Series or parallel toehold-mediated strand displacement and its application in circular RNA detection and logic gates

Split T7 switch-based orthogonal logic operation of fluorogenic RNA aptamer for small molecules detection

Recent advances in fluorescent biosensors have stimulated the development of molecular detection. We herein developed a new orthogonal logic operation of fluorescent biosensor with cell-free to accomplish the detection of atrazine (ATZ) and tetrachlorobiphenyls (PCB77). The transcriptional process to generate fluorescent RNA aptamers (Mango) was controlled by molecules-probe bindings, which regulate split T7 promoter transcription switches ON or OFF. Leveraging the rapid in vitro T7 transcription process and high signal-to-background ratio of the Mango-TO1-Biotin complex, this biosensor demonstrates remarkable sensitivity in detecting ATZ and PCB77, with detection limit of 1.56 pM and 10.2 pM. Moreover, the orthogonality of four logic gates (AND, NOR, INHIBT, NIMPLY) were utilized the ATZ and PCB77 as input to construct, which could be activated by utilizing the target probe-driven association. The output of the fluorescence signal was controlled by split/intact fluorescent RNA aptamer (Mango) to achieve flexible and sensitive orthogonal operations. Significantly, the development of two-input logic gates has enabled the modular detection of various small molecules, offering a promising approach to intelligent multi-input analysis. Predictably, with the advantages of sensitivity, flexibility and easy-to-operate, this orthogonal logic gate platform holds immense potential in small molecules detection.

Combination of exciton-plasmon interaction and programmable DNA cyclic amplification for electrochemiluminescence/photoelectrochemical sensing of serotonin

A novel dual-mode electrochemiluminescence (ECL)/photoelectrochemistry (PEC) biosensor was developed for sensitive serotonin detection. In this system, the PEC signal was produced by CdS quantum dots (QDs), while the ECL signal originated from L-Au NPs (luminol decorated Au nanoparticles), thereby avoiding the external interference and signal fluctuations that typically arose from using the same materials for both signals. The presence of target serotonin initiated the non-enzymatic toehold-mediated strand displacement reaction (TSDR) on magnetic bead (MB), which was followed by catalytic hairpin assembly (CHA) on the sensing interface, leading to the aggregation of many L-Au NPs. The strong exciton-plasmon interactions (EPI) induced the energy transfer between CdS QDs and Au NPs, causing the significant suppression of the photocurrent. In addition, this design assured that the ECL and PEC respond in opposing manners and that no background ECL signal was detected, thereby greatly improving the sensitivity of the biosensor. Ultimately, the biosensor demonstrated a broad linear range from 5 pM to 1 μM with a detection limit of 1.6 pM, and also could be used for the assay of serum and urine samples with satisfactory results. With the advantages of high sensitivity, selectivity, accuracy and signal stability, this sensing strategy was helpful for disease diagnosis and the fundamental research of neurotransmitters.

Fluorescent biosensor for ultra-stability detection of Pax-5a based on a double cascade amplification strategy

The development of B-lymphoblastic leukemia is tightly associated with aberrant expression of Pax-5a. This work presented a novel dual signal amplification strategy-based Pax-5a detection method by combining the rolling circle amplification reaction (RCA) and the Entropy-driven toehold-mediated strand displacement (ETSD). Particularly noteworthy is the employed ETSD, which effectively improves the rate and stability of the reaction due to its unique entropy-driven principle. The uniqueness of this method is the combination of two amplification techniques, each utilizing its own strengths to achieve our intended purpose. This sensing method has been effectively used to determine the Pax-5a gene which with a reliable linear correlation for detection within a range and achieving a detection limit of 3.34 pM, calculated using the formula (3σ/S). Furthermore, even in 1 % of human serum samples, the biosensor can identify the target gene with exceptional sensitivity. The recovery rates fall within the range of 96.68-101.76 %, with a relative standard deviation (RSD) of 5.47 %. The method has a strong specificity based on sequence-specific hybridization of nucleic acids, thereby effectively preventing potential false-positive results. This fluorescent biosensor has a high detection capability for Pax-5a, and offers stable results. It provides a new way for early clinical diagnosis of acute lymphoblastic leukemia.

