A path-choice-based biosensor to detect the activity of the alkaline phosphatase as the switch

The development of biosensors for alkaline phosphatase activity detection based on a phosphorylated DNA probe

Alkaline phosphatase (ALP) is a zinc-containing metalloprotein that shows very great significance in clinical diagnosis, which can catalyze the hydrolysis of phosphorylated species. ALP has the potential to serve as a valuable biomarker for detecting liver dysfunction and bone diseases. On the other hand, ALP is an efficient biocatalyst to amplify detection signals in the enzyme-linked assay. It has always been a major research focus to develop novel biosensors that can detect ALP activity with high selectivity and sensitivity. There have been numerous reports on the development of biosensors to determine ALP activity using a phosphorylated DNA probe. Among them, various beneficial strategies, such as λ exonuclease-mediated cleavage reaction, terminal deoxynucleotidyl transferase-triggered DNA polymerization, and Klenow fragment polymerase-catalyzed elongation, are employed to generate amplified and more intuitive signal. This review discusses and summarizes the development and advances of biosensors for ALP activity detection that use a well-designed phosphorylated DNA probe, aiming to provide some guidelines for the design of more sophisticated sensing strategies that exhibit improved sensitivity, selectivity, and adaptability in detecting ALP activity.

Programmable Molecular Signal Transmission Architecture and Reactant Regeneration Strategy Driven by EXO λ for DNA Circuits

The characteristics of DNA hybridization enable molecular computing through strand displacement reactions, facilitating the construction of complex DNA circuits, which is an important way to realize information interaction and processing at a molecular level. However, signal attenuation in the cascade and shunt process hinders the reliability of the calculation results and further expansion of the DNA circuit scale. Here, we demonstrate a novel programmable exonuclease-assisted signal transmission architecture, where DNA strand with toehold employed to inhibit the hydrolysis process of EXO λ is applied in DNA circuits. We construct a series circuit with variable resistance and a parallel circuit with constant current source, ensuring excellent orthogonal properties between input and output sequences while maintaining low leakage (<5%) during the reaction. Additionally, a simple and flexible exonuclease-driven reactant regeneration (EDRR) strategy is proposed and applied to construct parallel circuits with constant voltage sources that could amplify the output signal without extra DNA fuel strands or energy. Furthermore, we demonstrate the effectiveness of the EDRR strategy in reducing signal attenuation during cascade and shunt processes by constructing a four-node DNA circuit. These findings offer a new approach to enhance the reliability of molecular computing systems and expand the scale of DNA circuits in the future.

Unlocking the Full Potential of Cas12a: Exploring the Effects of Substrate and Reaction Conditions on Trans-Cleavage Activity

The trans-cleavage activity of Cas12a has been widely used with various applications. Here, we report that the trans-cleavage activity of Cas12a can be significantly affected by the fluorescent probe length and reaction buffer. The optimal probe length for Cas12a is found to be 15 nucleotides, and the optimal buffer is NEBuffer 4. Compared to the popularly used reaction conditions, the activity of Cas12a is improved by about 50-fold. In addition, the detection limit of Cas12a for DNA targets has been reduced by nearly three orders of magnitude. Our method provides a powerful tool for Cas12a trans-cleavage activity applications.

Multicolor and photothermal dual-mode assay of alkaline phosphatase based on the UV light-assisted etching of gold nanorods

A multicolor and photothermal dual-mode assay for sensitive alkaline phosphatase (ALP) determination was realized based on the 3,3',5,5'-tetramethylbenzidine (TMB)-induced etching of gold nanorods (AuNRs). TMB was oxidized under ultraviolet light irradiation to form TMB⁺. In the presence of ALP, ascorbic acid phosphate (AAP) is converted to ascorbic acid, which can then reduce the levels of TMB⁺, resulting in lower concentrations of TMB⁺. The remaining TMB⁺ was transformed into TMB²⁺ after the addition of HCl solution. AuNRs were etched by TMB²⁺ to produce a multicolor and photothermal change. Based on the degree of AuNRs etching, this highly sensitive dual-mode assay provided a linear range of 1.0-8.0 mU/mL, with detection limits of 0.34 mU/mL for the multicolor assay and 0.11 mU/mL for the photothermal assay. This method was successfully applied to the determination of ALP in serum samples.

An Exonuclease I-Aided Turn-Off Fluorescent Strategy for Alkaline Phosphatase Assay Based on Terminal Protection and Copper Nanoparticles

As an important DNA 3'-phosphatase, alkaline phosphatase can repair damaged DNA caused by replication and recombination. It is essential to measure the level of alkaline phosphatase to indicate some potential diseases, such as cancer, related to alkaline phosphatase. Here, we designed a simple and fast method to detect alkaline phosphatase quantitively. When alkaline phosphatase is present, the resulting poly T-DNA with a 3'-hydroxyl end was cleaved by exonuclease I, prohibiting the formation of fluorescent copper nanoparticles. However, the fluorescent copper nanoparticles can be monitored with the absence of alkaline phosphatase. Hence, we can detect alkaline phosphatase with this turn-off strategy. The proposed method is able to quantify the concentration of alkaline phosphatase with the LOD of 0.0098 U/L. Furthermore, we utilized this method to measure the effects of inhibitor Na₃VO₄ on alkaline phosphatase. In addition, it was successfully applied to quantify the level of alkaline phosphatase in human serum. The proposed strategy is sensitive, selective, cost effective, and timesaving, having a great potential to detect alkaline phosphatase quantitatively in clinical diagnosis.