Selection of a Structure-Switching Aptamer for the Specific Methotrexate Detection

Amplified Assembly of G-Quadruplex-Decorated DNA Network Nanostructure toward AIE Signaling-Based Sensitive Biosensing

Aggregation-induced emission (AIE) has offered a promising approach for developing low-background fluorescent methods; however, its applications often suffer from complex probe synthesis and poor biocompatibility. Herein, a novel AIE biosensing method for kanamycin antibiotic assays was developed by utilizing a DNA network nanostructure assembled from an aptamer recognition reaction to capture a large number of tetraphenylethylene fluorogen-labeled signal DNA (DTPE) probes. Due to the excellent hydrophilicity of the oligonucleotides, DTPE exhibited excellent water solubility without obvious background signal emission. Based on an ingenious nucleotide design, an abundance of G-quadruplex blocks neighboring the captured DTPE were formed on the DNA nanostructure. Because of the greatly restricted free motion of DTPE by this unique nanostructure, a strong AIE fluorescence signal response was produced to construct the signal transduction strategy. Together with target recycling and rolling circle amplification-based cascade nucleic acid amplification, this method exhibited a wide linear range from 75 fg mL-1 to 1 ng mL-1 and a detection limit down to 24 fg mL-1. The excellent analytical performance and effective manipulation improvement of the method over previous approaches determine its promising potential for various applications.

Development of Better Aptamers: Structured Library Approaches, Selection Methods, and Chemical Modifications

Systematic evolution of ligands by exponential enrichment (SELEX) has been used to discover thousands of aptamers since its development in 1990. Aptamers are short single-stranded oligonucleotides capable of binding to targets with high specificity and selectivity through structural recognition. While aptamers offer advantages over other molecular recognition elements such as their ease of production, smaller size, extended shelf-life, and lower immunogenicity, they have yet to show significant success in real-world applications. By analyzing the importance of structured library designs, reviewing different SELEX methodologies, and the effects of chemical modifications, we provide a comprehensive overview on the production of aptamers for applications in drug delivery systems, therapeutics, diagnostics, and molecular imaging.

An optical sensing platform for the detection of anti-cancer drugs and their cytotoxicity screening using a highly selective phosphorene-based composite

Monitoring therapeutic drugs and their elimination is crucial because they may cause severe side effects on the human body. Methotrexate (MTX) is a widely used anti-cancer drug, which is highly expensive, and the detection of unwanted overdoses of MTX using traditional procedures is time-consuming and involves complex instrumentation. In this work, we have developed a nanocomposite material using phosphorene, cystine, and gold (Ph-Cys-Au) that shows excellent optical properties. This nanocomposite can be used as an optical sensing platform for the detection of MTX in the range 0-260 μM. The synthesized sensing platform is very sensitive, selective, and cost-effective for the detection of MTX. Ph-Cys-Au can effectively detect MTX in aqueous media with a limit of detection (LOD) of about 0.0266 nM (for a linear range of 0-140 μM) and 0.0077 nM (for a linear range of 160-260 μM). The nanocomposite is equally selective for real samples, such as human blood serum (HBS) and artificial urine (AU) with a LOD of 0.0914 nM and 0.0734 nM, respectively. We have also determined the limit of quantification (LOQ); the LOQ values for the aqueous media were 0.0807 nM (for a linear range of 0-140 μM) and 0.0234 nM (for a linear range of 160-260 μM), whereas, the values for HBS and AU were around 0.2771 nM and 0.2226 nM, respectively. Moreover, the nanocomposite also provides a feasible platform for cytotoxicity screening in cancerous cells (Caco-2 cell lines) and non-cancerous cells (L-929 cell lines).

