Nucleic Acid Aptamers for Molecular Diagnostics and Therapeutics: Advances and Perspectives

Dual-mode monolithic column with zwitterion antifouling and aptamer affinity for online specific recognition of okadaic acid

Developing a functional media for precise identification of trace shellfish toxin would underpin the effective assessment of marine pollution. Herein, a novel monolithic column with a dual-mode strategy integrating antifouling and aptamer bionic affinity recognition was proposed for online specific identification of the marine toxin okadaic acid (OA). The zwitterionic monomer 2-(methacryloyloxy)ethylphosphorylcholine (MPC) and aptamers were synergistically employed to enable efficient reduction of matrix interferences and selective capture of target OA. Preparation optimization, characterization, and fouling-resistant mechanism of the dual-mode bionic monolith were evaluated. The zwitterion phosphorylcholine MPC introduced into the monolith significantly improved the fouling resistance to biomass substrates, meanwhile the aptamers were able to provide a high specific recognition capacity. Coupled with LC-MS, the as-prepared monolith provided an effective approach for highly selective and sensitive identification of OA. Good recovery yields of over 90 % in shellfish tissue extracts and human serum were achieved with a sensitive limit of detection (LOD) as low as 0.1 ng/mL, as well as excellent specificity and low interference from proteins, fatty acids and analogues. Applied to popular shellfishes (such as clams, mussels, and oysters) and serum samples, trace OA toxin was accurately distinguished and quantified with satisfactory recoveries as 93.8 ± 2.2 % - 99.9 ± 1.9 % (n = 3). Compared to the traditional HLB cartridge and other materials in the LC-MS method, the resulting anti-fouling aptamer monolith provided a more advanced online analysis mode with higher sensitivity and better resolution of OA in biological samples. It might provide an attractive access to an online bionic recognition platform with LC-MS for efficient, anti-interference and sensitive specific detection of trace marine toxin OA in biological samples.

Nanostructured aptasensors for ricin detection and tumor therapy: exploring aptamer-protein interactions and conformational stability in biological complexities

Aptamers are distinctive single-stranded oligonucleotides derived through in vitro evolution, and exhibit exceptional ability in binding to target proteins. Structural modifications of aptamers can profoundly regulate their interactions with proteins, thereby influencing associated cellular behavior. Recent research focused on modulating aptamer-protein interaction in complex biological environments to regulate various biological processes. However, in such crowded conditions, aptamer conformation and stability are susceptible to nuclease degradation, which can impair stable binding to target. Ricin is recognized as a significant biological toxin protein, distinguished by its widespread availability, remarkable dissemination, and resilience including wide pH tolerance, remarkable thermostability, and solubility. RTA is an enzymatic subunit of ricin, that can inactivate approximately 2000 ribosomes per minute, rapidly halting protein synthesis, making it a powerful candidate for tumor therapy. By leveraging the potent cytotoxicity of ricin, coupled with the targeting precision of aptamers and the versatility of nanomaterials, a powerful approach emerges for both targeted tumor therapy and highly sensitive detection of ricin. Although there have been some insightful reports on aptamers applied in ricin detection, a systematic discussion remains limited. In this context, we provide an in-depth overview of techniques used to analyze aptamer-ricin interactions and explore the potential of ricin-aptamer interactions in clinical diagnosis.

Refinement and Truncation of DNA Aptamers Based on Molecular Dynamics Simulations: Computational Protocol and Experimental Validation

Aptamers have proven useful for a wide variety of applications, such as drug delivery systems and analytical reagents for diagnosis or food safety control. Conventional aptamer selection methods typically produce sequences longer than necessary, which are optimized through a postselection trial and error process to obtain the shortest-length sequence that preserves binding affinity. Herein, we describe a general strategy to obtain the tridimensional structure of DNA aptamers using a semiautomated molecular dynamics protocol, which serves as a guide to rationally improve experimentally selected candidates. Based on this approach, we designed truncated aptamers from previously described ligands recognizing different peptides and proteins, which are 20-35% shorter than the original candidates and present similar or even improved binding affinities. Moreover, we also discriminate between energetically similar secondary structures in terms of the energetic scoring of the molecular dynamics trajectories and rationally explain the role of poly thymine spacers in the (de)stabilization of the structure. This work demonstrates how a protocol for generating the aptamers tridimensional structure can accelerate their optimization for obtaining better analytical reagents and therapeutic agents.

Aptamer-modified GSH-degradable honokiol polyprodrug nanoparticles for ovarian cancer-specific targeting therapy

Honokiol (HK) is a polyphenol isolated from the Magnolia genus, a component of traditional Chinese herbal medicine, which can effectively suppress the growth of various tumors, including ovarian cancer. However, its low water solubility and lack of tumor-targeting ability have greatly hindered the clinical application of HK. Herein, a glutathione (GSH)-sensitive HK polyprodrug was prepared using HK as the backbone. An EpCAM-specific aptamer and poly(ethylene glycol) (PEG) were then conjugated to the HK polyprodrug, and the resulting polyprodrug was assembled into nanoparticles (NPs) in water. The HK polyprodrug-formed NPs achieved high drug loading and GSH-responsive drug release. Moreover, after optimization, HK polyprodrug NPs (A/P-PHK NP40), formed by aptamer-modified and PEG-modified prodrug at a feed molar ratio of 2: 3, exhibited the highest ability to target EpCAM-overexpressing ovarian cancer cells. A/P-PHK NP40 also demonstrated a greater cell growth inhibition effect in ovarian cancer cells compared to free HK and control HK NPs. All in all, this work reported a novel strategy for HK delivery based on microenvironment responsiveness polyprodrug, which provided a potential method for ovarian cancer targeting therapy.

Engineering Covalent Aptamer Chimeras for Enhanced Autophagic Degradation of Membrane Proteins

Targeted degradation of membrane proteins represents an attractive strategy for eliminating pathogenesis-related proteins. Aptamer-based chimeras hold great promise as membrane protein degraders, however, their degradation efficacy is often hindered by the limited structural stability and the risk of off-target effects due to the non-covalent interaction with target proteins. We here report the first design of a covalent aptamer-based autophagosome-tethering chimera (CApTEC) for the enhanced autophagic degradation of cell-surface proteins, including transferrin receptor 1 (TfR1) and nucleolin (NCL). This strategy relies on the site-specific incorporation of sulfonyl fluoride groups onto aptamers to enable the cross-linking with target proteins, coupled with the conjugation of an LC3 ligand to hijack the autophagy-lysosomal pathway for targeted protein degradation. The chemically engineered CApTECs exhibit enhanced on-target retention and improved structural stability. Our results also demonstrate that CApTECs achieve remarkably enhanced and prolonged degradation of membrane proteins compared to the non-covalent designs. Furthermore, the CApTEC targeting TfR1 is combined with 5-fluorouracil (5-FU) for synergistic tumor therapy in a mouse model, leading to substantial suppression of tumor growth. Our strategy may provide deep insights into the LC3-mdiated autophagic degradation, affording a modular and effective strategy for membrane protein degradation and precise therapeutic applications.

Advances in RNA therapy for the treatment of autoimmune diseases

Autoimmune diseases (ADs) are a group of complex, chronic conditions characterized by disturbance of immune tolerance, with examples including systemic lupus erythematosus, rheumatoid arthritis, multiple sclerosis, and psoriasis. These diseases have unclear pathogenesis, and traditional therapeutic approaches remain limited. However, advances in high-throughput histology technology and scientific discoveries have led to the identification of various pathogenic factors contributing to ADs. Coupled with improvements in RNA nucleic acid-based drug synthesis, design, and delivery, RNA-based therapies have been extensively investigated for their potential in treating ADs. This paper reviews the progress in the use of miRNAs, lncRNAs, circRNAs, siRNAs, antisense oligonucleotides (ASOs), aptamers, mRNAs, and other RNA-based therapies in ADs, focusing on their therapeutic potential and application prospects, providing insights for future research and clinical treatment of autoimmune diseases.

