Theophylline detection in serum using a self-assembling RNA aptamer-based gold nanoparticle sensor

Advances of aptamer-based small-molecules sensors in body fluids detection

The field of aptamer-based sensing has evolved considerably over the past three decades. The aptamer sensor-based detection of small-molecule targets in body fluids is designed for real-time or rapid, low-cost, non- or minimally invasive tracking and diagnosis of human health status. It can be achieved by specifically monitoring biomarkers or metabolites excreted from various body fluids, including blood, urine, cerebrospinal fluid, saliva, ect. This article reviews a comprehensive collection of aptamer-based sensors for detecting small-molecule in various body fluids. A comparative analysis of aptamer features, emerging chemistry, advanced sensing materials, transduction techniques, and detection performance is conducted, and the strengths and pitfalls of each approach are discussed. Finally, the development process and application challenges of aptamer-based sensors in the detection of small-molecule in body fluids are presented and discussed.

A novel fluorescent aptasensor for the detection of theophylline based on cryonase-driven signal amplification strategy

In the study, we have developed an expedient and efficient method for the detection of theophylline based on the amplification of the signal intensity of fluorescence based on oxidized single-walled carbon nanohorns (oxSWCNHs)/cryonase. When theophylline was not present in the system, oxSWCNHs can adequately adsorb nucleic acid probes labeled by carboxyfluorescein (FAM). In the presence of theophylline, the nucleic acid probe forms the tertiary probe-theophylline complex, which detaches from the surface of the oxSWCNHs. Then, upon reaction with cryonase, the complex can release the FAM and theophylline into the next cycle. The fluorescence signal of the system exhibits a 1:N magnification, enabling quantitative detection of theophylline. The linear range was 30-150 ng/mL, and the limit of detection (LOD) was 6.04 ng/mL. At the same time, it can also be used to detect theophylline in mouse serum.

Improving aptamer performance: key factors and strategies

Aptamers are functional single-stranded oligonucleotide fragments isolated from randomized libraries by Systematic Evolution of Ligands by Exponential Enrichment (SELEX), exhibiting excellent affinity and specificity toward targets. Compared with traditional antibody reagents, aptamers display many desirable properties, such as low variation and high flexibility, and they are suitable for artificial and large-scale synthesis. These advantages make aptamers have a broad application potential ranging from biosensors, bioimaging to therapeutics and other areas of application. However, the overall performance of aptamer pre-selected by SELEX screening is far from being satisfactory. To improve aptamer performance and applicability, various post-SELEX optimization methods have been developed in the last decade. In this review, we first discuss the key factors that influence the performance or properties of aptamers, and then we summarize the key strategies of post-SELEX optimization which have been successfully used to improve aptamer performance, such as truncation, extension, mutagenesis and modification, splitting, and multivalent integration. This review shall provide a comprehensive summary and discussion of post-SELEX optimization methods developed in recent years. Moreover, by discussing the mechanism of each approach, we highlight the importance of choosing the proper method to perform post-SELEX optimization.

Bio-SCAN V2: A CRISPR/dCas9-based lateral flow assay for rapid detection of theophylline

Rapid, specific, and robust diagnostic strategies are needed to develop sensitive biosensors for small molecule detection, which could aid in controlling contamination and disease transmission. Recently, the target-induced collateral activity of Cas nucleases [clustered regularly interspaced short palindromic repeats (CRISPR)-associated nucleases] was exploited to develop high-throughput diagnostic modules for detecting nucleic acids and small molecules. Here, we have expanded the diagnostic ability of the CRISPR-Cas system by developing Bio-SCAN V2, a ligand-responsive CRISPR-Cas platform for detecting non-nucleic acid small molecule targets. The Bio-SCAN V2 consists of an engineered ligand-responsive sgRNA (ligRNA), biotinylated dead Cas9 (dCas9-biotin), 6-carboxyfluorescein (FAM)-labeled amplicons, and lateral flow assay (LFA) strips. LigRNA interacts with dCas9-biotin only in the presence of sgRNA-specific ligand molecules to make a ribonucleoprotein (RNP). Next, the ligand-induced ribonucleoprotein is exposed to FAM-labeled amplicons for binding, and the presence of the ligand (small molecule) is detected as a visual signal [(dCas9-biotin)-ligRNA-FAM labeled DNA-AuNP complex] at the test line of the lateral flow assay strip. With the Bio-SCAN V2 platform, we are able to detect the model molecule theophylline with a limit of detection (LOD) up to 2 μM in a short time, requiring only 15 min from sample application to visual readout. Taken together, Bio-SCAN V2 assay provides a rapid, specific, and ultrasensitive detection platform for theophylline.

