Simultaneous colorimetric determination of bisphenol A and bisphenol S via a multi-level DNA circuit mediated by aptamers and gold nanoparticles

Empowering DNA-Based Information Processing: Computation and Data Storage

Information processing is a critical topic in the digital age, as silicon-based circuits face unprecedented challenges such as data explosion, immense energy consumption, and approaching physical limits. Deoxyribonucleic acid (DNA), naturally selected as a carrier for storing and using genetic information, possesses unique advantages for information processing, which has given rise to the emerging fields of DNA computing and DNA data storage. To meet the growing practical demands, a wide variety of materials and interfaces have been introduced into DNA information processing technologies, leading to significant advancements. This review summarizes the advances in materials and interfaces that facilitate DNA computation and DNA data storage. We begin with a brief overview of the fundamental functions and principles of DNA computation and DNA data storage. Subsequently, we delve into DNA computing systems based on various materials and interfaces, including microbeads, nanomaterials, DNA nanostructures, hydrophilic-hydrophobic compartmentalization, hydrogels, metal-organic frameworks, and microfluidics. We also explore DNA data storage systems, encompassing encapsulation materials, microfluidics techniques, DNA nanostructures, and living cells. Finally, we discuss the current bottlenecks and obstacles in the fields and provide insights into potential future developments.

Dual-amplification colorimetric detection of bisphenol A based on catalytic hairpin assembly and DNAzyme-caused fragment self-assembly hybridization chain reaction

An efficient and innovative strategy for colorimetric detection of bisphenol A (BPA) is shown here based on target-induced catalytic hairpin assembly (CHA) and DNAzyme-caused fragment self-assembly hybridization chain reaction (HCR). BPA can bind with its aptamer hairpin to trigger CHA, thus forming Y-shaped DNA nanostructures with an enzyme-strand (E-DNA) tail. Subsequently, the E-DNA can cyclically cleave the substrate hairpin, generating many fragments which can cause self-assembly HCR to form long strand DNA. Finally, the formed long strand DNA can hybridize with short single strand DNA on AuNPs, causing the color change of AuNPs from red to blue. Six important detection conditions of the proposed aptasensor were optimized. Under optimal conditions, the biosensor has high sensitivity for BPA detection at concentrations ranging from 0.8 pM to 500 pM and the detection limit is as low as 0.2 pM, providing a promising prospective ultrasensitive detection of BPA.

Tailoring diameters of carbon nanofibers with optimal mesopores to remarkably promote hemin adsorption toward ultrasensitive detection of bisphenol A

Bisphenol A (BPA) is a worldwide used endocrine disrupting chemical that can migration from food containers and packaging, resulting in bioaccumulation of BPA in humans and causing adverse health effects. Porous electrodes have been proved with large surface areas and high sensing abilities in electrochemical detection of BPA. However, how to tailor the pore sizes to further improve the sensing performance is still a great challenge. Here, we delicately tailored the diameters of carbon nanofibers (CNFs) by adjusting electrospinning parameters to have optimal mesopore structure for strong adsorption of hemin that has been demonstrated with high electrocatalytic activity for BPA sensing. Benefiting from the optimal mesopores structure of CNFs and the synergistic effect of hemin and CNFs, this hemin@CNFs based sensor achieves an ultrahigh sensitivity of 40.97 μA cm^-2 μM^-1, a low detection limit of 3.1 nM and satisfactory recoveries from 90.2% to 104.2% in the direct detection of BPA in liquors. This work offers a promising sensing platform for ultrasensitive monitoring of BPA.

Borderline Boolean states improve the biosensing applications of DNA circuits

Molecular circuits have been used in a wide range of diagnosis applications, from the detection of chemical molecules in solution to the complex processing of cell surface receptors. One of the most important challenges of these systems is the lack of distinguishability between different circuit states when each circuit state represents a specific disease. In this work, we designed a molecular amplification circuit with borderline Boolean states that each state can be distinguished with different color intensity. For this purpose, two DNA complexes and four DNA hairpin structures were designed to detect miR-218 and miR-215 biomarkers. One of the designed DNA complexes has two G-quadruplex structures and the other has only one G-quadruplex structure. In the absence of the inputs, all three G-quadruplex structures are active and produce a high-intensity signal, while in the other three states, including the presence of miR-218, the presence of miR-215, and the presence of both inputs, respectively, one, two, and zero G-quadruplex structures are active. Therefore, the designed system can identify two different biomarkers simultaneously with different signal ratios, which can easily distinguish the different states of the circuit. This strategy is very promising to identify diseases in which any combination of biomarkers leads to a particular disease.