Recent advances in nucleic acid-functionalized metallic nanoparticles

Nucleic acid-functionalized metallic nanoparticles (N-MNPs) precisely integrate the advantageous characteristics of nucleic acids and metallic nanomaterials, offering various abilities such as resistance to enzymatic degradation, penetration of physiological barriers, controllable mobility, biomolecular recognition, programmable self-assembly, and dynamic structure-function transformation. These properties demonstrate significant potential in the field of biomedical diagnostics and therapeutics. In this review, we examine recent advancements in the construction and theranostic applications of N-MNPs. We briefly summarize the methodologies employed in the conjugation of nucleic acids with metallic nanoparticles and the formation of their superstructural assemblies. We highlight recent representative applications of N-MNPs in biomolecular diagnosis, imaging, and smart delivery of theranostic agents. We also discuss challenges currently faced in this field and provide an outlook on future development directions and application prospects.

Dual signal output detection of acetamiprid residues in medicine and food homology products via nanopore biosensor

Acetamiprid (ACE) is used in plant cultivation and their accumulation is a threat to ecology and health. Herein, a fluorescence/ion current dual-readout nanopore biosensor was designed for ACE detection. The carboxyfluorescein (FAM) labeled ACE aptamer was hybridized with complementary DNA (cDNA) to form partially hybridized double stranded DNA (dsDNA), and modified on the nanopore surface. ACE could specifically interact with FAM-aptamer and compete it against the nanopore surface. The probe changed from dsDNA to single-stranded DNA (ssDNA), which triggering the ionic current signal switched from "closed" to "open" and the fluorescence signal changed from "on" to "off". The sensor exhibited linear range 0.5-100 ng/mL and with detection limit of 0.12 ng/mL. Meanwhile, the sensor can be employed for the detection of ACE residues in medicine and food homology (MFH) products. More importantly, the dual signal output detection results can be cross-verified, ensuring the accuracy of the detection.

A supramolecular FRET signal amplification nanoprobe for high contrast and synchronous in situ imaging of cell surface receptor homodimers/heterodimers

Epidermal growth factor receptor (EGFR) homodimers and heterodimers play significant roles in a variety of tumors, but current imaging probes remain problematic due to restricted contrast and sensitivity. Thus, we have developed aptamer-mediated activated conformational transitions to target the EGFR and HER2. Furthermore, based on signal amplification techniques, especially the FRET fluorescence enhancement properties of poly-β-CD, supramolecular FRET signal amplification nanoprobes were constructed to improve imaging contrast and sensitivity. The results confirmed that the fluorescence intensity of the supramolecular FRET group probe is 1.2 to 1.3 times that of the multi-FRET group and 11.3 to 23.2 times that of the single-FRET group. The results further confirmed that the supramolecular nanoprobe could not only be activated by tumor cells and tissues to achieve high-contrast imaging of EGFR/EGFR and EGFR/HER2 dimers, but also successfully distinguish tumor cells and tissues from normal cells and tissues. The strategy provides a generalized platform for high-contrast imaging of other dimers intending to deepen the understanding of the central roles of multiple dimers in cancer development.

Aptamers in dentistry: diagnosis, therapeutics, and future perspectives

Oral health is essential to general health. The diagnosis of dental diseases and treatment planning of dental care need to be straightforward and accurate. Recent studies have reported the use of aptamers in dentistry to achieve a simple diagnosis and facilitate therapy. Aptamers comprise nucleic acid sequences that possess a strong affinity for their target. Synthesized chemically, aptamers have several advantages, including smaller size, higher stability, and lower immunogenicity compared with monoclonal antibodies. They can be used to detect biomarkers in saliva and the presence of various pathogens, or can be used as a targeted drug delivery system for disease treatment. This review highlights current research on aptamers for dental care, especially the recent progress in oral disease diagnosis and therapeutics. The challenges and unresolved problems faced by the clinical use of aptamers are also discussed. In the future, the clinical applications of aptamers will be further extended to include, for example, dental indications and regenerative dentistry.

Cascaded Strand Displacement Amplification and CRISPR/Cas12a Aptasensor Utilizing MoS2 Nanoflowers for Colorectal Cancer Biomarker Porphyromonas gingivalis Detection

Colorectal cancer (CRC) ranks as the third most prevalent cancer globally, both in terms of diagnoses and cancer-related mortality. Increasing evidence suggests that an imbalance in intestinal flora can contribute to the progression of CRC, and fecal microbiota may serve as potential biomarkers for its screening and diagnosis. Notably, Porphyromonas gingivalis has been identified in the malignant tissues and feces of CRC patients, establishing it as a significant biomarker for early screening, diagnosis, and prognostic assessment of CRC. Current methods for detecting P. gingivalis face numerous challenges, including high costs, complex procedures, and lengthy implementation times. Therefore, developing rapid, highly specific, and sensitive detection methods for P. gingivalis is of great importance. In this study, we utilized the whole-bacterium systematic evolution of ligands by exponential enrichment method to identify highly specific and high-affinity aptamers targeting P. gingivalis through 15 selection cycles. Subsequently, we developed an aptasensor driven by MoS2 nanoflowers, which integrates strand displacement amplification and CRISPR/Cas12a double amplification for sensitive detection of P. gingivalis, achieving a limit of detection of 10 CFU/mL. Using this aptasensor, we evaluated the abundance of P. gingivalis in clinical fecal samples and observed significantly higher levels in the feces of CRC patients compared to healthy individuals, corroborating the results obtained from quantitative polymerase chain reaction. In summary, we developed a highly specific and sensitive aptasensor for the first time, representing a promising new approach for the identification of P. gingivalis, with significant potential for CRC screening and diagnosis.

Molecular Modeling on Duplexes with Threose-Based TNA and TPhoNA Reveals Structural Basis for Different Hybridization Affinity toward Complementary Natural Nucleic Acids

Synthetic nucleic acids, also defined as xenobiotic nucleic acids (XNAs), opened an avenue to address the limitations of nucleic acid therapeutics and the development of alternative carriers for genetic information in biotechnological applications. Two related XNA systems of high interest are the α-l-threose nucleic acid (TNA) and (3'-2') phosphonomethyl threosyl nucleic acid (tPhoNA), where TNAs show potential in antisense applications, whereas tPhoNAs are investigated for their predisposition toward orthogonal genetic systems. We present predictions on helical models of TNA and tPhoNA chemistry in homoduplexes and in complex with native ribose chemistries. A stretched right-handed helical structure with a sugar puckering preference for the 4'3'T (C3'- endo/C4'- exo) and O4'1'T (C1'- endo/O4'- exo) is found for the in silico model of dsTNA, while for the in silico model of dstPhoNA a B-type structure is found with a sugar puckering preference for O4'1'T (C1'- endo/O4'- exo). Simulations with complementary DNA and RNA provided insight into the distinct pairing capabilities of TNA and tPhoNA.

Self-assembled aptamer nanoparticles for enhanced recognition and anticancer therapy through a lysosome-independent pathway

Aptamers and aptamer-drug conjugates (ApDCs) have shown some success as targeted therapies in cancer theranostics. However, their stability in complex media and their capacity to evade lysosomal breakdown still need improvement. To address these challenges, we herein developed a one-step self-assembly strategy to improve the stability of aptamers or ApDCs, while simultaneously enhancing their delivery performance and therapeutic efficiency through a lysosome-independent pathway. This strategy involves the formation of stable complexes between disulfide monomer and aptamers (Sgc8) or ApDCs (Gem-Sgc8). Self-assembled Sgc8 NPs resisted nuclease degradation for up to 24 h, whereas the aptamer alone degraded within just 3 h. These self-assembled Sgc8 NPs, as well as Gem-Sgc8 NPs, demonstrated enhanced binding capabilities compared to Sgc8 aptamers or Gem-Sgc8 alone. Furthermore, lysosome-independent cellular uptake was significantly improved, which in turn increased the therapeutic efficacy of Gem-Sgc8 NPs by 2.5 times compared to Gem-Sgc8 alone. In vivo results demonstrated that Gem-Sgc8 NPs can effectively suppress the growth of tumors. The same self-assembly strategy was successfully applied to other aptamers, such as MJ5C and cMET, showing the generalizability of our method, Overall, this aptamer self-assembly strategy not only overcomes the limitations associated with instability and lysosomal degradation but also demonstrates its broad applicability, highlighting its potential as a promising avenue for advancing targeted cancer theranostics. STATEMENT OF SIGNIFICANCE: We developed a one-step self-assembly strategy to improve the stability of aptamers or ApDCs and enhance their drug therapeutic efficiency through a lysosome-independent pathway. The stability of self-assembled Sgc8 nanoparticles (NPs) was significantly improved. The resulting Sgc8 NPs or GEM-Sgc8 NPs exhibited enhanced binding ability compared to Sgc8 aptamers or GEM-Sgc8 alone, and they also facilitated lysosome-independent cellular uptake, resulting in a 2.5-fold increase in therapeutic efficacy of GEM-Sgc8-NPs. The same self-assembly strategy was successfully applied to other aptamers, such as MJ5C and cMET, showing the generalizability of our method.