Interactions between Caffeine, Theophylline and Derivatives with Gold Nanoparticles and Implications for Aptamer-Based Label-Free Colorimetric Detection

Caffeine, theophylline, and other methylxanthines have interesting biological activities and are consumed in high quantities globally, causing health and environmental concerns. Gold nanoparticles (AuNPs) have excellent optical properties for biosensor development, although little is known about the adsorption of these xanthine derivatives to AuNPs. In this work, interactions of these compounds with AuNPs were studied. Caffeine, theophylline and theobromine are adsorbed in a manner that affords protection against salt-induced aggregation, whereas xanthine and paraxanthine are adsorbed to destabilize and thus aggregate the AuNPs. Caffeine and theophylline are able to protect AuNPs starting at concentrations as low as 6.3 μM. Xanthine and paraxanthine induce significant AuNP aggregation at 5 μM. Adsorption was also confirmed by surface-enhanced Raman scattering (SERS). Using two recently selected DNA aptamers for caffeine and theophylline, the label-free colorimetric sensing method was tested; our results indicated that due to adsorption of these target molecules, this method cannot be directly used for their detection. The adsorption of these compounds to AuNPs may enable various detection methods such as SERS, but at the same time, it may complicate other detection methods.

A DNA Aptamer for Theophylline with Ultrahigh Selectivity Reminiscent of the Classic RNA Aptamer

Since the report of the RNA aptamer for theophylline, theophylline has become a key molecule in chemical biology for designing RNA switches and riboswitches. In addition, theophylline is an important drug for treating airway diseases including asthma. The classic RNA aptamer with excellent selectivity for theophylline has been used to design biosensors, although DNA aptamers are more desirable for stability and cost considerations. In this work, we selected DNA aptamers for theophylline, and all the top sequences shared the same binding motifs. Binding was confirmed using isothermal titration calorimetry and a nuclease digestion assay, showing a dissociation constant (K_d) around 0.5 μM theophylline. The Theo2201 aptamer can be truncated down to 23-mer while still has a K_d of 9.8 μM. The selectivity for theophylline over caffeine is around 250,000-fold based on a strand-displacement assay, which was more than 20-fold higher compared to the classic RNA aptamer. For other tested analogs, the DNA aptamer also showed better selectivity. Using the structure-switching aptamer sensor design method, a detection limit of 17 nM theophylline was achieved in the selection buffer, and a detection limit of 31 nM was obtained in 10% serum.

Nano optical and electrochemical sensors and biosensors for detection of narrow therapeutic index drugs

For the first time, a comprehensive review is presented on the quantitative determination of narrow therapeutic index drugs (NTIDs) by nano optical and electrochemical sensors and biosensors. NTIDs have a narrow index between their effective doses and those at which they produce adverse toxic effects. Therefore, accurate determination of these drugs is very important for clinicians to provide a clear judgment about drug therapy for patients. Routine analytical techniques have limitations such as being expensive, laborious, and time-consuming, and need a skilled user and therefore  the nano/(bio)sensing technology leads to high interest.

The method for integrating dual-color fluorescence colocalization and single molecule photobleaching technology on the theophylline sensing platform

• Smart usage of single molecule photobleaching technology and dual-color fluorescence colocalization is of critical importance for exploiting the sensing platform. Here, we provide the detailed protocols related to the article “A split aptamer sensing platform for highly sensitive detection of theophylline based on dual-color fluorescence colocalization and single molecule photobleaching” (published online by Biosensors and Bioelectronics) (Liu et al., 2020). The protocols contain: (1) how to clean the slides; (2) how to prepare the probe and detection sample; (3) Single molecule imaging; 4) Data processing by using the Image J. Finally, we used a simple model to confirm the feasibility of the method for integrating dual-color fluorescence colocalization and single molecule photobleaching technology on the theophylline sensing platform.

