Addition of mirror-image L-DNA elements to DNA amplification circuits to distinguish leakage from target signal

Refined design of a DNA logic gate for implementing a DNA-based three-level circuit

DNA computing circuits are favored by researchers because of their high density, high parallelism, and biocompatibility. However, compared with electronic circuits, current DNA circuits have significant errors in understanding the OFF state and logic "0". Nowadays, DNA circuits only have two input states: logic "0" and logic "1", where logic "0" also means the OFF state. Corresponding to an electronic circuit, it is more like an on-off switch than a logic circuit. To correct this conceptual confusion, we propose a three-level circuit. The circuit divides the input signal into three cases: "none", logic "0" and logic "1". In subsequent experiments, 34 input combinations of the primary AND gate, OR gate as well as secondary AND-OR and OR-AND cascade circuits were successfully implemented to perform the operation, which distinguished the OFF state and logic "0" correctly. Based on this, we successfully implemented a more complex voting operation with only 12 strands. We believe that our redefinition of the OFF state and logic "0" will promote tremendous developments in DNA computing circuits.

A novel entropy-driven dual-output mode integrated with DNAzyme for enhanced microRNA detection

Accurate microRNA (miRNA) detection is pivotal in the diagnosis and monitoring of cancer. Entropy-driven catalysis (EDC) has attracted widespread attention as an enzyme-free, isothermal technique for miRNA detection owing to its inherent simplicity and reliability. However, conventional EDC is a single-output mode, limiting the efficiency of signal amplification. In this study, a novel EDC dual-output mode was employed in conjunction with DNAzyme, resulting in the development of an EDC dual-end DNAzyme (EDC-DED) approach for highly sensitive miRNA detection. In this system, miRNA-21 initiated the EDC reaction, producing a large amount of catalytically active dual-end Mg2+-dependent DNAzyme. The DNAzyme further cleaved the reporter cyclically, generating a notably amplified fluorescence signal. The proposed method achieved a low detection limit of 2 pM. Compared with the traditional EDC single-end DNAzyme (EDC-SED) strategy, the present method exhibited superior amplification efficiency, enhancing detection sensitivity by approximately 46.5-fold. Furthermore, this platform demonstrated ideal specificity, satisfactory reproducibility and acceptable detection capabilities in clinical serum samples. Therefore, the straightforward and convenient strategy is a potential tool for miRNA analysis, which may provide a new perspective for biological analysis and clinical application.

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.

Two-layer cascaded catalytic hairpin assemblies based on locked nucleic acids for one-step and highly sensitive ctDNA detection

Enzyme-free signal amplification of catalytic hairpin assembly (CHA) has enabled sensitive detection of circulating tumor DNA (ctDNA) in early clinical diagnosis. Conventional CHA strategies are restrained by the limited amplification efficiency of the single-stage system, and signal leakage from "breathing" influence and nuclease degradation. Here, we introduced two-layer cascaded locked nucleic acid (LNA)-assisted CHA circuits with the intelligent incorporation of LNA in the hairpins and reporter for the highly sensitive one-step detection of scarce ctDNA. The target-triggered upstream CHA reaction continuously generates hybrid products to catalyze the downstream CHA reaction for transducing the primary sensing event, and the released target and the produced hybrid product trigger the next catalytic reaction round at the same time and finally cascade to amplify the target ctDNA fluorescence output signal. Meanwhile, the stronger binding affinity of the LNA-DNA duplex endows the two-layer LNA-assisted CHA system with thermodynamic stability and nuclease resistance, and thus our designed system exhibits an excellent detection performance for target ctDNA in the range from 2 pM to 5 nM with a low detection limit of 0.6 pM. Significantly, the two-layer LNA-assisted CHA circuits have been successfully implemented for the feasible analysis of clinical samples. This two-layer cascaded LNA-assisted CHA strategy provides a promising high sensitivity tool for one-step detection of scarce ctDNA from complex clinical samples and would facilitate the reconfiguration of DNA circuit-based DNA nanotechnology for the precise analysis of other biomarkers in clinical research fields.

Nanosensor Based on the Dual-Entropy-Driven Modulation Strategy for Intracellular Detection of MicroRNA

The entropy-driven strategy has been proposed as a milestone work in the development of nucleic acid amplification technology. With the characteristics of an enzyme-free, isothermal, and relatively simple design, it has been widely used in the field of biological analysis. However, it is still a challenge to apply entropy-driven amplification for intracellular target analysis. In this study, a dual-entropy-driven amplification system constructed on the surface of gold nanoparticles (AuNPs) is developed to achieve fluorescence determination and intracellular imaging of microRNA-21 (miRNA-21). The dual-entropy-driven amplification strategy internalizes the fuel chain to avoid the complexity of the extra addition in the traditional entropy-driven amplification strategy. The unique self-locked fuel chain system is established by attaching the three-stranded structure on two groups of AuNPs, where the Cy5 fluorescent label was first quenched by AuNPs. After the target miRNA-21 is identified, the fuel chain will be automatically unlocked, and the cycle reaction will be driven, leading to fluorescence recovery. The self-powered and waste-recycled fuel chain greatly improves the automation and intelligence of the reaction process. Under the optimal conditions, the linear response range of the nanosensor ranges from 5 pM to 25 nM. This nanoreaction system can be used to realize intracellular imaging of miRNA-21, and its good specificity enables it to distinguish tumor cells from healthy cells. The development of the dual-entropy-driven strategy provides an integrated and powerful way for intracellular miRNA analysis and shows great potential in the biomedical field.