Aptamer-Modified MOFs (Aptamer@MOF) for Efficient Detection of Bacterial Pathogens: A Review

Detecting pathogenic bacteria is crucial for controlling infectious diseases, safeguarding public health, and ensuring food and water safety. The integration of metal-organic frameworks (MOFs) with aptamers offers a promising approach to enhance bacterial detection. Aptamers provide high specificity for target recognition, while MOFs contribute tunable porous structures and stability, forming robust biosensors. This synergy improves sensitivity, selectivity, and versatility, enabling real-time and quantitative detection. Applications span food safety, environmental monitoring, and point-of-care diagnostics. This review highlights the significance of aptamer@MOF biosensors, discussing various detection techniques and aptamer immobilization methods. It also addresses challenges like enhancing sensitivity, improving selectivity, minimizing interference, ensuring stability, and advancing scalability for real-world applications. Additionally, limitations such as the need for miniaturization, multimode detection, and multiplex analysis are highlighted. Future directions focus on optimizing the design and expanding applications to overcome these limitations. The versatility and potential of aptamer@MOF biosensors underscore their promise as high-performance platforms for bacterial detection in diverse fields.

Aptamer based immunotherapy: a potential solid tumor therapeutic

Aptamer-based immunotherapy can be a new hope for treating solid tumors with personalized and specific approaches toward cancer therapies. Aptamers are small synthetic single-stranded nucleic acids that may bring in a paradigm shift in treating solid tumors. These are highly selective drugs applied in cellular immunotherapy, cytokine modulation, and immune checkpoint suppression. This review provides an overview of the recent advances in aptamer-based technologies with specific key clinical trials involving AON-D21 and AM003. Aptamers are potently active in immune regulation and tumor targeting. However, aptamer stability and bioavailability are seriously compromised by the issues relating to renal clearance and rapid degradation through nucleases. The latter are reviewed here along with novel improvements, some of which involve chemical modifications that greatly enhance stability and prolong the circulation time; exemplary such modifications are PEGylation, cholesterol conjugation, and the synthesis of circular nucleic acids. The regulatory aspect is also crucial. For example, in addition to specific strategies to prevent drug-drug interactions (DDIs) in cancer remediation medications, this paper underscores the need of risk assessment, particularly because of immunogenicity and organ failure. The use of aptamers is expanded by the development of SOMAmers, X-aptamers, and bioinformatics. To make aptamer-based drugs a major part of cancer treatment, future research should concentrate more on resolving existing issues and expanding their beneficial uses.

An autocatalytic hybridization circuit-based FRET aptasensor for detection of low-abundant sulfameter in human serum

Exposure to antibiotics is considered a potential risk factor for human health. Yet, the extensive and cost-effective detection of low-abundant antibiotics in complex matrices remains a significant challenge. Herein, an aptamer and an autocatalytic hybridization circuit (AHC) were used to fabricate a fluorescence resonance energy transfer (FRET) platform to detect sulfameter (SME) in human serum. The AHC system comprised two mutually motivated hybridization chain reactions (HCR) modules, ultimately producing long-branched DNA copolymeric nanowires. This mutually reciprocal activation of two HCR modules enables continuous signal amplification, providing the AHC system with wide linear range and high sensitivity for the SME detection. Compared to the HCR-based aptasensor, the AHC-based aptasensor exhibited a wider linear range and improved sensitivity (3.3 times greater). Under optimal conditions, the fluorescent AHC-based aptasensor demonstrated a linear range (R2 was 0.996) from 0.5 to 2000 nM, with a low detection limit of 0.301 nM (S/N = 3). The fluorescent aptasensor was also validated by SME-spiked human serum samples, showing average recoveries ranging from 96.40 % to 109.30 %, with a relative standard deviation below 10.45 %. Furthermore, when tested on six human serum samples, the aptasensor results were consistent with those obtained from the commercial ELISA method. These findings demonstrate that the proposed aptasensor provides a promising approach for the practical monitoring of low-abundant SME in human serum.

Bispecific Aptamer-Drug Conjugates Selectively Eliminate Malignant Hematologic Cells for Treating Acute Myeloid Leukemia

Surface antigen-directed immunotherapy is a curative treatment modality for acute myeloid leukemia (AML) that is characterized by the abundance and stability expression of surface antigens. However, current surface antigen-directed immunotherapies have shown poor outcomes and undesirable mortality rates in treating AML patients, primarily due to acquired resistance that arises from using single-target therapies to address the heterogeneous expression of surface antigens. Hence, in order to improve the efficacy of antigen-specific therapies for treating AML, we designed a bispecific aptamer-drug conjugate. In particular, cell-SELEX incorporating cell lysate-SELEX for aptamers with HEL cells yielded AptCD117, which specifically binds to CD117 (a highly expressed marker on both hematopoietic stem cells and primary AML cells) and has excellent performance in targeting human AML cells. Combined with CD71-binding aptamer LXD-11b (another broadly expressed surface antigen on leukemia cells), bispecific aptamers were designed to couple with monomethyl auristatin F (MMAF) for fabricating aptamer-drug conjugates. Results demonstrated that bispecific aptamer-MMAF conjugates efficiently kill different CD117 and CD71 expression levels of target AML cell lines in vitro. Importantly, the exposure of AML marrow specimens to bispecific aptamer-MMAF conjugates resulted in the selective elimination of primary AML cells in vitro and had no effect on healthy lymphocytes within the same specimens. Thus, these results provide a proof of concept for the generation of bispecific aptamer-drug conjugates directed against human AML cells, which hold the promise of advancing treatment strategies and improving AML patient outcomes.

Multiple aptamer recognition-based quantum dot lateral flow platform: ultrasensitive point-of-care testing of respiratory infectious diseases

Respiratory infectious diseases spread rapidly and have a wide range of impacts, posing a serious threat to public health security. The development of a sensitive, accurate, and rapid detection method for respiratory viruses is crucial for disease prevention and control. However, existing methods are inadequate in satisfying the demand for accurate and convenient detection simultaneously. Therefore, an ultrasensitive point-of-care testing (POCT) platform based on a multiple aptamer recognition-based quantum dot lateral flow immunoassay (MARQ-LFIA) was developed in this work. This platform consisted of multiple high-affinity aptamers for recognizing different sites on a respiratory infectious virus protein, enhancing the efficiency of virus identification in complex environments. By combining a multiple aptamer recognition strategy with quantum dot fluorescent technique to construct LFIA test strips and pairing them with a high-gain portable fluorescence reader, excellent detection sensitivity and specificity were achieved in the case of coronavirus disease 2019 (COVID-19). The limits of detection were 1.427 pg mL-1 and 1643 U mL-1 towards the nucleocapsid protein and inactivated viruses, respectively, indicating that MARQ-LFIA improved detection sensitivity compared to reported methods. More critically, by testing thirty COVID-19 positive and twenty negative patient samples, the positive detection rate increased from 55.17% to 86.67% compared with commercially similar products. The universality of MARQ-LFIA was also investigated for diagnosing influenza B. We believe that MARQ-LFIA can be a promising POCT tool with potential applications in the areas of public health for the growing demand for precision diagnosis and treatment.