• A simple, ultrasensitive method for the detection of theophylline.

• The method is easily comprehensible.

• Both strategy formulation and data processing are simple, learnability, and highly reproducible.

Engineering and Application of a Myoglobin Binding Split Aptamer

Given that a split aptamer provides a chance for the development of a sandwich assay for targets with only one aptamer, it has received extensive attention in biosensing. However, due to the lack of binding mechanisms and reliable methods, there were still a few split aptamers that bind to proteins. In this work, cardiac biomarker myoglobin (Myo) was selected as a model, a new strategy of engineering split aptamers was explored with atomic force spectroscopy (AFM), and split aptamers against target protein could be achieved by choosing the optimal binding probability between split aptamers and target. Then, the obtained split aptamers were designed for Myo detection based on dynamic light scattering (DLS). The results demonstrated that the obtained split aptamers could be used to detect targets in human serum. The strategy of engineering split aptamers has the advantages of being intuitive and reliable and could be a general strategy for obtaining split aptamers.

Aptamer-Modified Nanoparticles in Medical Applications

Since aptamers have been selected against a broad range of target structures of medical interest and nanoparticles are available with diverse properties, aptamer-modified nanoparticles can be used in various diagnostic and therapeutic applications. While the aptamer is responsible for specificity and affinity of the conjugate, the nanoparticles' function varies from signal generation in diagnostic approaches to drug loading in drug delivery systems. Within this chapter different medical applications of aptamer-modified nanoparticles will be summarized and underlying principles will be described.

A split aptamer sensing platform for highly sensitive detection of theophylline based on dual-color fluorescence colocalization and single molecule photobleaching

A new split aptamer sensing platform is developed for highly sensitive and selective detection of theophylline based on single molecule photobleaching (SMPB) technique. The sensing system contains two probes. One is formed by one streptavidin and four biotinylated RNA fragments labelled with fluorescein isothiocyanate (FITC). Each biotinylated RNA fragment contains two repeating aptamer fragments. The other probe is the complementary aptamer fragment labelled with Cy5 dye. The existence of theophylline can trigger the first probe to bind as many as eight Cy5-labelled probes. The average combined number depends on the theophylline concentration and can be measured by SMPB technique. In the sensing system, the dual-color fluorescence colocalization is performed by the red fluorophore (Cy5) and green fluorophore (FITC), in which the red fluorophore is utilized for quantitative counting of photobleaching steps, while the green fluorophore serves as a counting reference to increase detection efficiency. On basis of the principle, an ultra-sensitive sensing platform of theophylline is created with a low limit of detection (LOD) of 0.092 nM. This work provides not only a highly sensitive method for theophylline detection but also a novel perspective for the applications of SMPB technology to construct biosensors.

7,8-Dihydro-8-oxoguanosine Lesions Inhibit the Theophylline Aptamer or Change Its Selectivity

Aptamers are attractive constructs due to their high affinity/selectivity towards a target. Here 7,8-dihydro-8-oxoguanosine (8-oxoG) has been used, due in part to its unique H-bonding capabilities (Watson-Crick or Hoogsteen), to expand the "RNA alphabet". Its impact on the theophylline RNA aptamer was explored by modifying its binding pocket at positions G11, G25, or G26. Structural probing, with RNases A and T1 , showed that modification at G11 leads to a drastic structural change, whereas the G25-/G26-modified analogues exhibited cleavage patterns similar to that of the canonical construct. The recognition properties towards three xanthine derivatives were then explored through thermophoresis. Modifying the aptamer at position G11 led to binding inhibition. Modification at G25, however, changed the selectivity towards theobromine (Kd ≈160 μm), with a poor affinity for theophylline (Kd >1.5 mm) being observed. Overall, 8-oxoG can have an impact on the structures of aptamers in a position-dependent manner, leading to altered target selectivity.

