Browsing by Author "Zheng, Jinkai"

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Comparison of the peroxidase activities of iron oxide nanozyme with DNAzyme and horseradish peroxidase
(Royal Society of Chemistry, 2023-04-20) Lu, Chang; Zandieh, Mohamad; Zheng, Jinkai; Liu, Juewen
Peroxidase-based assays are the most extensively used in bioanalytical sensors because of their simple colorimetric readout and high sensitivity owing to enzymatic signal amplification. To improve the stability, modification, and cost of protein-based enzymes, such as horseradish peroxidase (HRP), various enzyme mimics, such as DNAzymes and nanozymes, have emerged over the last few decades. In this study, we compared the peroxidase activities of HRP, a G-quadruplex (G4)-hemin DNAzyme, and Fe3O4 nanozymes in terms of activity and stability under different conditions. The reactions were much slower at pH 7 than at pH 4. At pH 4, the turnover rate of HRP (375 s−1) was faster than that of G4 DNAzyme (0.14 s−1) and Fe3O4 (6.1 × 10−4 s−1, calculated by surface Fe concentration). When normalized to mass concentrations, the trend was the same. Through observation of the reaction for a long time of 2 h, the changes in the color and UV-vis spectra were also different for these catalysts, indicating different reaction mechanisms among these catalysts. Moreover, different buffers and nanozyme sizes were found to influence the activity of the catalysts. Fe3O4 showed the highest stability compared to HRP and G4 DNAzyme after a catalytic reaction or incubation with H2O2 for a few hours. This study helps to understand the properties of catalysts and the development of novel catalysts with enzyme-mimicking activities for application in various fields.
DNA-Directed Seeded Synthesis of Gold Nanoparticles without Changing DNA Sequence
(Asian Chemical Editorial Society (ACES), 2022-05-06) Lu, Chang; Zandieh, Mohamad; Zheng, Jinkai; Liu, Juewen
DNA has been used for directing the growth of noble metal nanoparticles into different morphologies. Most previous studies focused on the effect of DNA sequence, while the effect of DNA adsorption was not thoroughly explored. In this work, we controlled the seeded growth of AuNPs by using the same DNA sequence but under different initial adsorption conditions: room temperature and heating. DNA adsorbed by heating induced more anisotropic nanoparticle growth, and the most effect was observed with 100 nM C30 DNA, where nanoflowers were obtained for the heated sample. By measuring DNA adsorption and desorption, heating did not increase DNA adsorption density but increased the adsorption affinity. The percentage of adsorbed DNA before the growth was only about 10%, regardless of heating, while after the growth, the associated DNA reached 75% or more, indicating that the free DNA also influenced the growth. This study offers fundamental insights into the effect of DNA adsorption on seeded AuNP growth, providing a method to tune the morphology of nanoparticles without changing DNA sequence.
Protection of DNA by metal ions at 95 °C: from lower critical solution temperature (LCST) behavior to coordination-driven self-assembly
(Royal Society of Chemistry, 2022-09-05) Lu, Chang; Xu, Yuancong; Huang, Po-Jung Jimmy; Zandieh, Mohamad; Wang, Yihao; Zheng, Jinkai; Liu, Juewen
While polyvalent metal ions and heating can both degrade nucleic acids, we herein report that a combination of them leads to stabilization. After incubating 4 mM various metal ions and DNA oligonucleotides at 95 °C for 3 h at pH 6 or 8, metal ions were divided into four groups based on gel electrophoresis results. Mg2+ can stabilize DNA at pH 6 without forming stable nanoparticles at room temperature. Co2+, Cu2+, Cd2+, Mn2+ and Zn2+ all protected the DNA and formed nanoparticles, whereas the nanoparticles formed with Fe2+ and Ni2+ were so stable that they remained even in the presence of EDTA. At pH 8, Ce3+ and Pb2+ showed degraded DNA bands. For Mg2+, better protection was achieved with higher metal and DNA concentrations. By monitoring temperature-programmed fluorescence change, a sudden drop in fluorescence intensity attributable to the lower critical solution temperature (LCST) transition of DNA was found to be around 80 °C for Mg2+, while this transition temperature decreased with increasing Mn2+ concentration. The unexpected thermal stability of DNA enabled by metal ions is useful for extending the application of DNA at high temperatures, forming coordination-driven nanomaterials, and it might offer insights into the origin of life on the early Earth.
Reversible and Irreversible HAuCl4 Binding to DNA for Seeded Gold Nanoparticle Growth and Opposite DNA and Aptamers Colorimetric Sensing Outcomes
(Wiley, 2022-08-09) Lu, Chang; Zandieh, Mohamad; Zheng, Jinkai; Liu, Juewen
DNA-directed seeded growth of gold nanoparticles has been used for the development of aptamer-based biosensors with the assumption that target analytes can modulate the adsorption of aptamers to the gold seeds and thus affect the growth reaction. To understand the reaction, the effect of single- and double-stranded DNA is first examined, and it is found that they have a similar promotion effect of anisotropic growth, suggesting that DNA cannot be detected using this method. By studying the interaction between HAuCl4 and DNA, both weak reversible binding and strong irreversible binding are identified, with the latter becoming dominating with a longer incubation time. Single- and double-stranded DNA have similar weak binding to HAuCl4, and this weak binding is more important for the growth reaction. Then three aptamers are tested, where only cortisol appeared to modulate its aptamer adsorption and the growth reaction reflected aptamer binding. Hg2+ shows no advantage for its aptamer, and quinine induced aggregation of AuNPs cannot be detected by this reaction either. Therefore, each aptamer target needs to be individually studied to test if this method is applicable. It is also noted that DNA and aptamers have opposite outcomes for the target-dependent growth reactions.