Aptamer and DNAzyme Based Colorimetric Biosensors for Pathogen Detection

The detection of pathogens is critical for preventing and controlling health hazards across clinical, environmental, and food safety sectors. Functional nucleic acids (FNAs), such as aptamers and DNAzymes, have emerged as versatile molecular tools for pathogen detection due to their high specificity and affinity. This review focuses on the in vitro selection of FNAs for pathogens, with emphasis on the selection of aptamers for specific biomarkers and intact pathogens, including bacteria and viruses. Additionally, the selection of DNAzymes for bacterial detection is discussed. The integration of these FNAs into colorimetric biosensors has enabled the development of simple, cost-effective diagnostic platforms. Both non-catalytic and catalytic colorimetric biosensors are explored, including those based on gold nanoparticles, polydiacetylenes, protein enzymes, G-quadruplexes, and nanozymes. These biosensors offer visible detection through color changes, making them ideal for point-of-care diagnostics. The review concludes by highlighting current challenges and future perspectives for advancing FNA-based colorimetric biosensing technologies for pathogen detection.

The Emergence of Oligonucleotide Building Blocks in the Multispecific Proximity-Inducing Drug Toolbox of Destruction

Oligonucleotides are a rapidly emerging class of therapeutics. Their most well-known examples are informational drugs that modify gene expression by binding mRNA. Despite inducing proximity between biological machinery and mRNA when applied to modulating gene expression, oligonucleotides are not typically labeled as "proximity-inducing" in literature. Yet, they have recently been explored as building blocks for multispecific proximity-inducing drugs (MPIDs). MPIDs are unique because they can direct endogenous biological machinery to destroy targeted molecules and cells, in contrast to traditional drugs that inhibit only their functions. The unique mechanism of action of MPIDs has enabled the targeting of previously "undruggable" molecular entities that cannot be effectively inhibited. However, the development of MPIDs must ensure that these molecules will selectively direct a potent, destruction-based mechanism of action toward intended targets over healthy tissues to avoid causing life-threatening toxicities. Oligonucleotides have emerged as promising building blocks for the design of MPIDs because they are sequence-controlled molecules that can be rationally designed to program multispecific binding interactions. In this Review, we examine the emergence of oligonucleotide-containing MPIDs in the proximity induction space, which has been dominated by antibody and small molecule MPID modalities. Moreover, examples of oligonucleotides developed as MPID candidates in immunotherapy and protein degradation are discussed to demonstrate the utility of oligonucleotides in expanding the scope and selectivity of the MPID toolbox. Finally, we discuss the utility of programming "AND" gates into oligonucleotide scaffolds to encode conditional responses that have the potential to be incorporated into MPIDs, which can further enhance their selectivity, thus increasing the scope of this drug category.

Effects of pain in lumbosacral stenosis and lifestyle-related factors on brain-derived neurotrophic factor expression profiles

This study investigated the role of brain-derived neurotrophic factor (BDNF) in patients with degenerative lumbar stenosis, focusing on its expression and correlation with pain intensity. The study examined 96 patients with lumbar stenosis and 85 control participants. BDNF levels in the yellow ligamentum flavum were measured using reverse transcription quantitative polymerase chain reaction (RT-qPCR), enzyme-linked immunosorbent assay (ELISA), and western blot analysis. The results showed significantly higher BDNF expression at both messenger ribonucleic acid (mRNA; fold change = +1.35 ± 0.23; p < 0.05) and protein levels in patients (28.98 ± 6.40 pg/mg) compared to controls (4.56 ± 1.98 pg/mg; p < 0.05). Furthermore, BDNF levels correlated positively with pain intensity reported by patients, with higher expression observed in those experiencing more severe pain. The study also explored the influence of lifestyle factors, such as smoking and alcohol consumption, and related diseases, such as diabetes, on BDNF expression. Smoking, alcohol use, and diabetes were associated with significantly elevated BDNF levels (p < 0.05). These findings suggest that BDNF could serve as a biomarker for pain severity in degenerative lumbar stenosis at the protein level, although this was not consistently observed at the mRNA level; this highlights the potential for BDNF-targeted therapies in managing pain. Future research should involve larger longitudinal studies to validate these findings and explore therapeutic interventions. This study underscores the importance of considering molecular and lifestyle factors in the treatment of degenerative lumbar stenosis, aiming to improve patient outcomes through comprehensive, targeted approaches.

Targeted APT8(16-34) obtained by cell-SELEX and its internalization with miR-23-5p into activated hepatic stellate cells

BACKGROUND

The activation of hepatic stellate cells play a pivotal role in the pathogenesis of hepatic fibrosis. However, the current lack of specifically identified targets on these cells poses a significant challenge in developing targeted delivery tools for effective anti-hepatic fibrosis therapeutics in clinical practice.

METHODS

Cell-systematic evolution of ligands by exponential enrichment method was conducted on HSC-T6 cell line to screen out activated hepatic stellate cell-specific aptamers. The specificity of the selected aptamers in targeting hepatic stellate cells was confirmed after truncation optimization. Furthermore, the optimal aptamer was conjugated with miR-23b-5p via C6 linkage to evaluate the targeting specificity of this complex and assess its potential in downregulating liver fibrosis-related proteins and slowing down the progression of liver fibrosis.

RESULTS

The present study successful identified 11 highly enriched single-stranded DNA sequences (APT1-11) that specifically target activated hepatic stellate cells. Subsequent affinity detection and optimization truncation led to the selection of APT8(16-34), which effectively targeted activated hepatic stellate cells both in vivo and in vitro. Moreover, when conjugated with miR-23b-5p, APT8(16-34) also exhibited internalization ability into activated hepatic stellate cells. The delivered cargo miR-23b-5p by APT8 (16-34) effectively targeted to mRNA, leading to translational inhibition and subsequent downregulation of related proteins.

CONCLUSIONS

We have identified APT8 (16- 34), which exhibits specific targeting and internalization capabilities into activated hepatic stellate cells. Moreover, when conjugated with miR-23b-5p, APT8 (16-34) also internalizes into activated hepatic stellate cells, enabling miR-23b-5p exert their respective functions.

3D Printing in Biocatalysis and Biosensing: From General Concepts to Practical Applications

3D printing has matured into a versatile technique that offers researchers many different printing methods and materials with varying properties. Nowadays, 3D printing is deployed within a myriad of different applications, ranging from chemistry to biotechnology -including bioanalytics, biocatalysis or biosensing. Due to its inherent design flexibility (which enables rapid prototyping) and ease of use, 3D printing facilitates the relatively quick and easy creation of new devices with unprecedented functions.. This review article describes how 3D printing can be employed for research in the fields of biochemistry and biotechnology, and specifically for biocatalysis and biosensor applications. We survey different relevant 3D printing techniques, as well as the surface activation and functionalization of 3D-printed materials. Finally, we show how 3D printing is used for the fabrication of reaction ware and enzymatic assays in biocatalysis research, as well as for the generation of biosensors using aptamers, antibodies, and enzymes as recognition elements.

Aptamer Proteolysis-Targeting Chimeras (PROTACs): A Novel Strategy to Combat Drug Resistance in Estrogen Receptor α-Positive Breast Cancer

Breast cancer with positive expression of estrogen receptor α (ERα+) accounts for 70% of breast cancer cases, whose predominant treatment is currently endocrine therapy. The main strategy of endocrine therapy for ERα+ breast cancer is to inhibit the ERα signaling pathway and downregulate ERα levels, which often results in mutations in the ligand-binding domain (LBD) of ERα, leading to significant resistance to subsequent treatment in patients. To combat drug resistance, we first proposed a novel aptamer PROTAC strategy through specifically targeted degradation of ERα via targeting the DNA-binding domain (DBD) of ERα. We proved that this strategy is capable of targeting ERα for degradation through ubiquitination, leading to the inhibition of proliferation in ERα+ breast cancer cells and tamoxifen-resistant breast cancer cells. Furthermore, we investigated the mechanisms involved in overcoming resistance. By circumventing drug resistance associated with LBD mutations in ERα, our approach provides a promising avenue for the discovery of new therapeutic agents.