Identifying conformational changes of aptamer binding to theophylline: A combined biolayer interferometry, surface-enhanced Raman spectroscopy, and molecular dynamics study

Theophylline is a potent bronchodilator for the treatment of asthma, bronchitis, and emphysema. Its narrow therapeutic window (20-100 μM) demands that the blood concentration of theophylline be monitored carefully, which can be achieved by aptamer capture. Thus, an understanding of what occurs when aptamers bind to theophylline is critical for identifying a high-affinity and high-specificity aptamer, which improve the sensitivity and selectivity of theophylline detection. Consequently, there is an urgent need to develop a simple, convenient, and nondestructive method to monitor conformational changes during the binding process. Here, we report the determination of the affinity of a selected aptamer and theophylline via biolayer interferometry (BLI) experiments. Additionally, using surface-enhanced Raman spectroscopy (SERS), the conformational changes on theophylline-aptamer binding were identified from differences in the SER spectra. Finally, molecular dynamics (MD) simulations were used to identify the specific conformational changes of the aptamer during the binding process. Such a combined BLI-SERS-MD method provides an in-depth understanding of the theophylline-aptamer binding processes and a comprehensive explanation for conformational changes, which helps to select, design, and modify an aptamer with high affinity and specificity. It can also be used as a scheme for the study of other aptamer-ligand interactions, which can be applied to the detection, sensing, clinical diagnosis, and treatment of diseases.

The Theophylline Aptamer: 25 Years as an Important Tool in Cellular Engineering Research

The theophylline aptamer was isolated from an oligonucleotide library in 1994. Since that time, the aptamer has found wide utility, particularly in synthetic biology, cellular engineering, and diagnostic applications. The primary application of the theophylline aptamer is in the construction and characterization of synthetic riboswitches for regulation of gene expression. These riboswitches have been used to control cellular motility, regulate carbon metabolism, construct logic gates, screen for mutant enzymes, and control apoptosis. Other applications of the theophylline aptamer in cellular engineering include regulation of RNA interference and genome editing through CRISPR systems. Here we describe the uses of the theophylline aptamer for cellular engineering over the past 25 years. In so doing, we also highlight important synthetic biology applications to control gene expression in a ligand-dependent manner.

Facile caffeine electrochemical detection via electrodeposited Ag nanoparticles with modifier polymers on carbon paste sensor at aqueous and micellar media

The analysis and detection of caffeine (Caf) is very useful due to its widespread usage in several daily consumed beverages, food products, and pharmacological preparations with various physiological effects. The preparation of a newly electrodeposited Ag nanoparticles – cellulose acetate phthalate (CAP) – chitosan (Chit) modified carbon paste (ACCMCP) sensor for sensitive determination of Caf in 0.01 mol L−1 H3PO4 solution (pH 1.0–5.0) both in aqueous and micellar media (0.5 mmol L−1 SDS) was achieved. The interaction of Caf was monitored using electrochemical techniques such as cyclic voltammetry, differential pulse voltammetry, electrochemical impedance spectroscopy, and chronoamperometry, and surface characterization was carried out using X-ray diffraction, scanning electron microscope, and energy dispersive X-ray techniques. The linear detection range of Caf was between 4 and 500 μmol L−1 (r2 = 0.955) and the limit of detection obtained from the calibration plot was 0.252 μmol L−1. The sensor was applicable for detecting Caf in numerous real samples with recoveries from 98.03% to 101.60% without interference of any accompanying species, which ensures high method selectivity.

Gold Nanoparticles in Conjunction with Nucleic Acids as a Modern Molecular System for Cellular Delivery

Development of nanotechnology has become prominent in many fields, such as medicine, electronics, production of materials, and modern drugs. Nanomaterials and nanoparticles have gained recognition owing to the unique biochemical and physical properties. Considering cellular application, it is speculated that nanoparticles can transfer through cell membranes following different routes exclusively owing to their size (up to 100 nm) and surface functionalities. Nanoparticles have capacity to enter cells by themselves but also to carry other molecules through the lipid bilayer. This quality has been utilized in cellular delivery of substances like small chemical drugs or nucleic acids. Different nanoparticles including lipids, silica, and metal nanoparticles have been exploited in conjugation with nucleic acids. However, the noble metal nanoparticles create an alternative, out of which gold nanoparticles (AuNP) are the most common. The hybrids of DNA or RNA and metal nanoparticles can be employed for functional assemblies for variety of applications in medicine, diagnostics or nano-electronics by means of biomarkers, specific imaging probes, or gene expression regulatory function. In this review, we focus on the conjugates of gold nanoparticles and nucleic acids in the view of their potential application for cellular delivery and biomedicine. This review covers the current advances in the nanotechnology of DNA and RNA-AuNP conjugates and their potential applications. We emphasize the crucial role of metal nanoparticles in the nanotechnology of nucleic acids and explore the role of such conjugates in the biological systems. Finally, mechanisms guiding the process of cellular intake, essential for delivery of modern therapeutics, will be discussed.