Label-free colorimetric assay for arsenic(III) determination based on a truncated short ssDNA and gold nanoparticles

A short ssDNA (Apt-21) rationally truncated from the parent 100 nt As(III) aptamer was used for colorimetric determination of As(III). Apt-21 serves dual functions, i.e., recognition of trace As(III) and regulation of AuNPs dispersion by surface attachment, while gold nanoparticles (AuNPs) functioned as colorimetric signal reporters. Under the optimal conditions, the ratio of the absorbance at 650 nm to 520 nm (A₆₅₀/A₅₂₀) of AuNPs changed proportionally with increasing concentration of As(III), which showed a linear relationship within the concentration ranges 1-30 ppb and 30-100 ppb with a detection limit of 0.18 ppb. The feasibility of this assay was demonstrated by determining As(III) in spiked water samples with mean recoveries ranging from 96.5-107.1%. Schematic representation of colorimetric detection of As(III) based on the short ssDNA (Apt-21) and gold nanoparticles (AuNPs).

Electrochemical detection of bisphenols in food: A review

Bisphenols (BPs) are worldwide used organic compounds in plastics, belonging to the group of endocrine disrupting chemicals (EDCs) which exhibits endocrine disruption to beings. Migration of BPs from food contact materials like plastic containers, epoxy coatings in metal cans and thermal papers, would results in bioaccumulation of BPs in human beings, causing adverse health effects. Therefore, sensitive and selective determination of BPs in food is needed. Among different strategies have been explored for the detection of BPs, electrochemical sensors with relatively high sensitivity and fast response are promising. This paper is devoted to comprehensively review the developed electrochemical methods for BPs sensing in food, so that to find a direction for developing low cost, high accuracy and compatibility sensors toward the sensitive and selective detection of BPs. Different electrochemical technologies categorized by recognition agents, aptamers, enzymes, molecularly imprinted polymers and nanomaterials are discussed and summarized in their mechanisms, usages, merits and limitations. The challenges and further perspectives in the development of electrochemical sensors is also discussed.

Propelling DNA Computing with Materials' Power: Recent Advancements in Innovative DNA Logic Computing Systems and Smart Bio-Applications

DNA computing is recognized as one of the most outstanding candidates of next-generation molecular computers that perform Boolean logic using DNAs as basic elements. Benefiting from DNAs' inherent merits of low-cost, easy-synthesis, excellent biocompatibility, and high programmability, DNA computing has evoked substantial interests and gained burgeoning advancements in recent decades, and also exhibited amazing magic in smart bio-applications. In this review, recent achievements of DNA logic computing systems using multifarious materials as building blocks are summarized. Initially, the operating principles and functions of different logic devices (common logic gates, advanced arithmetic and non-arithmetic logic devices, versatile logic library, etc.) are elaborated. Afterward, state-of-the-art DNA computing systems based on diverse "toolbox" materials, including typical functional DNA motifs (aptamer, metal-ion dependent DNAzyme, G-quadruplex, i-motif, triplex, etc.), DNA tool-enzymes, non-DNA biomaterials (natural enzyme, protein, antibody), nanomaterials (AuNPs, magnetic beads, graphene oxide, polydopamine nanoparticles, carbon nanotubes, DNA-templated nanoclusters, upconversion nanoparticles, quantum dots, etc.) or polymers, 2D/3D DNA nanostructures (circular/interlocked DNA, DNA tetrahedron/polyhedron, DNA origami, etc.) are reviewed. The smart bio-applications of DNA computing to the fields of intelligent analysis/diagnosis, cell imaging/therapy, amongst others, are further outlined. More importantly, current "Achilles' heels" and challenges are discussed, and future promising directions of this field are also recommended.

Logic Gates Based on DNA Aptamers

DNA bio-computing is an emerging trend in modern science that is based on interactions among biomolecules. Special types of DNAs are aptamers that are capable of selectively forming complexes with target compounds. This review is devoted to a discussion of logic gates based on aptamers for the purposes of medicine and analytical chemistry. The review considers different approaches to the creation of logic gates and identifies the general algorithms of their creation, as well as describes the methods of obtaining an output signal which can be divided into optical and electrochemical. Aptameric logic gates based on DNA origami and DNA nanorobots are also shown. The information presented in this article can be useful when creating new logic gates using existing aptamers and aptamers that will be selected in the future.

A novel turn-off fluorescent aptasensor for ampicillin detection based on perylenetetracarboxylic acid diimide and gold nanoparticles

Herein, a novel turn-off fluorescent aptasensor was developed for selective detection of ampicillin (AMP) at picomolar level based on 3,4,9,10-perylenetetracarboxylic acid diimide (PTCDI) as an affordable and low-cost fluorophore. This aptasensor was designed using aptamer, its complementary strand (CS) and gold nanoparticles (AuNPs). The principle of the sensing method is a decrease in the fluorescence intensity of PTCDI in the presence of free CS. Following the addition of AMP, Aptamer/CS-modified AuNPs releases CS and so, the fluorescence intensity of PTCDI is reduced. The designed analytical method indicated a good linear range from 100 pM to 1000 pM and a limit of detection (LOD) of 29.2 pM was obtained. Furthermore, the sensing strategy indicated satisfactory results for the detection of AMP in the spiked human serum samples. By changing the sequences of aptamer and its CS, the presented analytical approach can be easily applied for detection of other antibiotics.