AptamerRunner: An accessible aptamer structure prediction and clustering algorithm for visualization of selected aptamers

Aptamers are short single-stranded DNA or RNA molecules with high affinity and specificity for targets and are generated using the iterative systematic evolution of ligands by exponential enrichment (SELEX) process. Next-generation sequencing (NGS) revolutionized aptamer selections by allowing a more comprehensive analysis of SELEX-enriched aptamers as compared to Sanger sequencing. The current challenge with aptamer NGS datasets is identifying a diverse cohort of candidate aptamers with the highest likelihood of successful experimental validation. Here we present AptamerRunner, an aptamer sequence and/or structure clustering algorithm that synergistically integrates computational analysis with visualization and expertise-directed decision making. The visual integration of networked aptamers with ranking data, such as fold enrichment or scoring algorithm results, represents a significant advancement over existing clustering tools by providing a natural context to depict groups of aptamers from which ranked or scored candidates can be chosen for experimental validation. The inherent flexibility, user-friendly design, and prospects for future enhancements with AptamerRunner have broad-reaching implications for aptamer researchers across a wide range of disciplines.

Aptamer-based sensitive fluorescence β-lactoglobulin food allergen bioassay via dual and cyclic bidirectional strand displacement amplifications

β-Lactoglobulin (β-Lg) is a prevalent allergenic protein found in most dairy products, which poses great food safety risks for individuals with allergies, especially for infants. Sensitive and effective detection methods for such allergens are essential to reduce the risk of allergies in daily life. Herein, a fluorescent aptamer bioassay based on a dual and cyclic bidirectional strand displacement means is developed for the sensitive detection of β-Lg in infant rice porridge and milk. The aptamer in the duplex DNA probe binds β-Lg to release the assistance strand to further hybridize with two hairpins, which triggers the initiation of two cyclic amplification cycles through the polymerization, displacement, and nicking of the strands under the action of DNA polymerase and endonuclease restriction enzymes. The amplification cycles lead to the unfolding of many fluorescently quenched signal probes to exhibit substantially enhanced fluorescence recovery for detecting β-Lg. The assay can realize detection of β-Lg in concentrations as low as 4.41 pM within the range of 0.01 to 10 nM. Furthermore, our sensing method has the capability to discriminate β-Lg from other proteins with high selectivity, resulting in low levels of β-Lg detection in rice porridge and milk samples, demonstrating promising potentials of the developed sensing method for monitoring various food allergens.

Ultrasensitive electrochemiluminescencent multivalent aptamer sensor based on energy and electron transfer dual quenching tactics

An efficient "on-off-on" electrochemiluminescence (ECL) aptasensor utilizing dual-mechanism quenching was constructed for detecting furanyl fentanyl (FuF). The first signal "on" state was achieved by novel dual-ligand zinc metal-organic frameworks (Zn-MOFs), which were synthesized by self-assembly reaction using zinc atom clusters as metal nodes, achieving strong and stable ECL emission. The "off" state was realized by the energy and electron quenching effect of copper-doped WO3. Specifically, in addition to the overlap of the UV-Vis spectrum, energy transfer existed between the acceptor and donor after doping copper. Therefore, copper created a "highway" for electron transfer between the donor and acceptor, which greatly improved the quenching efficiency. Simultaneously, employing multivalent aptamers as capture probes augmented the binding affinity and probability of association between aptamer and target through a synergistic multivalent effect. Consequently, the second "on" state was the ECL signal restored by introducing FuF. Benefiting from the combination of the multivalent aptamers strategy with the "on-off-on" design, the developed aptasensor showed excellent linearity (1.0 × 10-13 to 1.0 × 10-6 g/L) with a low limit of detection of 5.5 × 10-14 g/L (S/N = 3). Additionally, it demonstrates a relative standard deviation (RSD) of less than 5% and good recovery ranging from 97.6 to 102%. The proposed aptasensor presents considerable potential for rapid, sensitive, and accurate determination of FuF.

Single-point mutated lanmodulin as a high-performance MRI contrast agent for vascular and kidney imaging

Magnetic resonance imaging contrast agents can enhance diagnostic precision but often face limitations such as short imaging windows, low tissue specificity, suboptimal contrast enhancement, or potential toxicity, which affect resolution and long-term monitoring. Here, we present a protein contrast agent based on lanmodulin, engineered with a single-point mutation at position 108 from N to D to yield maximum gadolinium binding sites. After loading with Gd3+ ions, the resulting protein complex, LanND-Gd, exhibits efficient renal clearance, high relaxivity, and prolonged renal retention compared to commercial agents. LanND-Gd enables high-performance visualization of whole-body structures and brain vasculature in male mice at a resolution finer than one hundred micrometers. In male ischemia mouse models, LanND-Gd also improves kidney dysfunction monitoring while minimizing risks of neural toxicity or immunogenic reactions. This protein-based contrast agent offers superior image quality, improved biocompatibility, and extended imaging timeframes, promising significant advancements in magnetic resonance-based diagnostics and patient outcomes.

Xeno Nucleic Acids as Functional Materials: From Biophysical Properties to Application

Xeno nucleic acid (XNA) are artificial nucleic acids, in which the chemical composition of the sugar moiety is changed. These modifications impart distinct physical and chemical properties to XNAs, leading to changes in their biological, chemical, and physical stability. Additionally, these alterations influence the binding dynamics of XNAs to their target molecules. Consequently, XNAs find expanded applications as functional materials in diverse fields. This review provides a comprehensive summary of the distinctive biophysical properties exhibited by various modified XNAs and explores their applications as innovative functional materials in expanded fields.

Novel ratiometric electrochemical aptasensor based on broad-spectrum aptamer recognition for simultaneous detection of penicillin antibiotics in milk

To effectively monitor multi-residues of penicillin antibiotics (PENs) in milk, we developed a novel ratiometric electrochemical aptasensor enabling simultaneous detection of PENs. The aptasensor employed a broad-spectrum aptamer as a recognition element, niobium carbide functionalized with methylene blue (Nb2C-MB) as a reference signal generator, and a ferrocene-labeled aptamer (Fc-Apt) as an output signal. Electrodes were modified with Fe-N-C doped carbon nanotubes (Fe-N-C-CNTs) to amplify detection signals further. During detection, Fc-Apt binding to PENs decreased Fc current intensity (IFc) and increased MB current intensity (IMB). The simultaneous detection of PENs was achieved using IMB/IFc as a quantitative signal. Under optimal conditions, a good linear relationship between IMB/IFc and antibiotic concentration was observed, indicating the aptasensor had a robustness. The limits of detection of aptasensor for four penicillin antibiotics and their mixed targets were 0.093-0.191 nM. This work provides a new approach to multi-residue detection of the same class of antibiotics.

Unite and Conquer: Association of Two G-Quadruplex Aptamers Provides Antiproliferative and Antimigration Activity for Cells from High-Grade Glioma Patients

Background: High-grade gliomas remain a virtually incurable form of brain cancer. Current therapies are unable to completely eradicate the tumor, and the tumor cells that survive chemotherapy or radiation therapy often become more aggressive and resistant to further treatment, leading to inevitable relapses. While the antiproliferative effects of new therapeutic molecules are typically the primary focus of research, less attention is given to their influence on tumor cell migratory activity, which can play a significant role in recurrence. A potential solution may lie in the synergistic effects of multiple drugs on the tumor. Objectives: In this study, we investigated the effect of combined exposure to bi-(AID-1-T), an anti-proliferative aptamer, and its analog bi-(AID-1-C), on the migratory activity of human GBM cells. Results: We examined the effects of various sequences of adding bi-(AID-1-T) and bi-(AID-1-C) on five human GBM cell cultures. Our findings indicate that certain sequences significantly reduced the ability of tumor cells to migrate and proliferate. Additionally, the expression of Nestin, PARP1, L1CAM, Caveolin-1, and c-Myc was downregulated in human GBM cells that survived exposure, suggesting that the treatment had a persistent antitumor effect on these cells.