Aptamer and nanomaterial based FRET biosensors: a review on recent advances (2014-2019)

Fluorescence resonance energy transfer, one of the most powerful phenomena for elucidating molecular interactions, has been extensively utilized as a biosensing tool to provide accurate information at the nanoscale. Numerous aptamer- and nanomaterial-based FRET bioassays has been developed for detection of a large variety of molecules. Affinity probes are widely used in biosensors, in which aptamers have emerged as advantageous biorecognition elements, due to their chemical and structural stability. Similarly, optically active nanomaterials offer significant advantages over conventional organic dyes, such as superior photophysical properties, large surface-to-volume ratios, photostability, and longer shelf life. In this report (with 175 references), the use of aptamer-modified nanomaterials as FRET couples is reviewed: quantum dots, upconverting nanoparticles, graphene, reduced graphene oxide, gold nanoparticles, molybdenum disulfide, graphene quantum dots, carbon dots, and metal-organic frameworks. Tabulated summaries provide the reader with useful information on the current state of research in the field. Graphical abstract Schematic representation of a fluorescence resonance energy transfer-based aptamer nanoprobe in the absence and presence of a given target molecule (analyte). Structures are not drawn to their original scales.

A fluorescence sensing platform of theophylline based on the interaction of RNA aptamer with graphene oxide

RNA, with a structure similar to DNA, should exhibit similar behaviors when it interacts with graphene. In this work, we designed a sensing platform of theophylline based on the interaction of an RNA aptamer with graphene oxide (GO) using the fluorescence as a sensing signal. Firstly, quantum dots (QDs) were modified with the selected ssRNA that can be used as an aptamer to recognize the theophylline. The fluorescence of QDs will be quenched in the presence of GO due to the noncovalent assembly between ssRNA aptamer and GO, leading to fluorescence resonance energy transfer (FRET) from QDs to GO, fluorescence "turn-off". Then, in the presence of theophylline, the ssRNA aptamer recognizes theophylline to form a dsRNA-theophylline complex. The weak affinity between the complex and GO makes QDs move away from the GO surface, leading to the fluorescence recovery of QDs, fluorescence "turn-on". Because of the high fluorescence quenching efficiency, unique structure of GO and specificity of the RNA aptamer, the proposed sensing platform exhibits high sensitivity and excellent selectivity for the determination of theophylline. The excellent performance of the sensor based on GO provides new opportunities for sensitive and selective detection of biorecognition events.

Nanomaterial based aptasensors for clinical and environmental diagnostic applications

Nanomaterials have been exploited extensively to fabricate various biosensors for clinical diagnostics and food & environmental monitoring. These materials in conjugation with highly specific aptamers (next-gen antibody mimics) have enhanced the selectivity, sensitivity and rapidness of the developed aptasensors for numerous targets ranging from small molecules such as heavy metal ions to complex matrices containing large entities like cells. In this review, we highlight the recent advancements in nanomaterial based aptasensors from the past five years also including the basics of conventionally used detection methodologies that paved the way for futuristic sensing techniques. The aptasensors have been categorised based upon these detection techniques and their modifications viz., colorimetric, fluorometric, Raman spectroscopy, electro-chemiluminescence, voltammetric, impedimetric and mechanical force-based sensing of a multitude of targets are discussed in detail. The bio-interaction of these numerous nanomaterials with the aptameric component and that of the complete aptasensor with the target have been studied in great depth. This review thus acts as a compendium for nanomaterial based aptasensors and their applications in the field of clinical and environmental diagnosis.

