DNA Aptamers Research Articles

Electrochemical sensor for vascular endothelial growth factor based on self-assembling DNA aptamer structure

Developing vascular endothelial growth factor (VEGF) protein is essential for early cancer diagnosis and cancer treatment monitoring. This study presents the design and characterisation of an electrochemical sensor utilising a self-assembling DNA aptamer structure for the sensitive and selective detection of VEGF. The aptamer structure comprises three different parts of single-stranded DNA that are assembled prior to integration into the sensor. Polypyrrole (Ppy)-based layers were deposited onto screen-printed carbon electrodes (SPCEs) using an electrochemical deposition technique, followed by the entrapment of a self-assembled DNA aptamer structure within electrochemically formed Ppy matrix ((DNA aptamer)/Ppy). The response to the sensor toward VEGF was measured by the pulsed amperometric detection (PAD), highlighting the enhanced performance of DNA aptamer/Ppy configuration compared to bare Ppy. The sensor exhibited high sensitivity, achieving a limit of detection (LOD) of 0.21 nM for VEGF. The interaction behaviour between VEGF in the solution and the immobilise DNA aptamer/Ppy-based structure was analysed using Langmuir isotherm model. The developed electrochemical biosensor in promising for in vitro applications in early cancer diagnostics and treatment monitoring, enabling rapid screening of patient samples.

Development of novel DNA aptamers and colorimetric nanozyme aptasensor for targeting multi-drug-resistant, invasive Salmonella typhimurium strain SMC25

Invasive, biofilm-forming Non-typhoidal Salmonella (iNTS), propagating through the global food and water supply chain, presents a significant risk to food safety and public health. Developing a robust detection system is crucial for enabling point-of-care, affordable, and equipment-free identification of this pathogen throughout the supply chain. In this study, we screened a novel pool of ssDNA aptamers specific to a multidrug resistant iNTS strain SMC25, previously isolated from Indian poultry products in our earlier research. Through 13 rounds of whole-cell SELEX, we identified, characterized, and selected seven full-length aptamers (ST18, ST19, ST25, ST28, ST29, ST31, and ST32). Flow cytometric analysis reveals superior binding of ST25, ST28, ST29, and ST31. These aptamers were translated onto Nanozyme-based aptasensing system for efficient, cost-effective detection of SMC25. This system harnesses the aptamer-mediated, reversible peroxidase-like activity of gold nanoparticles (GNPs) to oxidize the TMB substrate into a one-electron oxidation state, resulting in a blue-colored Diamine charge transfer complex (DCTC). The catalytic process, coupled with GNP aggregation, induces a visible color change in the test mixture from ruby-red to blue. Post-SELEX truncations identified the optimal aptamer sequence (T_ST31), which selectively detected SMC25 in water with a limit of detection (LOD) of ∼10⁴ CFU/mL. Lower concentrations (10 CFU/mL) of SMC25 could be detected after non-selective enrichment within 120 min. This research introduces a novel pool of iNTS-specific aptamers along with a cost-effective (0.25 USD per sample) solution for colorimetric detection by the naked eye.

An Ultrahigh Affinity DNA Aptamer for Quinine and Its Intrinsic Fluorescence Based Label-free Detection.

Measuring quinine is critical for the detection of its overdose, understanding its pharmacological and toxicological effects, and monitoring its pollution. While a previously reported aptamer named MN4 can bind quinine, it was not selected for it, leading to compromised binding affinity and specificity. In this work, a new quinine aptamer was isolated using the library immobilization capture-SELEX technique. The Q1 aptamer has a Kd value of 10 nM determined by an isothermal titration calorimetry experiment and 45 nM in a fluorescence binding assay. A 3.5 nM quinine limit of detection was obtained based on the aptamer binding-induced quenching of the intrinsic fluorescence of quinine. A large blue shift in fluorescence was observed for quinine upon binding to Q1, whereas binding to MN4 led to a very small red shift, indicating different ways of quinine binding by these two aptamers. Q1 did not bind cocaine based on NMR spectroscopy and fluorescence assays also indicated excellent selectivity against other tested molecules. This work has supplied a high affinity aptamer for quinine that can be useful for its detection and fundamental aptamer binding studies. It also highlights the advantages of using capture-SELEX to isolate aptamers for small molecules.