A rapid and highly sensitive ctDNA detection platform based on locked nucleic acid-assisted catalytic hairpin assembly circuits

As a promising biomarker of liquid biopsy, circulating tumor DNA (ctDNA) plays a paramount role in the early diagnosis of noninvasive cancer. The isothermal catalytic hairpin assembly (CHA) strategy has great potential for in vitro detection of ctDNA in low abundance. However, a traditional CHA strategy for ctDNA detection at the earlier stages of cancer remains extremely challenging, as annoying signal leakage from the 'breathing' phenomenon and nuclease degradation occur. Herein, we report a locked nucleic acid (LNA)-incorporated CHA circuit for the rapid and sensitive detection of target ctDNA. The target ctDNA intelligently catalyzed LNA-modified hairpins H1 and H2via a range of toehold-mediated strand displacement processes, leading to the continuous generation of an H1-H2 hybrid for the amplified fluorescence signal. In comparison to conventional CHA circuits, the stronger binding affinity of LNA-DNA bases greatly inhibited the breathing effect, which endowed it with greater thermodynamic stability and resistance to nuclease degradation in the LNA-assisted CHA system, thus achieving a high signal gain. The developed CHA circuit demonstrated excellent performance during target ctDNA detection, with a linear range from 10 pM to 5 nM, and its target detection limit was reached at 3.3 pM. Moreover, this LNA-assisted CHA system was successfully applied to the analysis of target ctDNA in clinical serum samples of breast cancer patients. This updated CHA system provides a general and robust platform for the sensitive detection of biomarkers of interest, thus facilitating the accurate identification and diagnosis of cancers.

Recent advances of catalytic hairpin assembly and its application in bioimaging and biomedicine

Catalytic hairpin assembly (CHA) appears to be a particularly appealing nucleic acid circuit because of its powerful amplification capability, simple protocols, and enzyme-free and isothermal conditions, and can combine with various signal output modes for the biosensing of various analytes. Especially in the last five years, vast CHA related studies have sprung up. With the deep exploration of the CHA mechanism, some novel and excellent CHA strategies have been proposed; meanwhile the CHA cascade strategies with various amplification techniques further improve the analysis performance. Furthermore, diverse CHA based biosensors have been tactfully engineered and extensively employed in imaging applications in living cells and in vivo ascribed to its gentle reaction, efficient amplification and universality. Hence, we present a comprehensive and systematic summary of the progress in CHA and its application in bioimaging and biomedicine to date. At first, we introduced the mechanism and diversification of CHA in detail, including the newly developed CHA and its ingenious combination with a variety of other technologies. Concurrently, we summarized the latest application progress of different CHA strategies in bioimaging and biomedicine, highlighting the merits and drawbacks of representative approaches. Finally, we put forward some views on the challenges and prospects of CHA in bioimaging and biomedicine in the future.

Mismatch-fueled catalytic hairpin assembly mediated ultrasensitive biosensor for rapid detection of MicroRNA

Herein, a mismatch-fueled catalytic hairpin assembly (MCHA) was rationally engineered, which possessed higher amplification efficiency and faster rate than catalytic hairpin assembly (CHA). Once input target microRNA-21(miRNA-21) triggers the MCHA, the hairpin DNA H1 will be opened to form the duplex H1-miRNA-21, then the mismatched hairpin DNA H2 could easily hybridize with H1-miRNA-21 to generate duplex H1-H2 and the miRNA-21 could be released to enter next cycle, thus generating amounts of output products. Impressively, the MCHA realizes a pretty shorter complete reaction time of 40 min and quite higher amplification efficiency of 9.56 × 10⁶, which dramatically transcended the barrier: low amplification times and long reaction time in traditional CHA. As a proof of the concept, the elaborated MCHA as a hyper-efficiency and high-speed DNA signal-magnifier was successfully applied in ultrasensitive and rapid detection of miRNA-21 with the detection limit of 0.17 fM, which exploited an ingenious nucleic acid signal amplification technique for sensitive and fast detection of biomarkers in biosensing assay and clinic diagnose.

Development of an Automated, Non-Enzymatic Nucleic Acid Amplification Test

Among nucleic acid diagnostic strategies, non-enzymatic tests are the most promising for application at the point of care in low-resource settings. They remain relatively under-utilized, however, due to inadequate sensitivity. Inspired by a recent demonstration of a highly-sensitive dumbbell DNA amplification strategy, we developed an automated, self-contained assay for detection of target DNA. In this new diagnostic platform, called the automated Pi-powered looping oligonucleotide transporter, magnetic beads capture the target DNA and are then loaded into a microfluidic reaction cassette along with the other reaction solutions. A stepper motor controls the motion of the cassette relative to an external magnetic field, which moves the magnetic beads through the reaction solutions automatically. Real-time fluorescence is used to measure the accumulation of dumbbells on the magnetic bead surface. Left-handed DNA dumbbells produce a distinct signal which reflects the level of non-specific amplification, acting as an internal control. The autoPiLOT assay detected as little as 5 fM target DNA, and was also successfully applied to the detection of S. mansoni DNA. The autoPiLOT design is a novel step forward in the development of a sensitive, user-friendly, low-resource, non-enzymatic diagnostic test.