Dynamic Nanostructure-Based DNA Logic Gates for Cancer Diagnosis and Therapy

DNA logic gates with dynamic nanostructures have made a profound impact on cancer diagnosis and treatment. Through programming the dynamic structure changes of DNA nanodevices, precise molecular recognition with signal amplification and smart therapeutic strategies have been reported. This enhances the specificity and sensitivity of cancer theranostics, and improves diagnosis precision and treatment outcomes. This review explores the basic components of dynamic DNA nanostructures and corresponding DNA logic gates, as well as their applications for cancer diagnosis and therapies. The dynamic DNA nanostructures would contribute to cancer early detection and personalized treatment.

Collaborative CRISPR-Cas System-Enabled Detection of Circulating Circular RNA for Reliable Monitoring of Acute Myocardial Infarction

Acute myocardial infarction (AMI) is one of the major causes of death worldwide, posing significant global health challenges. Circular RNA (circRNA) has recently emerged as a potential diagnostic biomarker for AMI, providing valuable information for timely medical care. In this work, a new electrochemical method for circRNA detection by engineering a collaborative CRISPR-Cas system is developed. This system integrates the unique circRNA-targeting ability with cascade trans-cleavage activities of Cas effectors, using an isothermal primer exchange reaction as the bridge. Using cZNF292, a circulating circRNA biomarker for AMI is identified by this group; as a model, the collaborative CRISPR-Cas system-based method exhibits excellent accuracy and sensitivity with a low detection limit of 2.13 × 10-15 m. Moreover, the method demonstrates a good diagnostic performance for AMI when analyzing whole blood samples. Therefore, the method may provide new insight into the detection of circRNA biomarkers and is expected to have great potential in AMI diagnosis in the future.

A DNA walker based on hairpin-shaped DNA aligner and fueled by nicking endonuclease for sensitive and rapid miRNA analysis

BACKGROUND

DNA walker-based strategies have gained significant attention in nucleic acid analysis. However, they face challenges related to balancing design complexity, sequence dependence, and amplification efficiency. Furthermore, most existing DNA walkers rely on walking and lock probes, requiring optimization of various parameters like DNA probe sequence, walking-to-lock probe ratio, lock probe length, etc. to achieve optimal performance. This optimization process is time-consuming and adds complexity to experiments. To enhance the performance and reliability of DNA walker nanomachines, there is a need for a simpler, highly sensitive, and selective alternative strategy.

RESULTS

A sensitive and rapid miRNA analysis strategy named hairpin-shaped DNA aligner and nicking endonuclease-fueled DNA walker (HDA-NE DNA walker) was developed. The HDA-NE DNA walker was constructed by modifying hairpin-shaped DNA aligner (HDA) probe and substrate report (SR) probe on the surface of AuNPs. Under normal conditions, HDA and SR remained stable. However, in the presence of miR-373, HDA underwent a conformational transition to an activated structure to continuously cleave the SR probe on the AuNPs with the assistance of Nt.AlwI nicking endonuclease, resulting in sensitive miRNA detection with a detection limit as low as 0.23 pM. Additionally, the proposed HDA-NE DNA walker exhibited high selectivity in distinguishing miRNAs with single base differences and can effectively analyze miR-373 levels in both normal and breast cancer patient serums.

SIGNIFICANCE

The proposed HDA-NE DNA walker system was activated by a conformational change of HDA probe only in the presence of the target miRNA, eliminating the need for a lock probe and without sequence dependence for SR probe. This strategy demonstrated a rapid reaction rate of only 30 min, minimal background noise, and a high signal-to-noise ratio (S/B) compared to capture/lock-based DNA walker. The method is expected to become a powerful tool and play an important role in disease diagnosis and precision therapy.

Sea Anemone-like Nanomachine Based on DNA Strand Displacement Composed of Three Boolean Logic Gates: Diversified Input for Intracellular Multitarget Detection

Efficient and accurate acquisition of cellular biomolecular information is crucial for exploring cell fate, achieving early diagnosis, and the effective treatment of various diseases. However, current DNA biosensors are mostly limited to single-target detection, with few complex logic circuits for comprehensive analysis of three or more targets. Herein, we designed a sea anemone-like DNA nanomachine based on DNA strand displacement composed of three logic gates (YES-AND-YES) and delivered into the cells using gold nano bipyramid carriers. The AND gate activation depends on the trigger chain released by upstream DNA strand displacement reactions, while the output signal relies on the downstream DNAzyme structure. Under the influence of diverse inputs (including enzymes, miRNA, and metal ions), the interconnected logic gates simultaneously perform logical analysis on multiple targets, generating a unique output signal in the YES/NO format. This sensor can successfully distinguish healthy cells from tumor cells and can be further used for the diagnosis of different tumor cells, providing a promising platform for accurate cell-type identification.