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

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.