Nanoscale Affinity Double Layer Overcomes the Poor Antimatrix Interference Capability of Aptamers

Recent advance on microextraction sampling technologies for bioanalysis

The contents of target substances in biological samples are usually at low concentration levels, and the matrix of biological samples is usually complex. Sample preparation is considered a very critical step in bioanalysis. At present, the utilization of microextraction sampling technology has gained considerable prevalence in the realm of biological analysis. The key developments in this field focus on the efficient microextraction media and the miniaturization and automation of adaptable sample preparation methods currently. In this review, the recent progress on the microextraction sampling technologies for bioanalysis has been introduced from point of view of the preparation of microextraction media and the microextraction sampling strategies. The advance on the microextraction media was reviewed in detail, mainly including the aptamer-functionalized materials, molecularly imprinted polymers, carbon-based materials, metal-organic frameworks, covalent organic frameworks, etc. The advance on the microextraction sampling technologies was summarized mainly based on in-vivo sampling, in-vitro sampling and microdialysis technologies. Moreover, the current challenges and perspective on the future trends of microextraction sampling technologies for bioanalysis were briefly discussed.

Precision-SELEX aptamer screening for the colorimetric and fluorescent dual-readout aptasensing of AFB1 in food

As nucleic acid-based affinity elements, aptamers have attracted significant attention for a wide range of analytical applications. Although several aflatoxin B1 (AFB1) aptamers have been identified, they are unsuitable for overcoming the unavoidable cross-reactions from interferents in complex food matrices due to their poor binding affinities and specificities. Herein, a novel precision-systematic evolution of ligands by exponential enrichment (P-SELEX) strategy through introducing the counter (matrix without target AFB1) and positive (with AFB1) screening steps was implemented to accurately identify AFB1 aptamers. A DNA aptamer A-42-2 at a 24-nt length was selected finally, which possessed nanomolar-level affinity of 5.55 nM, high specificity to other interferents, and strong anti-cross-reactivity ability for matrix components. Then, an A-42-2 aptamer-based ultra-sensitive colorimetric and fluorescent dual-readout aptasensor was fabricated for AFB1 detection in three kinds of complex food samples rich in starch without cross-reactions. The aptasensor displayed outstanding detection capacity with a wide liner range of 0.25-30 nM (1.95-234.4 μg/kg), while the detection limit for colorimetric measurement as low as 0.22 nM (1.72 μg/kg) and 0.048 nM (0.20 μg/kg) for fluorescent determination. P-SELEX is ideal for screening and applying aptamers in complex food matrices, creating more opportunities for the efficient and cost-effective development of high-quality aptamers and aptasensors for other targets.

Selection of regioselective DNA aptamer for detection of homocysteine in nondeproteinized human plasma

Small molecule-binding aptamers often suffer from high cross reactivity to structure analogues in biological samples, limiting their value for clinical diagnosis. Herein, we present a method to overcome this issue, by performing binding-inhibited organic reaction-based regioselective selection of aptamers against homocysteine (Hcy), which is a marker for diagnosing many disorders including stroke and Alzheimer's. This approach has led to isolation of a DNA aptamer that binds to the alkane thiol chain of Hcy with exceptional specificity against cysteine. It also binds with oxidized Hcy at weaker affinity. Using this new aptamer, we produced a reusable fluorescent optical fiber aptasensor for direct and validated detection of both free and total Hcy in nondeproteinized patient plasma in the diagnostic concentration range. The binding site-specific aptamer selection and optical-fiber-sensing strategy can expand the practical utility of aptamers in clinical diagnosis.

Ultrasensitive photoelectrochemical biosensor amplified by target induced assembly of cruciform DNA nanostructure for the detection of dibutyl phthalate

In this work, an ultra-sensitive signal quenched photoelectrochemical (PEC) aptasensor for dibutyl phthalate (DBP) detection was constructed by using a target induced cruciform DNA structure as signal amplifier and g-C₃N₄/SnO₂ composite as signal indicator. Impressively, the designed cruciform DNA structure shows high signal amplification efficiency due to the reduced reaction steric hindrance because of its mutually separated and repelled tails, multiple recognition domains, and a fixed direction for the sequential identification of the target. Therefore, the fabricated PEC biosensor demonstrated a low detection limit of 0.3 fM for DBP in a wide linear range of 1 fM to 1 nM. This work offered a novel nucleic acid signal amplification approach for enhancing the sensitivity of PEC sensing platforms for the detection of phthalates (PAEs)-based plasticizer, laying the foundation for its utilization in the determine of real environmental pollutants.

Recent Progress in Functional-Nucleic-Acid-Based Fluorescent Fiber-Optic Evanescent Wave Biosensors

Biosensors capable of onsite and continuous detection of environmental and food pollutants and biomarkers are highly desired, but only a few sensing platforms meet the "2-SAR" requirements (sensitivity, specificity, affordability, automation, rapidity, and reusability). A fiber optic evanescent wave (FOEW) sensor is an attractive type of portable device that has the advantages of high sensitivity, low cost, good reusability, and long-term stability. By utilizing functional nucleic acids (FNAs) such as aptamers, DNAzymes, and rational designed nucleic acid probes as specific recognition ligands, the FOEW sensor has been demonstrated to be a general sensing platform for the onsite and continuous detection of various targets ranging from small molecules and heavy metal ions to proteins, nucleic acids, and pathogens. In this review, we cover the progress of the fluorescent FNA-based FOEW biosensor since its first report in 1995. We focus on the chemical modification of the optical fiber and the sensing mechanisms for the five above-mentioned types of targets. The challenges and prospects on the isolation of high-quality aptamers, reagent-free detection, long-term stability under application conditions, and high throughput are also included in this review to highlight the future trends for the development of FOEW biosensors capable of onsite and continuous detection.