Ultrasonic energy-assisted in-situ synthesis of Ru0/PANI/g-C3N4 nanocomposite: Application for picomolar-level electrochemical detection of endocrine disruptor (Bisphenol-A) in humans and animals

Bisphenol A (BPA) is an endocrine-disrupting chemical which resembles structurally the hormone estrogen. Even a trace amount of BPA can bind estrogen receptors resulting in the inducement of reproductive disorders, cancers and problems related to sexual growth such as manliness in female and womanliness in male. So the determination of BPA in human and animal bodies is very essential. For this purpose, a new nanocomposite composed of ruthenium nanoparticles, polyaniline and graphitic carbon nitride (Ru⁰/PANI/g-C₃N₄) has been synthesized ultrasonically (40 ± 3 kHz, 200 W). A modification on glassy carbon electrode (GCE) with the nanocomposite detects BPA in human and animal urine samples with wide linear range (0.01-1.1 µM) and the limit of detection is pico molar-level. The synthesized nanocomposite was characterized by Ultraviolet-Visible and Fourier Transform-Infra Red spectroscopies, thermo gravimetric analysis, transmission electron microscopy, X-ray diffraction study, energy dispersive X-ray analysis, and elemental mapping analysis. This sensing system is selective, stable and reusable, by which the detection of BPA in various physiological fluids is very much possible.

Dual sensing reporter system of assembled gold nanoparticles toward the sequential colorimetric detection of adenosine and Cr(III)

A facile and sensitive sequential colorimetric detection strategy for adenosine and Cr³⁺ has been presented by using the aptamer and 11-mercaptoundecanoic acid assembled gold nanoparticles. The thiolated DNA and 11-mercaptoundecanoic acid was simultaneously assembled to the surface of gold nanoparticles in one step by gold-sulfur interaction. Adenosine aptamer was linked to functionalized gold nanaoparticles based on the strict complementary nature of the DNA base pairs. Conformational change of aptamer will be induced due to its specific binding with targets. As a result, this aptamer tethered aggregated nanoparticles underwent fast disassembly into dispersed nanoparticles upon binding of adenosine, and this distance change between particles induced a distinct solution color changing from blue to red. The dispersed particles were sensitive to Cr³⁺ due to the chelation effect between the carboxyl group of 11-mercaptoundecanoic acid and metal ions, and further occurred obvious aggregation accompanying with a color change from red to blue. Depended on this principle, a sensitive and selective sequential colorimetric sensor for detection of adenosine and Cr³⁺ was developed. The proposed colorimetric sensor exhibited wide linear ranges and low detection limits towards the detection of adenosine and Cr³⁺. Regarding adenosine, linear range was 1 × 10^-7 ∼ 1 × 10^-4 M with low detection limit of 1.8 × 10^-8 M, and the naked eye detection limit was estimated as 20 μM. With regard to Cr³⁺, good linear relationship was ranged from 1 × 10^-10 to 1 × 10^-6 M with low detection limit of 1.7 × 10^-11 M，and the naked eye detection limit was as low as 0.1 nM. Meanwhile, bifunctional recognition was successfully used for practical human urine samples with good recoveries from 89.0% to 112.6% for adenosine and 90.2%-113.4% for Cr³⁺. It also highlights the potential applications of other aptamers and ligands in cascade analysis of other analytes.

A multi-component Cu2O@FePO4 core-cage structure to jointly promote fast electron transfer toward the highly sensitive in situ detection of nitric oxide

Electrochemical sensors actually involve an electrocatalytic process in efficient and selective energy conversion. In this work, we use different components to innovatively produce a core@cage material, in which the outer cage, iron phosphate, offers a high electrocatalytic ability to electrochemically oxidize NO, while the inner material, cuprous oxide, could absorb the intermediary HO- ions to kinetically promote NO oxidation for fast electron transfer, resulting in a strong synergistic effect. The unique core@cage structure also increases the active surface area and provides plenty of channels via the porous cage for significantly enhanced mass transport. The as-prepared core@cage NO sensor shows a high sensitivity of 326.09 μA cm-2 μM-1, which is the highest among the reported non-noble metal-based NO biosensors based on the electrooxidation scheme. A free-standing flexible NO sensor was further fabricated with the material for the in situ detection of NO released from cancer cells, demonstrating a low detection limit (0.45 nM) and a fast response time (0.8 s). This work holds great promise for its practical applications in the diagnosis or research of complicated biological processes, especially in real-time in situ detection approaches.