The clinical potential of l-oligonucleotides: challenges and opportunities

Chemically modified nucleotides are central to the development of biostable research tools and oligonucleotide therapeutics. In this context, l-oligonucleotides, the synthetic enantiomer of native d-nucleic acids, hold great promise. As enantiomers, l-oligonucleotides share the same physical and chemical properties as their native counterparts, yet their inverted l-(deoxy)ribose sugars afford them orthogonality towards the stereospecific environment of biology. Notably, l-oligonucleotides are highly resistant to degradation by cellular nucleases, providing them with superior biostability. As a result, l-oligonucleotides are being increasingly utilized for the development of diverse biomedical technologies, including molecular imaging tools, diagnostic biosensors, and aptamer-based therapeutics. Herein, we present recent such examples that highlight the clinical potential of l-oligonucleotides. Additionally, we provide our perspective on the remaining challenges and practical considerations currently associated with the use of l-oligonucleotides and explore potential solutions that will lead to the broader adoption of l-oligonucleotides in clinical applications.

Unlocking precision in aptamer engineering: a case study of the thrombin binding aptamer illustrates why modification size, quantity, and position matter

The thrombin binding aptamer (TBA) is a prototypical platform used to understand the impact of chemically-modified nucleotides on aptamer stability and target affinity. To provide structural insight into the experimentally-observed effects of modification size, location, and number on aptamer performance, long time-scale molecular dynamics (MD) simulations were performed on multiple binding orientations of TBA-thrombin complexes that contain a large, flexible tryptophan thymine derivative (T-W) or a truncated analogue (T-K). Depending on modification position, T-W alters aptamer-target binding orientations, fine-tunes aptamer-target interactions, strengthens networks of nucleic acid-protein contacts, and/or induces target conformational changes to enhance binding. The proximity and 5'-to-3' directionality of nucleic acid structural motifs also play integral roles in the behavior of the modifications. Modification size can differentially influence target binding by promoting more than one aptamer-target binding pose. Multiple modifications can synergistically strengthen aptamer-target binding by generating novel nucleic acid-protein structural motifs that are unobtainable for single modifications. By studying a diverse set of modified aptamers, our work uncovers design principles that must be considered in the future development of aptamers containing chemically-modified nucleotides for applications in medicine and biotechnology, highlighting the value of computational studies in nucleic acids research.

DNAzyme and controllable cholesterol stacking DNA machine integrates dual-target recognition CTCs enable homogeneous liquid biopsy of breast cancer

Although circulating tumor cells (CTCs) have demonstrated considerable importance in liquid biopsy, their detection is limited by low concentrations and complex sample components. Herein, we developed a homogeneous, simple, and high-sensitivity strategy targeting breast cancer cells. This method was based on a non-immunological stepwise centrifugation preprocessing approach to isolate CTCs from whole blood. Precise quantification is achieved through the specific binding of aptamers to the overexpressed mucin 1 (MUC1) and human epidermal growth factor receptor 2 (HER2) proteins of breast cancer cells. Subsequently, DNAzyme cleavage and parallel catalytic hairpin assembly (CHA) reactions on the cholesterol-stacking DNA machine were initiated, which opened the hairpin structures T-Hg2+-T and C-Ag+-C, enabling multiple amplifications. This leads to the fluorescence signal reduction from Hg2+-specific carbon dots (CDs) and CdTe quantum dots (QDs) by released ions. This strategy demonstrated a detection performance with a limit of detection (LOD) of 3 cells/mL and a linear range of 5-100 cells/mL. 42 clinical samples have been validated, confirming their consistency with clinical imaging, pathology findings and the folate receptor (FR)-PCR kit results, exhibiting desirable specificity of 100% and sensitivity of 80.6%. These results highlight the promising applicability of our method for diagnosing and monitoring breast cancer.

AptaDiff: de novo design and optimization of aptamers based on diffusion models

Aptamers are single-stranded nucleic acid ligands, featuring high affinity and specificity to target molecules. Traditionally they are identified from large DNA/RNA libraries using $in vitro$ methods, like Systematic Evolution of Ligands by Exponential Enrichment (SELEX). However, these libraries capture only a small fraction of theoretical sequence space, and various aptamer candidates are constrained by actual sequencing capabilities from the experiment. Addressing this, we proposed AptaDiff, the first in silico aptamer design and optimization method based on the diffusion model. Our Aptadiff can generate aptamers beyond the constraints of high-throughput sequencing data, leveraging motif-dependent latent embeddings from variational autoencoder, and can optimize aptamers by affinity-guided aptamer generation according to Bayesian optimization. Comparative evaluations revealed AptaDiff's superiority over existing aptamer generation methods in terms of quality and fidelity across four high-throughput screening data targeting distinct proteins. Moreover, surface plasmon resonance experiments were conducted to validate the binding affinity of aptamers generated through Bayesian optimization for two target proteins. The results unveiled a significant boost of $87.9\%$ and $60.2\%$ in RU values, along with a 3.6-fold and 2.4-fold decrease in KD values for the respective target proteins. Notably, the optimized aptamers demonstrated superior binding affinity compared to top experimental candidates selected through SELEX, underscoring the promising outcomes of our AptaDiff in accelerating the discovery of superior aptamers.

Functional Aptamers In Vitro Evolution for Intranuclear Blockage of RNA-Protein Interaction

Over the last 30 years, despite considerable research and endeavors aimed at harnessing aptamers as pharmaceutical molecules, the progress in developing aptamer-based drugs has been falling short of expectations. Sequential steps of affinity molecule acquisition and functional screening are typically required for discovering affinity-based macromolecule therapeutics, which can be time-consuming and limiting in candidate selection. Additionally, aptamers often necessitate tedious postselection modifications to overcome pharmacokinetic limitations, which usually impede the binding affinity. Herein, we propose a novel in vitro screening platform termed Functional Aptamers in vitro Evolution (FAIVE), which integrates affinity molecule acquisition with functional screening and introduces chemical diversity during the process. This platform aims to rapidly generate functional aptamers capable of binding to target proteins and regulating their functions. Illustrated by targeting intranuclear RNA-protein interactions involving HIV-1 Tat protein and TAR RNA, FAIVE demonstrates a selection of functional aptamers with significant intracellular blocking effects. The study also explores lipid nanoparticle delivery systems to enhance intracellular delivery efficiency, expanding aptamer targeting potential to broader intracellular and intranuclear domains. This study emphasizes the potential of FAIVE to expedite the development of aptamer-based drugs and facilitate the creation of more versatile and effective therapeutics.

Facile Synthesis of Aptamer-Functionalized Polydopamine-Coated Magnetic Graphene Oxide Nanocomposites for Highly Efficient Purification of His-Tagged Proteins

Recombinant proteins hold significant importance in numerous disciplines. As the demand for expressing and purifying these proteins grows, the scientific community is in dire need of a simple yet versatile methodology that can efficiently purify these proteins. Aptamers as synthetic nucleic acid-based ligands with high affinity have shown promise in this regard, as they can capture targets through molecular recognition. In this study, novel aptamer-functionalized polydopamine-coated magnetic graphene oxide nanocomposites were facilely prepared, achieving an impressive average aptamer coverage density (45 nmol/mg). These nanocomposites exhibited a uniform structure and robust magnetic responsiveness. The findings indicated that they possess several advantages, such as rapid adsorption, substantial capacity (171.4 mg/g), and excellent reusability. Notably, due to the inherent properties of nucleic acids, the immobilized aptamer-magnetic beads can be utilized repeatedly with high purification efficiency. Finally, the nanocomposites were further employed to purify His-tagged proteins from actual samples. Remarkably, they were able to selectively and efficiently isolate His-tagged retinoid X receptor alpha protein from complex Escherichia coli lysate. The purified His-tagged retinoid X receptor alpha protein was analyzed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. This confirmed the efficacy of developed nanocomposites, reinforcing their vast potential for purification of His-tagged recombinant proteins.

Process, advances, and perspectives of graphene oxide-SELEX for the development of aptamer molecular probes: A comprehensive review

BACKGROUND

Aptamers are screened via the systematic evolution of ligands by exponential enrichment (SELEX) and are widely used in molecular diagnostics and targeted therapies. The development of efficient and convenient SELEX technology has facilitated rapid access to high-performance aptamers, thereby advancing the aptamer industry. Graphene oxide (GO) serves as an immobilization matrix for libraries in GO-SELEX, making it suitable for screening aptamers against diverse targets.