Evanescent Wave Optical-Fiber Aptasensor for Rapid Detection of Zearalenone in Corn with Unprecedented Sensitivity

Zearalenone (ZEN) is a common mycotoxin pollutant found in agricultural products. Aptamers are attractive recognition biomolecules for the development of mycotoxin biosensors. Even though numerous aptasensors have been reported for the detection of ZEN in recent years, many of them suffer from problems including low sensitivity, low specificity, tedious experimental steps, high-cost, and difficulty of automation. We report here the first evanescent wave optical-fiber aptasensor for the detection of ZEN with unprecedented sensitivity, high specificity, low cost, and easy of automation. In our aptasensor, a 40-nt ZEN-specific aptamer (8Z₃₁) is covalently immobilized on the fiber. The 17-nt fluorophore Cy5.5-labeled complementary DNA strand and ZEN competitively bind with the aptamer immobilized on the fiber, enabling the signal-off fluorescent detection of ZEN. The coating of Tween 80 enhanced both the sensitivity and the reproducibility of the aptasensor. The sensor was able to detect ZEN spiked-in the corn flour extract with a semilog linear detection range of 10 pM-10 nM and a limit of detection (LOD, S/N = 3) of 18.4 ± 4.0 pM (equivalent to 29.3 ± 6.4 ng/kg). The LOD is more than 1000-fold lower than the maximum ZEN residue limits set by China (60 μg/kg) and EU (20 μg/kg). The sensor also has extremely high specificity and showed negligible cross-reactivity to other common mycotoxins. In addition, the sensor was able to be regenerated for 28 times, further decreasing its cost. Our sensor holds great potential for practical applications according to its multiple compelling features.

Competitive Displacement Triggering DBP Photoelectrochemical Aptasensor via Cetyltrimethylammonium Bromide Bridging Aptamer and Perovskite

Here, a label-free perovskite-based photoelectrochemical (PEC) aptasensor was rationally designed for the displacement assay of dibutyl phthalate (DBP), a well-known endocrine disruptor, with the aid of cetyltrimethylammonium bromide (CTAB). In this method, CTAB significantly enhanced the PEC response and humidity resistance of the CH₃NH₃PbI₃ perovskite by forming a protecting layer and passivating the X- and A-sites vacancies of CH₃NH₃PbI₃. In addition, CTAB facilitated the immobilization of an aptamer through van der Waals and hydrophobicity forces, as well as the electrostatic interactions between the phosphate group of the aptamer and the cationic group of CTAB. When exposed to DBP in the affinity solution, the DBP aptamer was released from the electrode because the affinity between DBP and its aptamer competes with the interaction of the aptamer and CTAB. The displacement of the aptamer from the perovskite surface relieves the block effect and thus enhances the photoelectric signal of perovskite. By virtue of the good photoelectrochemical characters of CH₃NH₃PbI₃ and the specific recognition ability of aptamer, the linear range of the PEC sensor was 1.0 × 10^-13 to 1.0 × 10^-8 M and the detection and quantification limits were down to 2.5 × 10^-14 and 8.2 × 10^-14 M (S/N = 3), respectively. This work offers a novel strategy for designing aptasensors for the detection of various targets and exhibits the marvelous potential of organic-inorganic perovskite in the field of PEC analysis.

Shortened and multivalent aptamers for ultrasensitive and rapid detection of alternariol in wheat using optical waveguide sensors

Alternariol (AOH) is one of the common mycotoxins existing in a variety of foods at low level. Aptamers hold great promise for the development of sensitive and rapid aptasensors, but suffer from the excessive length and the difficulty in identification of critical binding domains (CBDs). In this study, the 5 nt CBD of the original 59-nt AOH aptamer (AOH-59, K_D = 423 nM) was identified to be a 'C' bulge in between two A-T base pairs. AOH-59 was successfully shortened to a 23 nt aptamer (AOH 6C, K_D = 701 nM). A 30 nt bivalent aptamer B-2-3 (K_D = 445 nM) and a 39 nt trivalent aptamer T-2-3 (K_D = 274 nM) were obtained by simply incorporating one or two CBDs into AOH 6C. The AOH 6C-, B-2-3-, and T-2-3-based optical waveguide aptasensors possessed the unprecedented detection of limits (LODs, S/N = 3) of 42 ± 3, 6 ± 1 and 2 ± 1 fM, respectively. Using the AOH 6C-based sensor as an example, we further demonstrated the detection of AOH spiked in wheat powder with a LOD of 37 pg/g, 20-230-fold lower than those achieved by ELISAs. The sensor was capable for 35 times 2-min regeneration and the assay time including the extraction of AOH from wheat was only about 1 h. We not only devised the first aptasensors for AOH detection, but also provided a simple strategy to design multivalent aptamers for small molecule targets.