Fluorescent immunochromatographic test strip for therapeutic drug monitoring of methotrexate with high sensitivity and wide dynamic range

As a front-line chemotherapeutic drug for maintenance and consolidation therapy, methotrexate (MTX) has widely been applied to treat various tumors and some inflammatory diseases. However, because of its severe toxicity ascribed to low selectivity, it is necessary to monitor therapeutic drugs in high-dose MTX therapeutic regimens to ensure treatment safety. In this work, we developed a fluorescent immunochromatographic test strip (FITS) for monitoring MTX by employing time-resolved fluorescent microspheres as signal probes. With a competitive immunoassay mode, the FITS for MTX shows a super-wide dynamic range of 10 pM-10 μM, covering the entire clinical therapeutic concentration range of MTX. Therapeutic drug monitoring of MTX can be achieved within 7 min with high specificity, facilitating the timely rescue of drug poisoning led by high-dose MTX treatment. The method was employed for monitoring MTX in the spiked human serum, urine, and milk, showing acceptable recoveries ranging from 94.0 to 110.0%. The established FITS has been applied to MTX detection in serum obtained from high-dose MTX treatment. The results from FITS and enzyme multiplied immunoassay technique showed no significant difference, suggesting its reliability for usage in real biological samples. The device shows promise in point-of-care therapeutic drug monitoring for resource-limited countries and institutes, which significantly facilitates overcoming the lag time between sampling and results.

Aptamer/proximity hybridization-based label-free and highly sensitive colorimetric detection of methotrexate via polymerization/nicking recycling amplifications

Methotrexate (MTX) is one of the commonly used therapeutic drugs for treating various tumors and autoimmune diseases. However, high dose usage of MTX may cause severe side effects and the monitoring of MTX is therefore critical. By coupling a new MTX aptamer-based proximity hybridization with polymerization/nicking reaction (PNR) recycling amplifications, we develop here a sensitive and label-free colorimetric approach for MTX detection in diluted human serums. The MTX molecules can bind and switch the conformation of aptamers in the DNA duplex probes to initiate subsequent proximity hybridization-induced PNR recycling processes for the yield of a great deal of G-quadruplexes with the assistance of two single-stranded assistant DNA sequences. Hemin subsequently combines with these G-quadruplexes to produce lots of G-quadruplex/hemin horseradish peroxidase (HRP) mimicking DNAzymes, which then catalyze intensified color transition of the substrate solution to exhibit highly magnified UV-Vis absorption for label-free and ultrasensitive detection of MTX at concentration as low as 5.66 nM in the range of 10 nM to 1 μM. High selectivity of the developed method also enables it to monitor low levels of MTX in diluted serum samples, which offers such a method enormous potentials for convenient and highly sensitive detection of other small molecule drugs for various clinical applications.

Terbium-triggered aggregation-induced emission of bimetallic nanoclusters for anticancer drugs sensing via the inner filter effect

The development of accurate and sensitive detection methods of anticancer drugs is of significant importance because they play vital roles in biological systems. In recent years, bimetallic nanoclusters (BMNCs) incorporating the advantages of two metals have gained more and more attention, and can be widely applied in sensing applications. In this work, for the first time, we designed a sensing platform based on terbium ion (Tb³⁺) triggered aggregation-induced emission (AIE) of BMNCs. Tb³⁺ hybrid glutathione (GS) protected Ag/Cu nanoclusters (Tb³⁺@GS-AgCuNCs) were facilely fabricated according to the complexation reaction between Tb³⁺ and the carboxyl group of GS. Due to the inner filter effect (IFE), the fluorescence of Tb³⁺@GS-AgCuNCs decreased significantly in the presence of anticancer drugs with 6-thioguanine and methotrexate as representatives. In addition, the sensing platform was applied to monitor 6-thioguanine and methotrexate in real serum samples, indicating that it has great potential in anticancer drugs related applications.

Real-Time, Seconds-Resolved Measurements of Plasma Methotrexate In Situ in the Living Body