Polyadenine-mediated Immobilization of Aptamers on a Gold Substrate for the Direct Detection of Bacterial Pathogens

Nucleic acid aptamers have been widely used as synthetic probes for bioanalytical applications. Herein, we carried out a detailed study on the immobilization of a series of aptamers ranging from 37 to 88 bases, which are specific to either Escherichia coli (E. coli) or Staphylococcus aureus (S. aureus), on a planar gold substrate via a polyadenine-mediated immobilization method. The resultant surfaces were characterized by both surface plasmon resonance spectroscopy (SPR) and X-ray photoelectron spectroscopy. The results clearly show that the aptamer solution at a lower ionic strength gives rise to a higher lateral density of the aptamer when compared to that at a higher ionic strength. The SPR aptasensors are then employed for detecting their corresponding bacteria (i.e., E. coli and S. aureus, respectively). The data indicate that the SPR aptasensor with a higher density of aptamer exhibits a better capture of target bacteria.

Fluorescent Sensors for the Detection of Heavy Metal Ions in Aqueous Media

Due to the risks that water contamination implies for human health and environmental protection, monitoring the quality of water is a major concern of the present era. Therefore, in recent years several efforts have been dedicated to the development of fast, sensitive, and selective sensors for the detection of heavy metal ions. In particular, fluorescent sensors have gained in popularity due to their interesting features, such as high specificity, sensitivity, and reversibility. Thus, this review is devoted to the recent advances in fluorescent sensors for the monitoring of these contaminants, and special focus is placed on those devices based on fluorescent aptasensors, quantum dots, and organic dyes.

Carbon nanoparticle-protected RNA aptasensor for amplified fluorescent determination of theophylline in serum based on nuclease-aided signal amplification

A carbon nanoparticle (CNP) and Cryonase-aided method that realizes the amplified fluorescent detection of theophylline was proposed.

An aptamer nanopore-enabled microsensor for detection of theophylline

This paper reports an aptamer-based nanopore thin film sensor for detecting theophylline in the buffer solution and complex fluids including plant extracts and serum samples. Compared to antibody-based detection, aptamer-based detection offers many advantages such as low cost and high stability at elevated temperatures. Experiments found that this type of sensor can readily detect theophylline at a concentration as low as 0.05µM, which is much lower than the detection limit of current lab-based equipment such as liquid chromatography (LC). Experiments also found that the aptamer-based sensor has good specificity, selectivity, and reasonable reusability with a significantly improved dynamic detection range. By using the same nanopore thin film sensors as the reference sensors to further mitigate the non-specific binding effect, the theophylline in plant extracts and serum has been detected. Only a small amount (~1μL) of plant extracts or serum samples is required to measure theophylline. Its low cost and ease-of-operation make this type of sensor suitable for point-of-care application to monitor the theophylline level of patients in real time.

Colorimetric theophylline aggregation assay using an RNA aptamer and non-crosslinking gold nanoparticles

The authors are presenting a rapid method for the determination of theophylline using unique non-crosslinking gold nanoparticle (AuNP) aggregation. An RNA aptamer against theophylline is firstly split into two RNA fragments which then interact with bare AuNPs. The two RNA probes cause an enhancement of the salt tolerance of AuNPs. However, in the presence of theophylline, the RNA probes form a complex with theophylline so that less RNA probes are available to protect the AuNPs from salt-induced aggregation. Theophylline induced aggregation of AuNPs is accompanied by a color change from red to blue. The color change can be detected visually and via UV-vis absorptiometry by ratioing the absorbances at 650 and 520 nm. The ratio increases linearly in the 0.1 to 20 μM theophylline concentration range, with a 67 nM limit of detection. The method is highly sensitive and selective. Graphical abstract Single-stranded split RNA aptamers (R1 and R2) protect gold nanoparticles (AuNPs) from salt-induced non-crosslinking aggregation. After recognition of theophylline by the RNA probe, the unprotected AuNPs aggregate and undergo a color change from red to blue, and this is used to quantify the theophylline concentration.

