermal stability, are highlighted. These characteristics contribute to the efficacy and reliability of DNA biosensors. Despite their great potential, challenges remain for the successful application of DNA biosensors, spanning storage and detection conditions, as well as associated costs. To overcome these limitations, we propose potential strategies that can be implemented to solve these issues. By offering these insights, we aim to inspire subsequent researchers in related fields.

INTRODUCTION:The pursuit of novel therapeutic agents for serious diseases such as cancer has been a global endeavor. Aptamers characteristic of high affinity, programmability, low immunogenicity, and rapid permeability hold great promise for the treatment of diseases. Yet obtaining the approval for therapeutic aptamers remains challenging. Consequently, researchers are increasingly devoted to exploring innovative strategies and technologies to advance the development of these therapeutic aptamers.AREAS COVERED:The authors provide a comprehensive summary of the recent progress of the SELEX (Systematic Evolution of Ligands by EXponential enrichment) technique, and how the integration of modern tools has facilitated the identification of therapeutic aptamers. Additionally, the engineering of aptamers to enhance their functional attributes, such as inhibiting and targeting, is discussed, demonstrating the potential to broaden their scope of utility.EXPERT OPINION:The grand potential of aptamers and the insufficient development of relevant drugs have spurred countless efforts for stimulating their discovery and application in the therapeutic field. While SELEX techniques have undergone significant developments with the aid of advanced analysis instruments and ingeniously updated aptameric engineering strategies, several challenges still impede their clinical translation. A key challenge lies in the insufficient understanding of binding conformation and susceptibility to degradation under physiological conditions. Despite the hurdles, our opinion is optimistic. With continued progress in overcoming these obstacles, the widespread utilization of aptamers for clinical therapy is envisioned to become a reality soon.

Materials and Methods 1.Genomic DNA preparation and whole-genome or whole-exome sequencing. 2.Reads mapping and somatic genetic alteration detection. 3. PCR and Sanger sequencing. 4.Immunohistochemistry Supplementary Figure 1. GISTIC analysis of rNPC and pNPC samples. Supplementary Figure 2. Recurrent somatic mutations in rNPC and pNPC. Supplementary Figure 3. Western blot (WB) assay with the indicated antibodies in 293T cell line and SUNE2 cell line. Supplementary Figure 4. Immunohistochemical (IHC) staining to examine the expression of specific SMGs in 148 rNPC samples and 122 pNPC samples.

Approaches to DNA probe-mediated precision medicine have been extensively explored for the diagnosis and treatment of diverse types of cancer. Despite this, simple nanoscale devices with the required recognition specificity and sensitivity for clinical application have remained elusive until now. Here, we report a pH-driven covalent nanoscale device that integrates pH-responsive, switchable structure and proximity-driven covalent cross-linking. A tumor acidic, pH-driven mechanism eliminates "on-target, off-tumor" nonspecific recognition. By manipulating covalent binding to target molecule on the cell surface, this nanodevice avoids binding-then-shedding to improve the sensitivity of tumor recognition. We envision that this pH-driven covalent nanoscale device will inspire more clinical applications toward specific, long-term tumor imaging in the cancer microenvironment.

DNA-templated silver nanoclusters (DNA-AgNCs) are promising fluorescent materials and have been used in cancer diagnosis. Although many different DNA-AgNC applications have been realized, most of them rely on individual DNA-AgNCs or assembled DNA-AgNCs with limited recognition abilities, resulting in low detection sensitivity or off-target effects, in turn, hindering the performance of DNA-AgNCs in cancer cell recognition. As a solution, we assembled DNA-AgNCs by a multibranched linear (MBL) DNA structure formed through a trigger-initiated hybridization chain reaction (HCR) regarding the natural compatibility of DNA-AgNCs with DNA programmability and the advantages of DNA assembly in incorporating repetitive and functional moieties into one structure. By the specific modification of the trigger, MBL-AgNCs tethered with the targeting aptamer and partially hybridized duplex, which works as a component of DNA logic platform relying on the combination of cascade strand displacement reaction and specific recognition ability of aptamers, were obtained, respectively. DNA-AgNCs assembled by the aptamer-tethered MBL structure exhibited about 20-fold enhanced detection sensitivity in recognizing cancer cells compared to individual aptamer-tethered DNA-AgNCs. DNA-AgNCs assembled by the duplex-attached MBL exhibited logic performance in analyzing dual cell surface receptors with the assistance of "AND" logic platform, thus identifying cancer cells with high sensitivity and resolution. The facile conjugation of the MBL structure with different functional DNA structures makes it an ideal platform to assemble DNA-AgNCs used for aptamer-based cell recognition, thus broadening the potential applications of DNA-AgNCs.

In the past decades, various nanomaterials with unique properties have been explored for bioapplications. Meanwhile, aptamers, generated from the systematic evolution of ligands by exponential enrichment technology, are becoming an indispensable element in the design of functional nanomaterials because of their small size, high stability, and convenient modification, especially endowing nanomaterials with recognition capability to specific targets. Therefore, the incorporation of aptamers into nanomaterials offers an unprecedented opportunity in the research fields of diagnostics and therapeutics. Here, we focus on recent advances in aptamer-embedded nanomaterials for bioapplications. First, we briefly introduce the properties of nanomaterials that can be functionalized with aptamers. Then, the applications of aptamer-embedded nanomaterials in cellular analysis, imaging, targeted drug delivery, gene editing, and cancer diagnosis/therapy are discussed. Finally, we provide some perspectives on the challenges and opportunities that have arisen from this promising area.