Dose-limiting toxicity and significant patient-to-patient pharmacokinetic variability often render it difficult to achieve the safe and effective dosing of drugs. This is further compounded by the slow, cumbersome nature of the analytical methods used to monitor patient-specific pharmacokinetics, which inevitably rely on blood draws followed by post-facto laboratory analysis. Motivated by the pressing need for improved "therapeutic drug monitoring", we are developing electrochemical aptamer-based (EAB) sensors, a minimally invasive biosensor architecture that can provide real-time, seconds-resolved measurements of drug levels in situ in the living body. A key advantage of EAB sensors is that they are generalizable to the detection of a wide range of therapeutic agents because they are independent of the chemical or enzymatic reactivity of their targets. Three of the four therapeutic drug classes that have, to date, been shown measurable using in vivo EAB sensors, however, bind to nucleic acids as part of their mode of action, leaving open questions regarding the extent to which the approach can be generalized to therapeutics that do not. Here, we demonstrate real-time, in vivo measurements of plasma methotrexate, an antimetabolite (a mode of action not reliant on DNA binding) chemotherapeutic, following human-relevant dosing in a live rat animal model. By providing hundreds of drug concentration values, the resulting seconds-resolved measurements succeed in defining key pharmacokinetic parameters, including the drug's elimination rate, peak plasma concentration, and exposure (area under the curve), with unprecedented 5 to 10% precision. With this level of precision, we easily identify significant (>2-fold) differences in drug exposure occurring between even healthy rats given the same mass-adjusted methotrexate dose. By providing a real-time, seconds-resolved window into methotrexate pharmacokinetics, such measurements can be used to precisely "individualize" the dosing of this significantly toxic yet vitally important chemotherapeutic.

Machine Learning Directed Aptamer Search from Conserved Primary Sequences and Secondary Structures

Computer-aided prediction of aptamer sequences has been focused on primary sequence alignment and motif comparison. We observed that many aptamers have a conserved hairpin, yet the sequence of the hairpin can be highly variable. Taking such secondary structure information into consideration, a new algorithm combining conserved primary sequences and secondary structures is developed, which combines three scores based on sequence abundance, stability, and structure, respectively. This algorithm was used in the prediction of aptamers from the caffeine and theophylline selections. In the late rounds of the selections, when the libraries were converged, the predicted sequences matched well with the most abundant sequences. When the libraries were far from convergence and the sequences were deemed challenging for traditional analysis methods, this algorithm still predicted aptamer sequences that were experimentally verified by isothermal titration calorimetry. This algorithm paves a new way to look for patterns in aptamer selection libraries and mimics the sequence evolution process. It will help shorten the aptamer selection time and promote the biosensor and chemical biology applications of aptamers.

Ultrasensitive therapeutic drug monitoring of methotrexate by a structure-switching aptamer with cascade primer exchange reaction

As a folate antagonist, methotrexate (MTX) has been widely used in clinics with good effects on various tumors and inflammatory diseases. While the optimum dosage and total body clearance of MTX usually varies between individuals and even low-dose MTX has side effects, high-dose MTX may cause life-threatening side effects. Therefore, a convenient and simple method toward MTX sensing is highly demanded. Herein, we report a highly sensitive and selective method for therapeutic drug monitoring (TMD) of MTX by integrating a highly specific MTX-dependent structure-switching aptamer with a primer exchange reaction-based signal amplification technique. The detection limit is down to 1.7 nM with a linear range from 0.01 to 1 μM in buffer. More importantly, the sensing strategy can effectively detect MTX in a complex bio-environment with a linear response range from 0.05 to 2 μM and a LOD of 12.4 nM in 10% FBS and a range of 0.2 to 5 μM with a LOD of 63.73 nM in 10% whole blood. Considering the high sensitivity and selectivity and good performance in blood, the method reported herein paves a new avenue for the effective determination of MTX in clinics.

Discovery of a Highly Specific Anti-methotrexate (MTX) DNA Aptamer for Antibody-Independent MTX Detection

High-dose methotrexate (MTX) therapy is used to treat a wide variety of cancers such as leukemia and lymphoma, while the resulting high blood concentration of MTX faces a risk of life-threatening side effects, so it is essential to monitor the concentration carefully. Currently, the MTX concentration is measured using antibody-based kits in a clinical setting; however, the heterogeneity and batch-to-batch variation of antibodies potentially compromise the detection limit. Here, we developed MTX detection systems with chemically synthesizable homogeneous oligonucleotides. Microbead-assisted capillary electrophoresis (MACE)-SELEX against MTX successfully identified MS^mt7 with a similar level of specificity to anti-MTX antibodies within three rounds. The 3'-end of MS^mt7 was coupled to a peroxidase-like hemin-DNAzyme to construct a bifunctional oligonucleotide for MTX sensing, where MTX in 50% human serum was detected with a limit of detection (LoD) of 118 nM. Furthermore, amplifying the DNAzyme region with rolling circle amplification significantly improved the sensitivity with an LoD of 290 pM. Presented oligonucleotide-based MTX detection systems will pave the way for antibody-independent MTX detection with reliability and less cost in the laboratory and the clinic.