A highly sensitive gold nanoparticle-based electrochemical aptasensor for theophylline detection

Theophylline is a common bronchodilator for the treatment of diseases like asthma, bronchitis and emphysema. However, it should be strictly used and monitored due to its toxicity when the concentration is above certain levels. In this work, an electrochemical biosensor for theophylline detection is proposed by recognition of RNA aptamer and gold nanoparticle (AuNP)-based amplification technique. First, RNA aptamer is splitted into two single-stranded RNA probes. One is hybridized with DNA tetrahedron and the resulted nanostructure is then immobilized onto a gold electrode; the other is modified on the surface of AuNPs which is also labeled with methylene blue (MB) as electrochemical species. The recognition process between the two RNA probes and theophylline causes the localization of AuNPs and the enrichment of MB on the electrode interface. A significant electrochemical response is thus generated which is related to the concentration of initial theophylline. This proposed aptasensor shows excellent sensitivity and selectivity which could also be applied in quantitatively detection of theophylline in serums samples.

Hand-in-hand RNA nanowire-based aptasensor for the detection of theophylline

Theophylline is a popular drug for many respiratory diseases. However, certain toxic side effects may be developed and the narrow safety range raises the demand for sensitive methods to constantly monitor theophylline levels. This study presents an electrochemical approach towards theophylline detection based on the recognition by split RNA aptamers. Target induced construction of hand-in-hand RNA nanowire on the electrode surface could further absorb silver nanoparticles (Ag NPs) as electrochemical species. When theophylline is not present, RNA probes are stable and their conformations remain unchanged. In contrast, theophylline is able to trigger the hairpin opening of RNA probe and subsequent self-assembly of RNA nanowire, which could be captured by DNA tetrahedron on the electrode interface. After further decorating Ag NPs on the nanowire, silver stripping current is measured to reveal initial theophylline concentration. The developed sensing strategy shows excellent specificity and sensitivity with the limit of detection of 50nM. Its practical utility is demonstrated by quantitative determination of theophylline levels in complex biological samples.

Bivalent Aptasensor Based on Silver-Enhanced Fluorescence Polarization for Rapid Detection of Lactoferrin in Milk

Here we report a novel type of bivalent aptasensor based on silver-enhanced fluorescence polarization (FP) for detection of lactoferrin (Lac) in milk powder with high sensitivity and specificity. The novel two split aptamers were obtained from the aptamer reported in our previous SELEX (systematic evolution of ligands by exponential enrichment) selection, and their minimal structural units were optimized on the basis of their affinity and specificity. Also, dual binding sites of split aptamers were verified. The bivalent aptamers were modified to be linked with signal-molecule fluorescein isothiocyanate (FITC) and enhancer silver decahedral nanoparticles (Ag₁₀NPs). The split aptamers could bind to different sites of Lac and assemble into a split-aptamers-target complex, narrowing the distance between Ag₁₀NPs and FITC dye. As a result, Ag₁₀NPs could produce a mass-augmented and metal-enhanced fluorescence (MEF) effect. In general, ternary amplification based on Ag₁₀NPs, split aptamers, and the MEF effect all contributed to the significant increase of FP values. It was proved that the sensitivity of this assay was about 3 orders of magnitude over traditional aptamer-based homogeneous assays with a detection limit of 1.25 pM. Furthermore, this design was examined by actual milk powder with rapid and high-throughout detection.

Multiparameter Particle Display (MPPD): A Quantitative Screening Method for the Discovery of Highly Specific Aptamers

Aptamers are a promising class of affinity reagents because they are chemically synthesized, thus making them highly reproducible and distributable as sequence information rather than a physical entity. Although many high-quality aptamers have been previously reported, it is difficult to routinely generate aptamers that possess both high affinity and specificity. One of the reasons is that conventional aptamer selection can only be performed either for affinity (positive selection) or for specificity (negative selection), but not both simultaneously. In this work, we harness the capacity of fluorescence activated cell sorting (FACS) for multicolor sorting to simultaneously screen for affinity and specificity at a throughput of 10⁷ aptamers per hour. As a proof of principle, we generated DNA aptamers that exhibit picomolar to low nanomolar affinity in human serum for three diverse proteins, and show that these aptamers are capable of outperforming high-quality monoclonal antibodies in a standard ELISA detection assay.

