A multiple primers-mediated exponential rolling circle amplification strategy for highly sensitive detection of T4 polynucleotide kinase and T4 DNA ligase activity

A rolling circle mediated exponential amplification reaction with suppressed nonspecific amplification to detect pathogen RNA with high sensitivity

Respiratory infections caused by pathogens such as influenza virus and SARS-CoV-2 seriously threaten human life and health. RNA has been widely recognized as an important biomarker for diagnosing these pathogens, creating a growing need for rapid and accurate RNA detection methods. Isothermal nucleic acid amplification has emerged as a promising molecular diagnostics approach. Exponential amplification reactions (EXPAR) is a commonly used RNA detection method, known for its simplicity and rapid signal amplification in a short time. However, traditional EXPAR is only suitable for detecting short-sequence RNA, and 3'-end template interactions in the amplification reaction can lead to nonspecific amplification, which greatly limits its practical application. Here, we established an isothermal amplification method comprising a three-way junction (3-WJ) structure and dumbbell probe (DP) for the rapid and sensitive detection of pathogen RNA in a single closed tube, termed the rolling circle mediated exponential amplification reaction (RC-EXPAR). The introduction of the DP eliminated the 3'-end of the template, suppressing nonspecific amplification caused by the 3'-end extension in the reaction. Although the trigger generation by the 3-WJ structure is a linear amplification process, the RC-EXPAR amplifies the triggers exponentially to enhance signal output further and increase sensitivity. The proposed method showed a high sensitivity with a limit of detection (LOD) of 103 copies/mL. Moreover, RC-EXPAR demonstrated strong anti-interference capability in complex biological matrices. This work opens up new ideas for suppressing nonspecific amplification and provides a promising signal amplification strategy for rapid, sensitive, and specific pathogen detection in clinical.

In situ surface oxygen vacancy effect synergistic with internal polarization effect in BiFeO3 for photoelectrochemical detection of T4 DNA ligase

Recently, the field of cathode photoelectrochemistry has advanced significantly, yet there remained a dearth of innovative approaches in signal transmission strategies. This paper introduced a novel concept where the dopamine (DA)-engineered surface vacancy (Ov) effect on BiFeO3 microspheres synergistically interacted with the intrinsic polarization of the material, leading to a significantly enhanced photocurrent when compared to that of Bi2O3 or Fe2O3 alone without a built-in electric field. Based on this finding, we proposed a PEC biosensor that leveraged the competitive binding reaction between single-base nucleotides and DA for photocurrent output, wherein the T4 DNA ligase-mediated ligation reaction governed the production of single-base nucleotides. The detection system demonstrated commendable performance for T4 DNA ligase analysis, with a linear detection range spanning from 0.0006 to 10 U/mL. The detection limit was determined to be 0.0001 U/mL. This ligase detection method requires no labeling, was straightforward to operate, and exhibited high sensitivity and excellent selectivity. This study not only elucidates the synergistic effect of in-situ surface Ov effect and the internal polarization effect the ferroelectric material to construct an efficient PEC sensing mechanism, but also introduces a new method for measuring T4 DNA ligase.

Triangle-toothed gear occlude-guided universal nanotechnology constructs 3D symmetric DNA polyhedra with high assembly efficiency for precision cancer therapy

Chemotherapy is commonly used to treat malignant tumors. However, conventional chemotherapeutic drugs often cannot distinguish between tumor and healthy cells, resulting in adverse effects and reduced therapeutic efficacy. Therefore, zigzag-shaped gear-occlude-guided cymbal-closing (ZGC) DNA nanotechnology was developed based on the mirror-symmetry principle to efficiently construct symmetric DNA polyhedra. This nanotechnology employed simple mixing steps for efficient sequence design and assembly. A targeting aptamer was installed at a user-defined position using an octahedron as a model structure. Chemotherapeutic drug-loaded polyhedral objects were subsequently delivered into tumor cells. Furthermore, anticancer drug-loaded DNA octahedra were intravenously injected into a HeLa tumor-bearing mouse model. Assembly efficiency was almost 100 %, with no residual building blocks identified. Moreover, this nanotechnology required a few DNA oligonucleotides, even for complex polyhedrons. Symmetric DNA polyhedrons retained their structural integrity for 24 h in complex biological environments, guaranteeing prolonged circulation without drug leakage in the bloodstream and promoting efficient accumulation in tumor tissues. In addition, DNA octahedra were cleared relatively slowly from tumor tissues. Similarly, tumor growth was significantly inhibited in vivo, and a therapeutic outcome comparable to that of conventional gene-chemo combination therapy was observed. Moreover, no systemic toxicity was detected. These findings indicate the potential application of ZGC DNA nanotechnology in precision medicine.

A label-free fluorescent biosensor for amplified detection of T4 polynucleotide kinase activity based on rolling circle amplification and catalytic hairpin assembly

T4 polynucleotide kinase (PNK) plays a key role in maintaining genome integrity and repairing DNA damage. In this paper, we proposed a label-free fluorescent biosensor for amplified detection of T4 PNK activity based on rolling circle amplification (RCA) and catalytic hairpin assembly (CHA). Firstly, we designed a padlock probe with a 5'-hydroxyl terminus for phosphorylation reaction, a complementary sequence of the primer for initiating RCA, and a complementary sequence of the trigger for triggering CHA. T4 PNK catalyzed the phosphorylation reaction by adding a phosphate group to the 5'-hydroxyl terminus of padlock probe, generating a phosphorylated padlock probe. Then it hybridized with the primer to generate a circular probe under the action of ligase. Subsequently, the primer initiated an RCA reaction along the circular probe to synthesize a large molecular weight product with repetitive trigger sequences. The triggers then triggered the cyclic assembly reactions between hairpin probe 1 and hairpin probe 2 to generate a large amount of complexes with free G-rich sequences. The free G-rich sequences folded into G-quadruplex structures, and the N-methylmesoporphyrin IXs were inserted into them to produce an amplified fluorescent signal. Benefiting from high amplification efficiency of RCA and CHA, this fluorescent biosensor could detect T4 PNK as low as 6.63 × 10^-4 U mL^-1, and was successfully applied to detect its activity in HeLa cell lysates. Moreover, this fluorescent biosensor could effectively distinguish T4 PNK from other alternatives and evaluate the inhibitory effect of inhibitor, indicating that it had great potential in drug screening and disease treatment.