Enzyme-assisted waste-to-reactant transformation to engineer renewable DNA circuits

Entropy-driven "two-way signal output" cyclic circuit: An ultra-sensitive electrochemical biosensor for non-invasive ORAOV 1 detection

The rapid, sensitive and reliable detection of oral cancer overexpressed 1 (ORAOV 1) is crucial for the early, non-invasive diagnosis of oral squamous cell carcinoma (OSCC). Herein, we are the first to construct an ultrasensitive electrochemical (EC) biosensor based on an entropy-driven "two-way signal output" (TWSO) cyclic circuit for salivary ORAOV 1 detection. This innovative TWSO cyclic circuit can skillfully convert by-products into desired signal-generating units, not only reducing the excessive accumulation of by-products but also improving the utilization efficiency of output chains, thereby achieving rapid reaction kinetics and high signal outputs. Furthermore, this novel EC biosensor leverages metal and metal-organic framework nanocomposites, which possess good stability and electrocatalytic activity, to enhance its electrochemical performance. We experimentally demonstrate that this EC biosensor exhibits ultra-high sensitivity (LOD as low as 135 aM), a wide linear range from 1 fM to 1 nM, good reproducibility and stability. Meanwhile, it can determine ORAOV 1 in human saliva samples with good anti-interference and well-pleasing recovery rates. Importantly, this newly developed EC biosensor can accurately discriminate patients with OSCC from clinical samples (AUC = 1), holding immense prospects for the sensitive and non-invasive diagnosis of OSCC.

Entropy driven-based catalytic biosensors for bioanalysis: From construction to application-A review

The rapid advancement of precision medicine and the continuous emergence of novel pathogens have presented new challenges for biosensors, necessitating higher requirements. Target amplification technology serves as the core component in biosensor construction. Enzyme-based amplification methods are often sensitive and selective but involve relatively complex operational steps, whereas enzyme-free amplification methods offer simplicity but frequently fail to meet both sensitivity and selectivity simultaneously. Existing research has confirmed that entropy-driven catalyst (EDC) biosensors not only fulfills the demands for sensitivity and selectivity concurrently but also offers ease of operation and flexibility in construction. In this review, we summarize the key advantages of EDC, explore how to construct DNA nanomachines based on these advantages to achieve intracellular detection and simultaneous detection of multiple targets, as well as point-of-care testing (POCT) to address practical issues in clinical diagnosis and treatment. We also anticipate potential challenges, propose corresponding solutions, and outline future development directions for EDC-based biosensors in practical clinical applications. We firmly believe that EDC sensors will emerge as a crucial branch within the realm of biosensor development.

A novel all-in-one target-powered entropy-driven dynamic DNA networks to regulate the activity of CRISPR/AsCas12a for enhanced DNA detection

BACKGROUND

The non-enzyme autonomous DNA nanodevices have been developed to detect various analytes through the programmability of Watson-Crick base pairing. Nevertheless, by comparison with enzymatic biosensors, the usage of enzyme-free DNA networks to create biosensors for testing low amounts of targets is still subject to the finite number of cycles. Besides, these biosensors still require the incorporation of other amplification strategies to improve the sensitivity, which complicates the detection workflow and lacks of a uniform compatible system to respond to the target in one pot.

RESULTS

Here, we put forward a novel way for rapid and sensitive DNA diagnostic via EDN (entropy-driven dynamic network) coupling with CRISPR/AsCas12a-powered amplification. In the absence of the target, the autonomous hybridization among the substrate and crRNA is kinetically hindered by enclosing complementary regions, which leads to the loss of the activation function of Cas12a. On the contrary, the target initiates the EDN, reconfiguring the activator strand from a duplex to branch construction, which provides a valid means to adjust the hybridization with crRNA, thereby controlling the indiscriminate collateral cleavage activities of the CRISPR/AsCas12a. Compared with the traditional EDN, synergistic activation between the EDN and the CRISPR catalyst could dramatically enhance the detection signal of the target in one pot. Furthermore, the proposed approach provides universal platforms through the rational functional and structural design of DNA assembly modules.

