Triplex-structure based DNA circuits with ultra-low leakage and high signal-to-noise ratio

An efficient DNAzyme-locked leakless enzyme-free amplification system for alpha-foetoprotein detection in liver cancer and breast cancer

Alpha-foetoprotein (AFP) is taken as a diagnostic tumor marker for the screening and diagnosis of cancer. Nucleic acid-based isothermal amplification strategies are emerging as a potential technology in early screening and clinical diagnosis of AFP. The leakages between hairpins dramatically increase the background and reduce the sensitivity. Thus, it is necessary to develop some strategies to reduce the leakage for isothermal amplification strategies. A DNAzyme-locked leakless enzyme-free amplification system was developed for AFP detection in liver cancer and breast cancer. AFP could open the apt-hairpin and initiate the catalytic hairpin assembly (CHA) reaction to produce a Y-shaped duplex. Two tails of a Y-shaped duplex cleaved the two kinds of leakless hairpins. Then, the third tail of the Y-shaped duplex catalyzed the second CHA between the cleaved leakless hairpins to recover the fluorescent intensity. The limit of detection reached 5 fg/mL by the two levels of signal amplifications. Importantly, the leakless hairpin design effectively reduced leakage between hairpins and weakened the background. In addition, it also showed a great promising potential for AFP detection in early screening and clinical diagnosis.

Inhibition of kinetic random-distribution in DNA Seesaw gates and biosensors for complete leakage prevention

DNA nanomaterials have a wide application prospect in biomedical field, among which DNA computers and biosensors based on Seesaw-based DNA circuit is considered to have the most development potential. However, the serious leakage of Seesaw-based DNA circuit prevented its further development and application. Moreover, the existing methods to suppress leakage can't achieve the ideal effect. Interestingly, we found a new source of leakage in Seesaw-based DNA circuit, which we think is the main reason why the previous methods to suppress leakage are not satisfactory. Therefore, based on this discovery, we use DNA triplex to design a new method to suppress the leakage of Seesaw-based DNA circuit. Its ingenious design makes it possible to perfectly suppress the leakage of all sources in Seesaw-based DNA circuit and ensure the normal output of the circuit. Based on this technology, we have constructed basic Seesaw module, AND gate, OR gate, secondary complex circuits and DNA detector. Experimental results show that we can increase the working range of the secondary Seesaw-based DNA circuit by five folds and keep its normal output signal above 90%, and we can improve the LOD of the Seesaw-based DNA detector to 1/11 of the traditional one(1.8pM). More importantly, we successfully developed a detector with adjustable detection range, which can theoretically achieve accurate detection in any concentration range. We believe the established triplex blocking strategy will greatly facilitate the most powerful Seesaw based DNA computers and biosensors, and further promote its application in biological systems.

DNAzyme-Based Dissipative DNA Strand Displacement for Constructing Temporal Logic Gates

Toehold-mediated DNA strand displacement is the foundation of dynamic DNA nanotechnology, encompassing a wide range of tools with diverse functions, dynamics, and thermodynamic properties. However, a majority of these tools are limited to unidirectional reactions driven by thermodynamics. In response to the growing field of dissipative DNA nanotechnology, we present an approach: DNAzyme-based dissipative DNA strand displacement (D-DSD), which combines the principles of dynamic DNA nanotechnology and dissipative DNA nanotechnology. D-DSD introduces circular and dissipative characteristics, distinguishing it from the unidirectional reactions observed in conventional strand displacement. We investigated the reaction mechanism of D-DSD and devised temporal control elements. By substituting temporal components, we designed two distinct temporal AND gates using fewer than 10 strands, eliminating the need for complex network designs. In contrast to previous temporal logic gates, our temporal storage is not through dynamics control or cross-inhibition but through autoregressive storage, a more modular and scalable approach to memory storage. D-DSD preserves the fundamental structure of toehold-mediated strand displacement, while offering enhanced simplicity and versatility.