Generation of Biostable L-aptamers against Achiral Targets by Chiral Inversion of Existing D-aptamers

In this paper, based on reciprocal chiral substrate specificity, taking achiral molecules, ethanolamine (EA) and malachite green (MG) as two model targets, biostable L- DNA aptamers and L-RNA aptamers were generated respectively by chiral inversion of existing D-aptamers. In the detection of EA with L-DNA aptamer-based sensors, the feasibility of our strategy was confirmed, while in the detection of MG with L-RNA aptamers, linear calibration curves were obtained in the range from 0.1 to 5µm with the detection limit of 0.065µm under optimized experimental conditions. The results demonstrated that the mirror-image L-aptamers have identical recognition capability as D-aptamers. Meanwhile, L-aptamers have superior biostability to resist nuclease digestion, protein binding interference and off-target effects, enabling their applications in complex practical samples, such as lake water and fish tissue extractions. Our work provides a simple, yet universal and efficient way to develop biostable aptamers.

Selection and Biosensor Application of Aptamers for Small Molecules

Small molecules play a major role in the human body and as drugs, toxins, and chemicals. Tools to detect and quantify them are therefore in high demand. This review will give an overview about aptamers interacting with small molecules and their selection. We discuss the current state of the field, including advantages as well as problems associated with their use and possible solutions to tackle these. We then discuss different kinds of small molecule aptamer-based sensors described in literature and their applications, ranging from detecting drinking water contaminations to RNA imaging.

A self-assembling RNA aptamer-based graphene oxide sensor for the turn-on detection of theophylline in serum

To date, few effective fluorescent biosensors based on RNA aptamers have been developed because the intrinsic instability of RNA in the presence of nucleases precludes the application of RNA aptamers for the analysis of biological fluids. In this study, we developed a simple, sensitive, selective turn-on fluorescent aptasensor for theophylline detection in serum, utilizing ligand-induced self-assembling RNA aptamers and two different interaction stages of the aptamer fragments with graphene oxide (GO). A single strand of the theophylline RNA aptamer (33-mer) was split at the end loop region into two shorter fragments, one of which was labeled with a fluorophore (FAM). In the absence of theophylline, the adsorption of the two individual fragments on GO brought the fluorophore in close proximity to the GO surface, resulting in highly efficient quenching of fluorescence. The system showed very low background fluorescence. Conversely, the fragments self-assembled into an RNA aptamer/theophylline complex and were dissociated from GO. The quenched fluorescence was significantly recovered, and theophylline could be detected at a wide range of concentrations from 1 to 100μM, with a detection limit of 0.155μM and good selectivity in serum. Moreover, because of the shorter RNA fragments and the effective protection ability of GO from nuclease cleavage, the RNA sequences remained stable during the experiments. This design may serve as an example for the application of RNA aptasensors in the clinical setting.

A self-assembling RNA aptamer-based nanoparticle sensor for fluorometric detection of Neomycin B in milk

To date, there are few reports regarding the development of RNA aptamer-based biosensors for the detection of small molecules. The possible reason is attributed to the weak nuclease resistance of RNA in biological environments. In this study, we have developed an RNA aptamer-based gold nanoparticle (AuNP) sensor for fluorometric detection of Neomycin B in milk. This aptasensor depends on the self-assembly of the RNA aptamer/Neomycin B complex and fluorescence quenching by AuNPs. This biosensor exhibited a low detection limit of 0.01 μM, with a linear dynamic range from 0.1 to 10 μM in milk, and a good selectivity toward Neomycin B. Specifically, because of the shorter RNA fragments and the nuclease inhibition ability of the RNA-modified AuNPs, the RNA sequences remained stable during the experiments. This work will serve as an example for the development of novel biosensors based on RNA aptamers. Graphical Abstract An RNA aptamer-based nanoparticle sensor, developed for the detection of Neomycin B in milk, shows high binding affinity and selectivity. This aptasensor depends on the self-assembly of the aptamer/ligand complex and fluorescence quenching by gold nanoparticles (AuNPs). Because of the shorter RNA fragments and the nuclease inhibition ability of RNA-modified AuNPs, RNA sequences remain stable during the detection.