SIGNIFICANCE AND NOVELTY

Overall, this target-triggered EDN switches the activator strand to regulate the activity of AsCas12a (called TERA), which showed nearly one orders of magnitude sensitivity than the conventional Cas12a alone assay, resulting in a devisable universal CRISPR sensing platform that favours the fast, robust and one-pot detection of nucleic molecules.

Erasable and Field Programmable DNA Circuits Based on Configurable Logic Blocks

DNA is commonly employed as a substrate for the building of artificial logic networks due to its excellent biocompatibility and programmability. Till now, DNA logic circuits are rapidly evolving to accomplish advanced operations. Nonetheless, nowadays, most DNA circuits remain to be disposable and lack of field programmability and thereby limits their practicability. Herein, inspired by the Configurable Logic Block (CLB), the CLB-based erasable field-programmable DNA circuit that uses clip strands as its operation-controlling signals is presented. It enables users to realize diverse functions with limited hardware. CLB-based basic logic gates (OR and AND) are first constructed and demonstrated their erasability and field programmability. Furthermore, by adding the appropriate operation-controlling strands, multiple rounds of programming are achieved among five different logic operations on a two-layer circuit. Subsequently, a circuit is successfully built to implement two fundamental binary calculators: half-adder and half-subtractor, proving that the design can imitate silicon-based binary circuits. Finally, a comprehensive CLB-based circuit is built that enables multiple rounds of switch among seven different logic operations including half-adding and half-subtracting. Overall, the CLB-based erasable field-programmable circuit immensely enhances their practicability. It is believed that design can be widely used in DNA logic networks due to its efficiency and convenience.

Controllable and reusable seesaw circuit based on nicking endonucleases

Seesaw circuits are essential for molecular computing and biosensing. However, a notable limitation of seesaw circuits lies in the irreversible depletion of components, precluding the attainment of system recovery and rendering nucleic acid circuits non-reusable. We developed a brand-new method for creating controllable and reusable seesaw circuits. By using the nicking endonucleases Nt.BbvCI and Nt.Alwi, we removed "functional components" while keeping the "skeletal components" for recurrent usage. T-inputs were introduced, increasing the signal-to-noise ratio of AND logic from 2.68 to 11.33 and demonstrating compatibility. We identified the logic switching feature and verified that it does not impair circuit performance. We also built intricate logic circuits, such as OR-AND gate, to demonstrate the versatility of our methodology. This controllable reusability extends the applications of nanotechnology and bioengineering, enhancing the practicality and efficiency of these circuits across various domains.

A ratiometric fluorescence sensor for 5-hydroxymethylfurfural detection based on strand displacement reaction

Since 5-hydroxymethylfurfural (HMF) becomes a neo-forming contaminant with latent harm to human health, development of new method for highly sensitive detection of HMF is extremely desirable. Herein, a novel ratiometric fluorescence sensor based on strand displacement reaction and magnetic separation was designed for sensitive and selective detection of HMF with the help of MnO₂ nanosheets. The aldehyde-functionalized DNA (S0-CHO) and HMF competed for binding to amino-functionalized magnetic beads (NH₂-MBs). Then, S0-CHO was collected from supernatant by magnetic separation. In the presence of HMF, the obtained S0-CHO induced the formation of T-shaped DNA by strand displacement reaction (SDR), lighting the fluorescence of FAM. In the absence of HMF, no S0-CHO was present to ignite T-shaped DNA. In this situation, fluorescence of Cy5 was turned on. Thus, a ratiometric fluorescence sensor for high-sensitive detection of HMF was developed. The sensor has a wide linear range from 5 nM to 5 μM. It also exhibited high selectivity against other potential interfering substances. It has been successfully applied to analyze HMF in food samples. The method has potential to be expanded to detect other molecules containing aldehyde groups and further be applied in food safety, environment and other fields.