RESULTS

This review summarizes the detailed steps involved in GO-SELEX, including monitoring methods, various sublibrary acquisition methods, and practical applications from its inception to the present day. In addition, the potential of GO-SELEX in the development of broad-spectrum aptamers is explored, and its current limitations for future development are emphasized. This review effectively promotes the application of the GO-SELEX technique by providing valuable insights and assisting researchers interested in conducting related studies.

SIGNIFICANCE AND NOVELTY

To date, no review on the topic of GO-SELEX has been published, making it challenging for researchers to initiate studies in this area. We believe that this review will broaden the SELEX options available to researchers, ensuring that they can meet the growing demand for molecular probes in the scientific domain.

Current status and trends in small nucleic acid drug development: Leading the future

Small nucleic acid drugs, composed of nucleotides, represent a novel class of pharmaceuticals that differ significantly from conventional small molecule and antibody-based therapeutics. These agents function by selectively targeting specific genes or their corresponding messenger RNAs (mRNAs), further modulating gene expression and regulating translation-related processes. Prominent examples within this category include antisense oligonucleotides (ASO), small interfering RNAs (siRNAs), microRNAs (miRNAs), and aptamers. The emergence of small nucleic acid drugs as a focal point in contemporary biopharmaceutical research is attributed to their remarkable specificity, facile design, abbreviated development cycles, expansive target spectrum, and prolonged activity. Overcoming challenges such as poor stability, immunogenicity, and permeability issues have been addressed through the integration of chemical modifications and the development of drug delivery systems. This review provides an overview of the current status and prospective trends in small nucleic acid drug development. Commencing with a historical context, we introduce the primary classifications and mechanisms of small nucleic acid drugs. Subsequently, we delve into the advantages of the U.S. Food and Drug Administration (FDA) approved drugs and mainly discuss the challenges encountered during their development. Apart from researching chemical modification and delivery system that efficiently deliver and enrich small nucleic acid drugs to target tissues, promoting endosomal escape is a critical scientific question and important research direction in siRNA drug development. Future directions in this field will prioritize addressing these challenges to facilitate the clinical transformation of small nucleic acid drugs.

Breaking Barriers: Nucleic Acid Aptamers in Gastrointestinal (GI) Cancers Therapy

Conventional cancer therapies can have significant adverse effects as they are not targeted to cancer cells and may damage healthy cells. Single-stranded oligonucleotides assembled in a particular architecture, known as aptamers, enable them to attach selectively to target areas. Usually, they are created by Systematic Evolution of Ligand by Exponential enrichment (SELEX), and they go through a rigorous pharmacological revision process to change their therapeutic half-life, affinity, and specificity. They could thus offer a viable substitute for antibodies in the targeted cancer treatment market. Although aptamers can be a better choice in some situations, antibodies are still appropriate for many other uses. The technique of delivering aptamers is simple and reasonable, and the time needed to manufacture them is relatively brief. Aptamers do not require animals or an immune response to be produced, in contrast to antibodies. When used as a medication, aptamers can directly suppress tumor cells. As an alternative, they can be included in systems for targeted drug delivery that administer medications specifically to tumor cells while reducing toxicity to healthy cells. The most recent and cutting-edge methods for treating gastrointestinal (GI) tract cancer with aptamers will be covered in this review, with a focus on targeted therapy as a means of conquering resistance to traditional medicines.

DNA/RNA-based electrochemical nanobiosensors for early detection of cancers

Nucleic acids, like DNA and RNA, serve as versatile recognition elements in electrochemical biosensors, demonstrating notable efficacy in detecting various cancer biomarkers with high sensitivity and selectivity. These biosensors offer advantages such as cost-effectiveness, rapid response, ease of operation, and minimal sample preparation. This review provides a comprehensive overview of recent developments in nucleic acid-based electrochemical biosensors for cancer diagnosis, comparing them with antibody-based counterparts. Specific examples targeting key cancer biomarkers, including prostate-specific antigen, microRNA-21, and carcinoembryonic antigen, are highlighted. The discussion delves into challenges and limitations, encompassing stability, reproducibility, interference, and standardization issues. The review suggests future research directions, exploring new nucleic acid recognition elements, innovative transducer materials and designs, novel signal amplification strategies, and integration with microfluidic devices or portable instruments. Evaluating these biosensors in clinical settings using actual samples from cancer patients or healthy donors is emphasized. These sensors are sensitive and specific at detecting non-communicable and communicable disease biomarkers. DNA and RNA's self-assembly, programmability, catalytic activity, and dynamic behavior enable adaptable sensing platforms. They can increase biosensor biocompatibility, stability, signal transduction, and amplification with nanomaterials. In conclusion, nucleic acids-based electrochemical biosensors hold significant potential to enhance cancer detection and treatment through early and accurate diagnosis.

Electrochemical aptasensors based on porous carbon derived from graphene oxide/ZIF-8 composites for the detection of Erwinia cypripedii

In this research, self-screening aptamer and MOFs-derived nanomaterial have been combined to construct electrochemical aptasensor for environmental detection. By utilizing the large specific surface area of reduced graphene oxide (rGO), ZIF-8 was grown in situ on surface of rGO, and the composites was pyrolyzed to obtain MOFs-derived porous carbon materials (rGO-NCZIF). Thanks to the synergistic effect between rGO and NCZIF, the complex exhibits remarkable characteristics, including a high electron transfer rate and electrocatalytic activity. In addition, the orderly arrangement of imidazole ligands within ZIF-8 facilitated the uniform doping of nitrogen elements into the porous carbon, thereby significantly enhancing its electrochemical performance. After carboxylation, rGO-NCZIF was functionalized with self-screening aptamer for fabricating electrochemical aptasensor, which can be used to detect Erwinia cypripedii, a kind of quarantine plant bacteria, with detection limit of 4.92 × 103 cfu/mL. Due to the simplicity and speed, the aptasensor is suitable for rapid customs inspection and quarantine. Additionally, the universality of this sensing strategy was verified through exosomes detection by changing the aptamer. The results indicated that the rGO-NCZIF-based electrochemical aptasensor had practical value in the environmental and medical fields.

Nano revolution of DNA nanostructures redefining cancer therapeutics-A comprehensive review

DNA nanostructures are a promising tool in cancer treatment, offering an innovative way to improve the effectiveness of therapies. These nanostructures can be made solely from DNA or combined with other materials to overcome the limitations of traditional single-drug treatments. There is growing interest in developing nanosystems capable of delivering multiple drugs simultaneously, addressing challenges such as drug resistance. Engineered DNA nanostructures are designed to precisely deliver different drugs to specific locations, enhancing therapeutic effects. By attaching targeting molecules, these nanostructures can recognize and bind to cancer cells, increasing treatment precision. This approach offers tailored solutions for targeted drug delivery, enabling the delivery of multiple drugs in a coordinated manner. This review explores the advancements and applications of DNA nanostructures in cancer treatment, with a focus on targeted drug delivery and multi-drug therapy. It discusses the benefits and current limitations of nanoscale formulations in cancer therapy, categorizing DNA nanostructures into pure forms and hybrid versions optimized for drug delivery. Furthermore, the review examines ongoing research efforts and translational possibilities, along with challenges in clinical integration. By highlighting the advancements in DNA nanostructures, this review aims to underscore their potential in improving cancer treatment outcomes.

DNA nanotechnology in ionic liquids and deep eutectic solvents

Nucleic acids have the ability to generate advanced nanostructures in a controlled manner and can interact with target sequences or molecules with high affinity and selectivity. For this reason, they have applications in a variety of nanotechnology applications, from highly specific sensors to smart nanomachines and even in other applications such as enantioselective catalysis or drug delivery systems. However, a common disadvantage is the use of water as the ubiquitous solvent. The use of nucleic acids in non-aqueous solvents offers the opportunity to create a completely new toolbox with unprecedented degrees of freedom. Ionic liquids (ILs) and deep eutectic solvents (DESs) are the most promising alternative solvents due to their unique electrolyte and solvent roles, as well as their ability to maintain the stability and functionality of nucleic acids. This review aims to be a comprehensive, critical, and accessible evaluation of how much this goal has been achieved and what are the most critical parameters for accomplishing a breakthrough.