Upconversion fluorescent aptasensor for bisphenol A and 17β-estradiol based on a nanohybrid composed of black phosphorus and gold, and making use of signal amplification via DNA tetrahedrons

This study describes an upconversion fluorescent aptasensor based on black phosphorus nanohybrids and self-assembled DNA tetrahedrons dual-amplification strategy for rapid detection of the environmental estrogens bisphenol A (BPA) and 17β-estradiol (E2). Tetrahedron complementary DNAs (T-cDNAs) were self-assembled in an oriented fashion on a 2D nanohybrid composed of black phosphorus (BP) and gold to give a materials of architecture BP-Au@T-cDNAs. In parallel, core-shell upconversion nanoparticles were modified with aptamers (UCNPs@apts) and used as capture probes. On complementary pairing, the BP-Au@T-cDNA quench the fluorescence of UCNPs@apts (measured at an excitation wavelength 808 nm and at main emission peaks at 545 nm and 805 nm.) Compared with single-stranded probes based on black phosphorus and gold, the dual-amplification strategy increases quenching efficiency by nearly 25%-30% and reduces capture time to 10 min. This is due to the higher optical absorption of 2D nanohybrid and the reduction of steric hindrance by T-cDNAs. Exposure to BPA or E2 cause the release of UCNPs@apts from the BP-Au@T-cDNAs due to stronger binding between aptamer and analyte. Hence, fluorescence recovers at 545 nm for BPA and 805 nm for E2. Based on these findings, a dually amplified aptamer assay was constructed that covers the 0.01 to 100 ng mL^-1 BPA concentration range, and the 0.1 to 100 ng mL^-1 E2 concentration range. The detection limits are 7.8 pg mL^-1 and 92 pg mL^-1, respectively. This method was applied to the simultaneous determination of BPA and E2 in spiked samples of water, food, serum and urine. Graphical abstract Schematic presentation of novel quenching probes designed by tetrahedron complementary DNAs oriented self-assembled on the surface of black phosphorus/gold nanohybrids. Combined with aptamer-modified upconversion nanoparticles, a dual-amplification self-assembled fluorescence nanoprobe was constructed for simultaneous detection of BPA and E2.

Critical Review: DNA Aptasensors, Are They Ready for Monitoring Organic Pollutants in Natural and Treated Water Sources?

There is a growing need to monitor anthropogenic organic contaminants detected in water sources. DNA aptamers are synthetic single-stranded oligonucleotides, selected to bind to target contaminants with favorable selectivity and sensitivity. These aptamers can be functionalized and are used with a variety of sensing platforms to develop sensors, or aptasensors. In this critical review, we (1) identify the state-of-the-art in DNA aptamer selection, (2) evaluate target and aptamer properties that make for sensitive and selective binding and sensing, (3) determine strengths and weaknesses of alternative sensing platforms, and (4) assess the potential for aptasensors to quantify environmentally relevant concentrations of organic contaminants in water. Among a suite of target and aptamer properties, binding affinity is either directly (e.g., organic carbon partition coefficient) or inversely (e.g., polar surface area) correlated to properties that indicate greater target hydrophobicity results in the strongest binding aptamers, and binding affinity is correlated to aptasensor limits of detection. Electrochemical-based aptasensors show the greatest sensitivity, which is similar to ELISA-based methods. Only a handful of aptasensors can detect organic pollutants at environmentally relevant concentrations, and interference from structurally similar analogs commonly present in natural waters is a yet-to-be overcome challenge. These findings lead to recommendations to improve aptasensor performance.

A novel colorimetric aptasensor for ultrasensitive detection of cocaine based on the formation of three-way junction pockets on the surfaces of gold nanoparticles

Herein, a novel colorimetric aptasensor was introduced for detection of cocaine based on the formation of three-way junction pockets on the surfaces of gold nanoparticles (AuNPs) and the catalytic activity of the surfaces of AuNPs. Simplicity and detection of cocaine in a short time (only 35 min) are some of the unique features of the proposed sensing strategy. In the presence of cocaine, triple-fragment aptamer (TFA) forms on the surfaces of AuNPs, leading to a significant decrease of the catalytic activity of AuNPs and the color of samples remains yellow. In the absence of target, TFA does not form on the surfaces of AuNPs and 4-Nitrophenol, as a colorimetric agent, has more access to the surfaces of AuNPs, resulting in the reduction of 4-Nitrophenol and the color of sample changes from yellow to colorless. The sensing strategy showed good specificity, a limit of detection (LOD) of 440 pM and a dynamic range over 2-100 nM. The sensing method was also successfully applied to detect cocaine in spiked human serum samples with recovery of 94.71-98.63%.