The Inhibitory Effects of a Factor B-Binding DNA Aptamer Family Supersede the Gain of Function of Factor B Variants Associated with Atypical Hemolytic Uremic Syndrome.

Aptamers are short, single-stranded oligonucleotides that selectively bind to target biomolecules. Although they generally exhibit good binding specificity, their affinities are often limited because of the relative lack of hydrophobic groups in nucleic acids. Chemically modified nucleotides incorporating hydrophobic structures into uracil have been synthesized to address this obstacle. Modified DNA aptamers containing such nonstandard nucleotides have been developed for >20 different complement proteins. These modified aptamers show increased affinity and enhanced serum stability and have potential value as therapeutic agents. We recently conducted a structure/function study on a family of modified DNA aptamers that bind specifically to complement Factor B (FB). This work revealed that these aptamers selectively inhibit the complement alternative pathway (AP) by preventing the formation of the AP complement component C3 (C3) proconvertase complex, C3bB. Certain patients with atypical hemolytic uremic syndrome express gain-of-function variants of FB that enhance the formation of the proconvertase complex and/or decrease the efficacy of endogenous regulators against the C3 convertases they form. To investigate whether these FB-binding aptamers could override the effects of disease-causing mutations in FB, we examined how they interacted with several FB variants, including D279G, F286L, K323E, and K350N, in various assays of complement function. We found that the inhibitory effect of the FB-binding aptamers superseded the gain-of-function mutations in FB, although the aptamers could not dissociate preformed C3 convertases. These findings suggest that FB-binding aptamers could be further developed as a potential treatment for certain atypical hemolytic uremic syndrome patients or those with other diseases characterized by excessive complement activity.

Demyelination detection in CSF based on electrochemical monitoring of myelin basic protein in comparison between Apta vs. Immuno sensing strategies

Multiple sclerosis (MS) is a recurrent inflammatory, demyelinating disease of the white matter in central nervous system (CNS). The number of MS patients is increasing, but the diagnostic process is still quite difficult, costly and requires combination of several methods. Myelin basic protein (MBP) makes up to 30 % of the myelin in CNS. It is known that MBP is released into the cerebrospinal fluid (CSF) as MS bioindicator. Herein, myelin specific DNA aptamer earlier developed for possible therapeutic purposes and anti-MBP antibody were applied as bioreceptors for MBP recognition on the same nanomodified sensor surfaces and their performances were compared. Biosensors were developed by using graphene oxide (GO) nanoparticles integrated onto pencil graphite electrodes (PGE) and bioreceptor molecules immobilized to create a bioactive layer for MBP binding. The measurements were run with electrochemical impedance spectroscopy (EIS). Selectivity of the biosensors was evaluated using human serum albumin (HSA). After optimization of binding parameters, biosensors were validated in artificial CSF. It was shown that LJM-5708 based aptasensor had LOD 0.65 ng/mL that was comparable to immunosensor LOD (0.36 ng/mL) in artificial CSF and showed its applicability in the clinical concentration range between 1 and 128 ng/mL.

Enhancing Target Detection: A Fluorescence-Based Streptavidin-Bead Displacement Assay.

Fluorescence-based aptasensors have been regarded as innovative analytical tools for the detection and quantification of analytes in many fields, including medicine and therapeutics. Using DNA aptamers as the biosensor recognition component, conventional molecular beacon aptasensor designs utilise target-induced structural switches of the DNA aptamers to generate a measurable fluorescent signal. However, not all DNA aptamers undergo sufficient target-specific conformational changes for significant fluorescence measurements. Here, the use of complementary 'antisense' strands is proposed to enable fluorescence measurement through strand displacement upon target binding. Using a published target-specific DNA aptamer against the receptor binding domain of SARS-CoV-2, we designed a streptavidin-aptamer bead complex as a fluorescence displacement assay for target detection. The developed assay demonstrates a linear range from 50 to 800 nanomolar (nM) with a limit of detection calculated at 67.5 nM and a limit of quantification calculated at 204.5 nM. This provides a 'fit-for-purpose' model assay for the detection and quantification of any target of interest by adapting and functionalising a suitable target-specific DNA aptamer and its complementary antisense strand.

Thieno[3,2-b]thiophene for the Construction of Far-Red Molecular Rotor Hemicyanines as High-Affinity DNA Aptamer Fluorogenic Reporters.

