A label-free fluorescent sensor for rapid and sensitive detection of ctDNA based on fluorescent PDA nanoparticles

Technological advances in the detection of circulating tumor DNA (ctDNA) have made new options available for diagnosis, classification, biological studies, and treatment selection. However, effective and practical methods for analyzing this emerging class of biomarkers are still lacking. In this work, a fluorescent biosensor was designed for the label-free detection of ctDNA (EGFR 19 del for non-small cell lung cancer, NSCLC). The biosensor was based on the fact that MnO2 nanosheets (MnO2 NSs) have stronger affinity towards single-stranded DNA (ssDNA), as compared with double-stranded DNA (dsDNA). As a high-performance nanoenzyme, MnO2 NSs could oxidize dopamine (DA) into fluorescent polydopamine nanoparticles (FL-PDA NPs), which could be used as a fluorescence signal. The probe ssDNA could be adsorbed on the surface of MnO2 NSs through π-π stacking, and the active site would be masked, causing a lower fluorescence. After the targets were recognized by probe ssDNA to form dsDNA, its affinity for MnO2 NSs decreased and the active site recovered, causing a restored fluorescence. It was verified that Mn ions, •OH radicals and electron transfer were the important factors in the catalytic oxidation of DA. Under the optimal experimental conditions, this biosensor exhibited a detection limit of 380 pM and a linear range of 25-125 nM, providing reliable readout in a short time (45 min). This sensor exhibited outstanding specificity, stability and reproducibility. In addition, this sensor was applied to the detection of ctDNA in serum samples and cell lysates. It is demonstrated that FL-PDA NPs can be used as a fluorescence signal for easy, rapid and label-free detection of ctDNA without any other amplification strategies, and the proposed strategy has great potential for biomarker detection in the field of liquid biopsy.

A label-free T4 polynucleotide kinase fluorescence sensor based on split dimeric G-quadruplex and ligation-induced dimeric G-quadruplex/thioflavin T conformation

The phosphorylation process of DNA by T4 polynucleotide kinase (T4 PNK) plays a crucial role in DNA recombination, DNA replication, and DNA repair. Traditional monomeric G-quadruplex (G4) systems are always activated by single cation such as K⁺ or Na⁺. The conformation transformation caused by the coexistence of multiple cations may interfere with the signal readout and limit their applications in physiological system. In view of the stability of dimeric G4 in multiple cation solution, we reported a label-free T4 PNK fluorescence sensor based on split dimeric G4 and ligation-induced dimeric G4/thioflavin T (ThT) conformation. The dimeric G4 was divided into two independent pieces of one normal monomeric G4 and the other monomeric G4 fragment phosphorylated by T4 PNK in order to decrease the background signal. With the introduction of template DNA, DNA ligase, and invasive DNA, the dimeric G4 could be generated and liberated to combine with ThT to show obvious fluorescence signal. Using our strategy, the linear range from 0.005 to 0.5 U mL^-1, and the detection limit of 0.0021 U mL^-1 could be achieved without the consideration of interference caused by the coexistence of multiple cations. Additionally, research in real sample determination and inhibition effect investigations indicated its further potential application value in biochemical process research and clinic diagnostics.

A highly sensitive fluorescent biosensor for the detection of cytochrome c based on polydopamine nanotubes and exonuclease I amplification

A novel fluorescence method for the detection of Cyt c was developed based on PDANTs and exonuclease I amplification.

Calcium ion assisted fluorescence determination of microRNA-167 using carbon dots-labeled probe DNA and polydopamine-coated Fe3O4 nanoparticles

A selective and sensitive fluorescence biosensor is described for determination of microRNA-167 using fluorescent resonant energy transfer (FRET) strategy. The FRET system comprises carbon dots (CDs, donor) labeled with probe DNA (pDNA) and polydopamine (PDA)-coated Fe₃O₄ nanoparticles (Fe₃O₄@PDA NPs, acceptor). The CDs-pDNA can be absorbed onto the surface of Fe₃O₄@PDA NPs because of the strong π interaction between pDNA and PDA. With the enhanced adsorption ability of Fe₃O₄@PDA NPs by Ca²⁺, the fluorescence intensity of CDs at 445 nm (excitation at 360 nm) is quenched. In presence of microRNA-167, the hybridized complex of CDs-pDNA-microRNA-167 will be released from the surface of Fe₃O₄@PDA NPs due to the weak π interaction of the complex and PDA. This results in the fluorescence recovery of CDs. By application of twice-magnetic separation, the biosensor shows a wide linear range of 0.5-100 nM to microRNA-167 with a 76 pM detection limit. The method was applied to the determination of microRNA-167 in samples of total microRNA extractions from A. thaliana seedlings, and the recoveries ranged from 96.4 to 98.3%.