The ultra-sensitive visual biosensor based on thermostatic triple step functional nucleic acid cascade amplification for detecting Zn2+

A competitive colorimetric aptasensor for simple and sensitive detection of kanamycin based on terminal deoxynucleotidyl transferase-mediated signal amplification strategy

We developed a rapid and sensitive colorimetric biosensor based on competitive recognition between kanamycin (KAN), magnetic beads-kanamycin (MBs-KAN) and aptamer and terminal deoxynucleotidyl transferase (TdT)-mediated signal amplification strategy. In the absence of KAN, aptamers recognize MBs-KAN. TdT can amplify oligonucleotides to the 3'-OH ends of aptamers, with biotin-dUTP being embedded in the long single stranded DNA (ssDNA). Then the assay produced visual readout due to the horseradish peroxidase (HRP)-catalyzed color change of the substrate after the linkage between biotin and streptavidin (SA)-HRP. In the presence of KAN, however, aptamers tend to bind free KAN rather than MBs-KAN. In this case, aptamers are isolated by magnetic separation, resulting in the failure of signal amplification and catalytic signals. This competitive colorimetric sensor showed excellent selectivity toward KAN with the limit of detection (LOD) as low as 9 pM. And recovery values were between 93.8 and 107.8% when spiked KAN in milk and honey samples.

Highly Sensitive and Selective Copper (II)-Catalyzed Dual-DNAzyme Colorimetric Biosensor Based on Exonuclease III-Mediated Cyclical Assembly

“Cu-DNAzyme” and “G4-DNAzyme” were used to develop a “turn-off” dual-DNAzyme colorimetric biosensor, which could be used to detect Cu2+ by employing exonuclease III-mediated cyclical assembly (EMCA). EMCA was based on the cleavage activity of Cu2+ to transfer the linkage sequences of the substrate strand and enzyme strand into the transition sequence. The horseradish peroxidase (HRP)-mimicking activity of the G4-DNAzyme was lost after binding with the complementary transition sequence and was hydrolyzed by Exo III. These results demonstrate that the proposed colorimetric biosensor was an effective method for ultradetection of trace metals in a high original signal background. Due to the high sensitivity of the biosensor, the limit of detection (LOD) of Cu2+ is 0.16 nM. This design offers a general purpose platform that could be applied for the detection of any metal ion target through adjustment of metal-dependent DNA-cleaving DNAzymes, which is of great significance for the rapid determination of food safety.

Developing a three-input cascade DNA logic gate based on the biological characteristics of metal ion-GO, combined with analysis and verification

Due to the limitation of technology, electronic computing is approaching the limit of technology, and new computing tools need to be developed. Here, we build a three-input cascade logic gate based on the advantages of biomolecules, particularly DNA, in the construction of computational logic systems, combined with metal ions and graphene oxide (GO). It is worth mentioning that this study uses a variety of research methods. In addition to the commonly used biological experiments, NUPACK and visual DSD simulation methods are used for analysis, and orthogonal, standardized and other statistical means are used to simplify the experimental process and make the results intuitive. Finally, the designed three-input logic gate is successfully constructed, and it is found that it may have the potential to realize complex computing.

Polysaccharide-enhanced ARGET ATRP signal amplification for ultrasensitive fluorescent detection of lung cancer CYFRA 21-1 DNA

An ultrasensitive fluorescence biosensor for detecting cytokeratin fragment antigen 21-1 (CYFRA 21-1) DNA of non-small cell lung carcinoma (NSCLC) is designed using polysaccharide and activator regenerated by electron transfer atom transfer radical polymerization (ARGET ATRP) signal amplification strategy. Thiolated peptide nucleic acid (PNA) is fixed on magnetic nanoparticles (MNPs) by a cross-linking agent and hybridized with CYFRA 21-1 DNA. Hyaluronic acid (HA) is linked to PNA/tDNA heteroduplexes in the form of carboxy-Zr⁴⁺-phosphate. Subsequently, multiple 2-bromo-2-methylpropionic acid (BMP) molecules are linked with HA to initiate ARGET ATRP reaction. Finally, a large number of fluorescein o-acrylate (FA) monomers are polymerized on the macro-initiators, and the fluorescence signal is significantly amplified. Under optimal conditions, this biosensor shows a significant linear correlation between the fluorescence intensity and logarithm of CYFRA 21-1 DNA concentration (0.1 fM to 0.1 nM), and the limit of detection is as low as 78 aM. Furthermore, the sensor has a good ability to detect CYFRA 21-1 DNA in serum samples and to recognize mismatched bases. It suggests that the strategy has broad application in early diagnosis by virtue of its high sensitivity and selectivity. Graphical abstract A novel and highly sensitive fluorescence biosensor for quantitatively detecting CYFRA 21-1 DNA via dual signal amplification of hyaluronic acid and ARGET ATRP reaction was developed. This proposed method has a low detection limit, wide detection range, high selectivity, and strong anti-interference.

TiO2 Nanoparticle-Enhanced Linker Recombinant Strand Displacement Amplification (LRSDA) for Universal Label-Free Visual Bioassays

The influence of nanomaterials on dynamic isothermal amplification and their morphology regulated by bionic biological reactions in vitro remain unknown. From a theoretical perspective, TiO₂ nanoparticles enhance the amplification efficiency and reaction specificity of recombinase polymerase amplification (RPA). These nanoparticles aggregated into larger nanoclusters by adsorbing RPA components, termed nanoscale RPA factories, which increased their local concentrations to enhance RPA. Following the nick/extension cycles mediated by a bifunctional linker located at the 5' end of the forward primers, the TiO₂ nanoparticle-enhanced LRSDA process produces single-stranded products, constituting the G-quadruplex DNAzymes and catalyzing the chromogenic substrate to facilitate colorimetric analysis for on-site bioassays. Salmonella spp. and genetically modified maize MON810 could be detected with a detection limit of 4 cfu/mL and 0.1% transgenic components, respectively. Briefly, TiO₂-assisted isothermal molecular amplification addressed the demands of practical on-site applications.