The construction of far-red fluorescent molecular rotors (FMRs) is an imperative task for developing nucleic acid stains that have superior compatibility with cellular systems and complex matrices. A typical strategy relies on the methine extension of asymmetric cyanines, which unfortunately fails to produce sensitive rotor character. To break free from this paradigm, we have synthesized far-red hemicyanines using a dimethylamino thieno[3,2-b]thiophene donor. The resultant probes, designated as ATh2Ind and ATh2Btz, possess excitation maxima (λmax) of >600 nm and have been rigorously characterized by NMR, electrochemistry, and computational methods. The dyes possess alternating charge patterns like indodicarbocyanine (Cy5), but with twisted intramolecular charge transfer (TICT) rotational barriers at 60°, akin to the classical FMR thiazole orange (TO1). ATh2Btz also displays cyanine characteristics, enhancing its response upon binding to nucleic acids and allowing for efficient staining of cellular nuclei. When binding to the DNA aptamer for quinine (MN4), ATh2Btz exhibits a Kd of 17 nM, a 660-fold light-up response, brightness (Φfl x εmax) of ∼37,000 M-1cm-1, and λex/λem of 655/677 nm. The resulting far-red DNA-based MN4-ATh2Btz platform has been termed "pomegranate."

AptBCis1, An Aptamer-Cisplatin Conjugate, Is Effective in Lung Cancer Leptomeningeal Carcinomatosis.

Treatment of lung cancer leptomeningeal carcinomatosis (LM) remains challenging partly due to the biological nature of the blood-brain barrier (BBB). Cisplatin has limited effects on LM, and it is notorious for neurotoxicity. Aptamers are small oligonucleotides considered as antibody surrogates. Here we report a DNA therapeutics, AptBCis1. AptBCis1 is a cisplatin-conjugated, BBB-penetrating, and cancer-targeting DNA aptamer. Its backbone, AptB1, was identified via in vivo SELEX using lung cancer LM orthotopic mouse models. The AptB1 binds to EAAT2, Nucleolin, and YB-1 proteins. Treatment with AptBCis1 1 mg/kg (equivalent to cisplatin 0.35 mg/kg) showed superior tumor suppressive effects compared to cisplatin 2 mg/kg in mice with lung cancer LM diseases. The cerebrospinal fluid platinum concentration in the AptBCis1 group was 10% of that in the cisplatin group. The data suggested the translational potential of AptBCis1 in lung cancer with LM and in cancers in which platinum-based chemotherapy remains as the standard of care.

In Silico Analysis of Binding Sites for a Novel ssDNA Aptamer Specific to Verrucarin A and Detection in Dust Extracts.

An aptamer is a single-stranded oligonucleotide that serves as a chemical antibody with a high specificity and binding affinity that can recognize a wide range of molecules. Effective modification and truncation of aptamers can enhance their binding affinities to particular targets while also broadening their application for uses, such as biosensors. However, a conventional trial-and-error methodology hinders this process. Herein, we demonstrate an in silico method to elucidate the binding site of single-stranded DNA aptamer specific to verrucarin A, a mycotoxin produced by molds in indoor buildings that causes adverse effects in living organisms. The novel ssDNA aptamer exhibited a binding affinity of 29.5 nM, demonstrating a relatively strong affinity compared to those of previously reported typical aptamers for small molecules. Furthermore, the selected aptamer was highly specific toward verrucarin A among structurally related mycotoxins (i.e., verrucarol and zearalenone). The specific binding site of the aptamer predicted via molecular dynamics and molecular docking simulations was highly consistent with the results observed via truncation, single base mutation, and circular dichroism experiments. The fluorescence assay revealed limits of detection and quantification of 4.1 and 12 nM for the aptamer, respectively. Comparing our developed aptasensor with LC-MS/MS methodology revealed that it could detect verrucarin A levels in phosphate-buffered saline and dust extracts with robust precision and consistency. Our findings provide insight for future studies exploring interaction mechanisms with intended targets and practical sensing applications, such as point-of-care detection of verrucarin A.

Streamlining RNA Aptamer Selection via Unique Molecular Identifiers and High-Throughput Sequencing.