MoS2 quantum dots as fluorescent probe for methotrexate detection

Herein, we developed a unique fluorescence biosensor for methotrexate assay based on MoS₂ quantum dots, which were synthesized in one step using sodium molybdate and cysteine as raw materials. The fluorescence of MoS₂ QDs could be quenched when encountered with methotrexate, which was attributed to the inner filter effect (IFE). Furthermore, this present IFE-based method showed the linearity between the MoS₂ QDs fluorescence intensity and the methotrexate concentration in the range of 0.05-1 μM with the LOD of 42 nM. The practical applicability of this strategy was successfully demonstrated by detecting methotrexate in real samples. Results indicated that the proposed method could be a promising sensing platform for methotrexate analysis.

Rapid nanomolar detection of methamphetamine in biofluids via a reagentless electrochemical aptamer-based biosensor

The availability of sensing platforms able to rapidly measure abused drugs directly in biological fluids in a single step would allow performing drugged driving screening on the site. The achievement of this goal is extremely important for preventing and controlling drug abuse and crime incidence. Motived by this, we constructed a simple, cost-effective and reagentless electrochemical aptamer-based (EAB) sensor with methamphetamine (MAMP) as the target molecule. This EAB sensor produced a nanomolar level of detection accuracy in unprocessed or minimally processed bio-samples. Specifically, circular dichroic spectrum was used to confirm that the truncated aptamer from the original sequence would undergo large binding-induced conformational changes. We then engineered the aptamer to work in the EAB platform and the resulting sensor enabled sensitive and specific detection of MAMP with the detection limit of 30 nM in undiluted serum, 50 nM in undiluted urine and 20 nM in 50% saliva. The sensor has good recovery rate, implying this method has good reliability and repeatability. The detection limit is far below the clinical detection threshold, it would be hopefully used for preliminary screening of drugged driving in real world.

Aptamer-engineered extended-gate field-effect transistor device for point-of-care therapeutic drug monitoring

A portable point-of-care testing (POCT) device based on an aptamer-engineered extended-gate field-effect transistor (EG-FET) was unveiled for therapeutic monitoring of the drug methotrexate.

Identification of a novel DNA aptamer that selectively targets lung cancer serum

Lung cancer is the leading cause of cancer-related deaths worldwide. Early diagnosis and treatment is critical to improving the 5 year survival rate of lung cancer. The identification of new options for early-stage diagnosis and therapy of lung cancer still represents a crucial challenge. Therefore, a new diagnostic method is urgently needed. In this study, we used a new modified SELEX, called serum-SELEX, to isolate aptamers that can specifically bind lung cancer serum, without any prior knowledge of their target. Among the obtained candidate aptamer sequences, Ap-LC-19 was identified as the optimal aptamer probe with the lowest dissociation constant (K d) value of 15 ± 8.6 nM and higher affinity assessed by qPCR. Furthermore, this molecule could be a suitable aptamer for lung cancer serum and could be used as a recognition element in aptamer-based biosensors for efficient early diagnosis of lung cancer or as an innovative tool for targeted therapy. In addition, we performed MALDI-TOF MS followed by secondary peptide sequencing MS analysis for the identification of the aptamer targeted proteins. CLEC3B could be useful biomarkers for early detection of lung cancer and in monitoring its evolution.

Recent Advances in Micro/Nanomaterial-Based Aptamer Selection Strategies

Aptamers are artificial nucleic acid ligands that have been employed in various fundamental studies and applications, such as biological analyses, disease diagnostics, targeted therapeutics, and environmental pollutant detection. This review focuses on the recent advances in aptamer discovery strategies that have been used to detect various chemicals and biomolecules. Recent examples of the strategies discussed here are based on the classification of these micro/nanomaterial-mediated systematic evolution of ligands by exponential enrichment (SELEX) platforms into three categories: bead-mediated, carbon-based nanomaterial-mediated, and other nanoparticle-mediated strategies. In addition to describing the advantages and limitations of the aforementioned strategies, this review discusses potential strategies to develop high-performance aptamers.