Trends and frontiers in signal amplification for aptamer-based tumor detection: A bibliometric analysis

BACKGROUND

Malignant tumors are one of the leading causes of death worldwide, imposing a substantial economic and social burden. Early detection is the key to improving cure rates and reducing mortality rates, which requires the development of sensitive early detection technologies. Signal amplification techniques play a crucial role in aptamer-based early detection of tumors and are increasingly garnering attention from researchers.

AIM

To investigate the current research status, developmental trajectories, and hotspots in signal amplification for aptamer-based tumor detection through bibliometric analysis.

METHODS

English publications pertaining to signal amplification in aptamer-based tumor detection were retrieved from the Web of Science Core Collection database. VOSviewer and CiteSpace software were employed to analyze various information within this field, including countries, institutions, authors, co-cited authors, journals, co-cited journals, cited references, and keywords.

RESULTS

A total of 757 publications were included in this study. China accounted for 85.47% of all publications, with Nanjing University (China) emerging as the institution with the highest publication output. The most influential authors and journals were Hasanzadeh M. from Iran and "Biosensors and Bioelectronics", respectively. Exosomes and carcinoembryonic antigen (CEA) stood out as the most researched tumor-related molecules. Currently, the predominant signal amplification technique, nanomaterial, and signal transduction method were identified as hybridization chain reactions, gold nanoparticles, and electrochemical methods, respectively. Over the past 3 years, exosomes, CEA, electrochemical biosensors, and nanosheets have emerged as research hotspots, exhibiting a robust burst of intensity.

CONCLUSION

This study is the first bibliometric analysis of literature on signal amplification in aptamer-based tumor detection and elucidates the current status, hotspots, and prospective research directions within this realm. Additionally, it provides an important reference for researchers.

Aptamer-functionalized triptolide with release controllability as a promising targeted therapy against triple-negative breast cancer

Targeted delivery and precise release of toxins is a prospective strategy for the treatment of triple-negative breast cancer (TNBC), yet the flexibility to incorporate both properties simultaneously remains tremendously challenging in the X-drug conjugate fields. As critical components in conjugates, linkers could flourish in achieving optimal functionalities. Here, we pioneered a pH-hypersensitive tumor-targeting aptamer AS1411-triptolide conjugate (AS-TP) to achieve smart release of the toxin and targeted therapy against TNBC. The multifunctional acetal ester linker in the AS-TP site-specifically blocked triptolide toxicity, quantitatively sustained aptamer targeting, and ensured the circulating stability. Furthermore, the aptamer modification endowed triptolide with favorable water solubility and bioavailability and facilitated endocytosis of conjugated triptolide by TNBC cells in a nucleolin-dependent manner. The integrated superiorities of AS-TP promoted the preferential intra-tumor triptolide accumulation in xenografted TNBC mice and triggered the in-situ triptolide release in the weakly acidic tumor microenvironment, manifesting striking anti-TNBC efficacy and virtually eliminated toxic effects beyond clinical drugs. This study illustrated the therapeutic potential of AS-TP against TNBC and proposed a promising concept for the development of nucleic acid-based targeted anticancer drugs.

Development of Bivalent Aptamer-DNA Carrier-Doxorubicin Conjugates for Targeted Killing of Esophageal Squamous Cell Carcinoma Cells

Esophageal cancer ranks the seventh in cancer incidence and the sixth in cancer death. Esophageal squamous cell carcinoma (ESCC) accounts for approximately 90% of the total cases of esophageal cancer. Chemotherapy is the most effective drug-based method for treatment of esophageal cancer. However, severe side effects of traditional chemotherapy limit its treatment efficacy. Targeted chemotherapy can deliver chemotherapeutic drugs to cancer cells and specifically kill these cells with reduced side effects. In the work, the bivalent aptamer-DNA carrier (BAD) was designed by using an ESCC cell-specific aptamer as the recognition molecule and a GC base-rich DNA sequence as the drug carrier. With doxorubicin (Dox) as chemotherapeutic drugs, the bivalent aptamer-DNA-Dox conjugate (BADD) was constructed for targeted killing of ESCC cells. Firstly, the truncated A2(35) aptamer with a retained binding ability was obtained through optimization of an intact A2(80) aptamer and was used to fuse with DNA carrier sequences for constructing the BAD through simple DNA hybridization. The results of gel electrophoresis and flow cytometry analysis showed that the BAD was successfully constructed and had a stronger binding affinity than monovalent A2(35). Then, the BAD was loaded with Dox drugs to construct the BADD through noncovalent intercalation. The results of fluorescence spectra and flow cytometry assays showed that the BADD was successfully constructed and can bind to target cells strongly. Confocal imaging further displayed that the BADD can be specifically internalized into target cells and release Dox. The results of CCK-8 assays, Calcein AM/PI staining, and wound healing assays demonstrated that the BADD can specifically kill target cells, but not control cells. Our results demonstrate that the developed BADD can specifically deliver doxorubicin to target ESCC cells and selectively kill these cells, offering a potentially effective strategy for targeted chemotherapy of ESCC.

Cell-SELEX and application research of a DNA aptamer against esophageal squamous cell carcinoma (ESCC) cell line TE-1

Esophageal cancer is a common cancer with high morbidity and mortality that severely threatens the safety and quality of human life. The strong metastatic nature of esophageal cancer enables it to metastasize more quickly and covertly, making it difficult for current diagnostic and treatment methods to achieve efficient early screening, as well as timely and effective treatment. As a promising solution, nucleic acid aptamers, a kind of special single-stranded DNA or RNA oligonucleotide selected by the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) technology, can specifically bind with different molecular targets. In this paper, random DNA single-stranded oligonucleotides were used as the initial library. Using TE-1 cells and HEEC cells as targets, specific binding sequences were selected by 15 rounds of the cell-SELEX method, and the aptamer sequence that binds to TE-1 cells with the most specificity was obtained and named Te4. The Te4 aptamer was further validated for binding specificity, binding affinity, type of target, in vitro cytotoxicity when conjugated with DOX(Te4-DOX), and in vivo distribution. Results of in vitro validation showed that Te4 has outstanding binding specificity with a Kd value of 51.16 ± 5.52 nM, and the target type of Te4 was preliminarily identified as a membrane protein. Furthermore, the cytotoxicity experiment showed that Te4-DOX has specific cytotoxicity towards cultured TE-1 cells. Finally, the results of the in vivo distribution experiment showed that the Te4 aptamer is able to specifically target tumor regions in nude mice, showing great potential to be applied in future diagnosis and targeted therapy of esophageal cancer.

Fructose@histone synergistically improve the performance of DNA-templated Cu NPs: rapid analysis of LAM in tuberculosis urine samples using a handheld fluorometer and a smartphone RGB camera

This study presented a nanoparticle-enhanced aptamer-recognizing homogeneous detection system combined with a portable instrument (NASPI) to quantify lipoarabinomannan (LAM). This system leveraged the high binding affinity of aptamers, the high sensitivity of nanoparticle cascade amplification, and the stabilization effect of dual stabilizers (fructose and histone), and used probe-Cu2+ to achieve LAM detection at concentrations ranging from 10 ag mL-1 to 100 fg mL-1, with a limit of detection of 3 ag mL-1 using a fluorometer. It can also be detected using an independently developed handheld fluorometer or the red-green-blue (RGB) camera of a smartphone, with a minimum detection concentration of 10 ag mL-1. We validated the clinical utility of the biosensor by testing the LAM in the urine of patients. Forty urine samples were tested, with positive LAM results in the urine of 18/20 tuberculosis (TB) cases and negative results in the urine of 6/10 latent tuberculosis infection cases and 10/10 non-TB cases. The assay results revealed a 100% specificity and a 90% sensitivity, with an area under the curve of 0.9. We believe that the NASPI biosensor can be a promising clinical tool with great potential to convert LAM into clinical indicators for TB patients.