Aptamers are valuable tools for applications such as cell imaging, drug delivery, and therapeutics. RNA aptamers, in particular, exhibit complex structural diversity and flexibility, affording higher affinity and specificity, broader target recognition, and easier chemical modification compared with DNA aptamers. However, traditional selection methods for RNA aptamers are time-consuming and involve numerous rounds of screening, thus limiting their widespread application. To overcome this challenge, we propose an efficient truncated selection approach termed ID-SELEX. This method incorporates a molecular identification marker whereby each template is labeled with a unique molecular identifier, or UMI. Such incorporation helps mitigate biases introduced by multiple polymerase chain reaction (PCR) amplification during high-throughput sequencing, ensuring accurate identification of aptamer candidates. Utilizing ID-SELEX, we successfully identified a panel of high-quality aptamers targeting the human colon cancer cell line HCT-8 in just 2 rounds of selection. Furthermore, we demonstrated the versatility of this strategy by selecting 6 RNA aptamers targeting mouse myoblast cell line C2C12 with only one round of selection. In summary, RNA aptamer selection based on ID-SELEX utilizes high-throughput sequencing and UMI labeling to enable the rapid screening of RNA aptamers across human and murine cell lines. As such, ID-SELEX has the potential to facilitate RNA aptamer discovery, providing a novel molecular tool for biomedical research, clinical applications, and precision medicine.

Ratiometric electrochemical and impedimetric dual-mode aptasensor based on thionine-functionalized Ti3C2Tx MXene/Pt and Au nanoparticle composites for reliable detection of aflatoxin B1

Rapid and reliable detection of aflatoxin B1 (AFB1) is critical in public health, food safety and environmental control. Herein, a ratiometric electrochemical (EC) and electrochemical impedance spectroscopy (EIS) dual-mode aptasensing platform based on thionine-functionalized Ti3C2Tx MXene/Pt and Au nanoparticle composites (MXene@Thi/PtAuNPs) was constructed for accurate and reliable detection of AFB1. The MXene@Thi/PtAuNPs composites were prepared by a facile and mild approach. The electroactive molecule Thi embedded in MXene could not only inhibit the aggregation of MXene nanosheets, but also act as an internal reference probe to form a ratiometric sensing strategy. The decoration of Pt and Au nanoparticles can further effectively enhance the conductivity and catalytic activity of the composites. The MXene@Thi/PtAuNPs composites were then served as a support to sequentially assemble hairpin DNA (hDNA) and ferrocene-labelled AFB1 aptamer (Fc-Apt) to construct the dual-mode sensor. The developed dual-mode sensor with both ratiometric EC detection (based on IThi/IFc) and EIS detection (based on Ret) can mutually verify the detection results obtained by two modes, offering more accurate and reliable results, which enabled sensitive and reliable AFB1 detection in the concentration range of 10.0 pg mL−1-30.0 ng mL−1 (ratiometric EC mode) and 3.0 pg mL−1-30.0 ng mL−1 (EIS mode), respectively. The sensing platform also demonstrated favorable selectivity, reproducibility and stability, and satisfactory applicability in corn sample, showing great potential in the sensing of mycotoxins in agricultural products.

A compact stem-loop DNA aptamer targets a uracil-binding pocket in the SARS-CoV-2 nucleocapsid RNA-binding domain.

SARS-CoV-2 nucleocapsid (N) protein is a structural component of the virus with essential roles in the replication and packaging of the viral RNA genome. The N protein is also an important target of COVID-19 antigen tests and a promising vaccine candidate along with the spike protein. Here, we report a compact stem-loop DNA aptamer that binds tightly to the N-terminal RNA-binding domain of SARS-CoV-2 N protein. Crystallographic analysis shows that a hexanucleotide DNA motif (5'-TCGGAT-3') of the aptamer fits into a positively charged concave surface of N-NTD and engages essential RNA-binding residues including Tyr109, which mediates a sequence-specific interaction in a uracil-binding pocket. Avid binding of the DNA aptamer allows isolation and sensitive detection of full-length N protein from crude cell lysates, demonstrating its selectivity and utility in biochemical applications. We further designed a chemically modified DNA aptamer and used it as a probe to examine the interaction of N-NTD with various RNA motifs, which revealed a strong preference for uridine-rich sequences. Our studies provide a high-affinity chemical probe for the SARS-CoV-2 N protein RNA-binding domain, which may be useful for diagnostic applications and investigating novel antiviral agents.

Ligand-Induced Folding in a Dopamine-Binding DNA Aptamer.

Aptamers are often employed as molecular recognition elements in the development of different types of biosensors. Many of these biosensors take advantage of the aptamer having a ligand-induced structure-formation binding mechanism. However, this binding mechanism is poorly understood. Here we use isothermal titration calorimetry, circular dichroism spectroscopy and NMR spectroscopy to study the binding and ligand-induced structural change exhibited by a dopamine-binding DNA aptamer. We analysed a series of aptamers where we shorten the terminal stem that contains the 5´and 3´termini of the aptamer sequence. All aptamers bind dopamine in an enthalpically driven process coupled with an unfavorable entropy. A general trend of the aptamer having a weaker binding affinity is observed as the terminal stem is shortened. For all aptamers studied, numerous signals appear in the imino region of the1H NMR spectrum indicating that new structure forms with ligand binding. However, it is only when this region of structure formation in the aptamer is brought close to the sensor surface that we obtain a functional electrochemical aptamer-based biosensor.

Selective quantification of estrogens in serum with aptamer-affinity and LC-MS/MS analysis

In the previous study, we developed an accurate and automated immunologic mass spectrometry (iMS) method for the simultaneous quantification of multiple steroid hormones by target capturing with monoclonal antibodies and LC-MS/MS analysis. However, antibodies are less accessible to a wide variety of low-molecular-weight analytes, which limited the application of iMS method. At the same time, multiple monoclonal antibodies needed also increased the complexity and cost of the iMS assay. In the present study, we developed an aptamer-affinity and LC-MS/MS analysis method with a class-specific aptamer for the selective enrichment and simultaneous determination of estrogens (estrone (E1) and estradiol (E2)) in human serum. The DNA aptamer was coupled to magnetic beads to enrich the target estrogens from serum sample after protein precipitation. The magnetic beads were then washed and eluted with acetonitrile solution, and targets were analyzed with LC-MS/MS. The sample preparation process of enrichment, washing and elution works in an automatic manner. Matrix effect was negligible as the high specificity of target recognition and enrichment by the aptamer. The aptamer-affinity assay for estrogen quantification was validated for sensitivity, linearity, accuracy and precision. The limit of detection (LOD) and quantification (LOQ) were0.01 ng/mLand0.02 ng/mL for E1 and E2, respectively. Satisfactory coefficients of variation (CVs) were obtained, with the intra-batch CVs of5.5 %-7.3 % and 5.2 %-6.0 % for E1 and E2, respectively, and inter-batch CVs of 3.8 %-10.0 % and 5.2 %-6.3 % for E1 and E2, respectively. Recoveries were in the range of99.1 %-107.0 % and 94.9 %-107.7 % for E1 and E2, respectively. Quantification results of 40 serum samples by the aptamer-affinity and solid-phase extraction (SPE) LC-MS/MS method showed good consistency, with the correlation coefficient of 0.93 and 0.98 for E1 and E2, respectively. Clinical application of the aptamer-affinity and LC-MS/MS method was further demonstrated for quantifying serum estrogen levels of 170 pregnant women at different gestational weeks.

Sandwich-Type Electrochemical Aptasensor with Supramolecular Architecture for Prostate-Specific Antigen.

A novel sandwich-type electrochemical aptasensor based on supramolecularly immobilized affinity bioreceptor was prepared via host-guest interactions. This method utilizes an adamantane-modified, target-responsive hairpin DNA aptamer as a capture molecular receptor, along with a perthiolated β-cyclodextrin (CD) covalently attached to a gold-modified electrode surface as the transduction element. The proposed sensing strategy employed an enzyme-modified aptamer as the signalling element to develop a sandwich-type aptasensor for detecting prostate-specific antigen (PSA). To achieve this, screen-printed carbon electrodes (SPCEs) with electrodeposited reduced graphene oxide (RGO) and gold nanoferns (AuNFs) were modified with the CD derivative to subsequently anchor the adamantane-modified anti-PSA aptamer via supramolecular associations. The sensing mechanism involves the affinity recognition of PSA molecules on the aptamer-enriched electrode surface, followed by the binding of an anti-PSA aptamer-horseradish peroxidase complex as a labelling element. This sandwich-type arrangement produces an analytical signal upon the addition of H2O2 and hydroquinone as enzyme substrates. The aptasensor successfully detected the biomarker within a concentration range of 0.5 ng/mL to 50 ng/mL, exhibiting high selectivity and a detection limit of 0.11 ng/mL in PBS.

A-348 Portable aptamer-based home monitoring system for blood phenylalanine measurement

Abstract Background Aptatek BioSciences, Inc. has developed a home monitoring tool for blood phenylalanine (phe) levels. The Aptatek system integrates a proprietary aptamer assay approach with a user-friendly handheld, smartphone-enabled test platform. PKU (phenylketonuria), is an inborn error of phenylalanine (Phe) metabolism If undiagnosed or untreated, phe accumulates in all body tissues, including the blood and brain, where it is especially neurotoxic and when untreated it can cause significant cognitive impairment and neurological defects. PKU management targets maintaining blood Phe concentration within the therapeutic range (120-360uM) to avoid severe neurological sequelae, mainly through nutritional therapy. Methods PheCheck™ includes a portable hand-held reader, software accessible as a mobile phone application, and a disposable single-use lateral flow cassette, blood collection, cap, and buffer chamber. PheCheck™ detects phe by binding of the phe in a small blood sample using small molecule-specific DNA aptamers. A patient (or caregiver) collects 5μl of capillary blood using a lancet to lance the fingertip and use the collection cap to collect the specimen. Once collected, the specimen is placed into the buffer chamber where the blood is diluted and processed in preparation for a lateral flow assay. The buffer chamber is placed on top of a lateral flow cassette to release the solution into the cassette. The lateral flow cassette is inserted into a small electronic reader after specimen incubation. The reader will detect a fluorescent signal from the strip and report the quantitative Phe concentration present in the specimen to the integrated mobile phone application. The reader has a simple design with a single operating push button, USB data connection port, and replaceable battery compartment. The reader reads the output of the lateral flow cassette and reports the result to a Smartphone app. The app is designed to either display the quantitative results or store the results without displaying the quantitative value. Results Twelve patients were trained on the PheCheck system and observed using the system for self-testing. Patients also prepared dried blood spot cards for comparative testing using LC-mass spectrometry. Patients were asked to return to the clinic within two weeks to retest. The blood phenylalanine levels measured by the PheCheck system were within targeted standard deviation of the dried blood spots demonstrating the feasibility of portable home-based testing for routine monitoring of blood phenylalanine levels in phenylketonuria patients. Such a portable system would enable real time monitoring and adjustment of diet or therapy for chronic diseases such as PKU. Conclusions Aptatek has developed a DNA aptamer based portable monitor for measuring blood phenylalanine levels. The system quantitatively measures phenylalanine from a 5-microliter finger stick blood sampler. Aptamer-based detection of phenylalanine provides reliable quantitation across a wide clinical concentration range and encouraging performance relative to gold standard testing of venous blood draw or dried blood spots. Analysis of samples from patients on Palynziq indicate that the PheCheck system could provide more reliable testing than venous blood draws. The system shows strong promise for routine home monitoring of blood phe levels by patients.

Synthesis and in vitro study of surface-modified and anti-EGFR DNA aptamer -conjugated chitosan nanoparticles as a potential targeted drug delivery system

Nowadays, finding effective approaches for cancer therapy is one of the significant issues related to human health all over the world. Hence, in this research, we designed and synthesized a novel targeted DDS based on surface-modified chitosan (CS) for the effective delivery of noscapine (NO). As the surface of CS nanoparticles was firstly modified with carboxyl groups and followed by covalent conjugation of DNA-aptamer (Ap) as targeting and receptor blocker agent. Secondly, NO, as a chemotherapeutic agent, was loaded into prepared nano-complex and synthetics were effectively characterized via various analytical devices, including FT-IR, 1H NMR, DLS, Zeta potential analyzer, TGA, TEM, and SEM to verify quality and quantity of synthetics. Drug loading was obtained about 25 % and sustained drug release was observed for nano-complex at different pHs. Then, the cell viability assay was performed on MCF-7 (as breast cancer cell) and HFF-1 (as normal cell) cell lines to investigate cancer cell inhibition potency of nano-complex. Cell viability of cancer cells was 19.84 ± 1.87 % (for C-CS-Ap-NO) and 75.43 ± 2.64 % (for C-CS-Ap) after 72 h of treatment with 400 nM concentration. These results have been confirming the excellent potency of synthesized novel nano-complex as practical DDS in cancer therapy.

A smartphone-assisted ultrasensitive colorimetric aptasensor based on DNA-encoded porous MXene nanozyme for visual detection of okadaic acid

The smartphone-assisted ultrasensitive colorimetric aptasensor based on DNA-encoded porous Ti3C2 nanozyme (Apt-P-Ti3C2) was exploited for real-time detection of OA. Porous Ti3C2 (P-Ti3C2) MXene with outstanding peroxidase-like activities were crafted using microwave combustion, facilitating the efficient catalysis of chromogenic substrate oxidation by H2O2. The integration of a considerable number of unsaturated Ti center edges and residual Mn2+ within the single-layer porous Ti3C2 framework augmented the adsorption capacity of DNA aptamer, thereby yielding a heightened catalytic efficacy of P-Ti3C2 nanoparticles. The enhanced catalytic activity of P-Ti3C2 can be partially diminished through specific recognition of OA. Concurrently, a smartphone platform was integrated for signal reading based on the colorimetric sensing strategy. The smartphone-based biosensor exhibited a reliable and ultrasensitive capability for OA detection with the detection limit of 0.38 ng·mL−1. It is anticipated that the developed smartphone-based biosensing platform can provide a prospective ultrasensitive detection method for marine algal toxin in food analysis.

A disposable paper-based electrochemical biosensor for detection of aflatoxin B1 based on a structure-switching aptamer

Aflatoxin B1 (AFB1) is a highly toxic mycotoxin that readily contaminates major food crops. This study presents a novel ratiometric electrochemical paper-based aptasensor for AFB1 detection that utilizes a structure-switching aptamer. The sensor detects AFB1 by folding the DNA aptamer, reducing the electron transfer efficiency between the methylene blue (MB) molecules attached to the DNA and the electrode surface. An inner reference element modified with ferrocene (Fc) is co-assembled on the electrode surface of the paper-based biosensor to enhance the accuracy of AFB1 detection. In the presence of target AFB1, a folded target–aptamer complex is formed, distancing the MB molecules from the electrode and generating a low current signal in a differential pulse voltammetry mode. The ratio of oxidation currents for MB and Fc serves as the metric for monitoring AFB1 levels. The detection range spans from 20.0 to 1000.0 ng mL−1, with a limit of detection of 7.6 ng mL−1. The paper-based aptasensor exhibits excellent specificity and stability. Additionally, its high reliability and applicability are validated by the strong correlation observed between the sensor results and the results obtained using UPLC−MS/MS analysis of real samples. This study offers a low-cost, readily available approach for portable detection of foodborne hazards.

Single-Molecule adenosine detection and chiral selectivity by DNA aptamer conformational changes using α-Hemolysin nanopore

Nucleic acid aptamers, which are short single-stranded RNA or DNA molecules, undergo conformational changes upon recognizing small molecules. However, their structural characterization is challenging due to the flexibility of single-stranded oligonucleotides. Nanopores provide a sensitive method for single-molecule analysis of molecular conformational changes as they transport through the pore. In this study, we employed α-hemolysin (α-HL) nanopore with high spatiotemporal resolution to investigate the conformational changes of DNA aptamer (ADO-23) upon binding to adenosine (Ado) molecules. Unlike the events generated by the aptamer alone, the DNA-Ado complex produced two distinct new characteristic events, indicating the formation of two unique secondary structures. By analyzing current events, the structures formed by the DNA-Ado complex were speculated to be hairpin DNA and G-quadruplex (G4) DNA. Furthermore, we demonstrated the potential of the aptamer as a chiral selector within the nanopore. The results showed that the aptamer specifically bound to D-Ado and not to L-Ado. Finally, we realized specific and sensitive detection of small molecule Ado by α-HL pore, with a detection limit as low as 10.5 nM, and successfully applied it to the detection of real human serum samples. The nanopore platform provides a powerful tool for studying small molecule-biomolecule conformational changes, and we constructed sensors for detecting adenosine through the aptamer. This work also offers a promising new approach to the recognition of enantiomers at the single-molecule level.