Simple Monovalent Metal Ion Logical Order to Regulate the Secondary Conformation of G-Quadruplex

Nanoscale Interaction of Endonuclease APE1 with DNA

Apurinic/apyrimidinic endonuclease 1 (APE1) is involved in DNA repair and transcriptional regulation mechanisms. This multifunctional activity of APE1 should be supported by specific structural properties of APE1 that have not yet been elucidated. Herein, we applied atomic force microscopy (AFM) to characterize the interactions of APE1 with DNA containing two well-separated G-rich segments. Complexes of APE1 with DNA containing G-rich segments were visualized, and analysis of the complexes revealed the affinity of APE1 to G-rich DNA sequences, and their yield was as high as 53%. Furthermore, APE1 is capable of binding two DNA segments leading to the formation of loops in the DNA-APE1 complexes. The analysis of looped APE1-DNA complexes revealed that APE1 can bridge G-rich segments of DNA. The yield of loops bridging two G-rich DNA segments was 41%. Analysis of protein size in various complexes was performed, and these data showed that loops are formed by APE1 monomer, suggesting that APE1 has two DNA binding sites. The data led us to a model for the interaction of APE1 with DNA and the search for the specific sites. The implication of these new APE1 properties in organizing DNA, by bringing two distant sites together, for facilitating the scanning for damage and coordinating repair and transcription is discussed.

Ratiometric G-quadruplex/hemin DNAzymes with low-dosage associative substrates

BACKGROUND

G-quadruplex (G4)/hemin DNAzymes with conversion of substrates into colorimetric readouts are well recognized as convenient biocatalysis tools in sensor development. However, the previously developed colorimetric G4/hemin DNAzymes are diffusive substrate-based DNAzymes (DSBDs). The current colorimetric DSBDs have several drawbacks including high dosage (∼mM) of diffusive substrates (DSs), colorimetric product toxicity, and single colorimetric readout without tolerance to fluctuation of experimental factors and background. In addition, the usage of high-dosage DSs can smear the G4 foldings and their discard is more harmful to environment. Therefore, exploring alternative DNAzymes with potential to overcome these drawbacks of DSBDs is urgently needed.

RESULTS

We herein developed associative substrate-based DNAzymes (ASBDs). Cyanine dyes were selected as associative substrates (ASs) due to their binding competency with G4/hemin DNAzymes. With respect to DSBDs, ASBDs needed only low dosage (∼10 μM) of ASs to be able to cause a rapid and visible substrate conversion. In addition, since cyanine dyes are NIR dyes with high extinction coefficients and their conversion products have absorption bands at shorter wavelength. Therefore, a colorimetric ratio response can be developed to follow activities of G4/hemin DNAzymes with competency to tolerate fluctuation of experimental factors and background. In particular, herein developed ASBDs can endure somewhat concentration fluctuation of H2O2. ASBDs are able to cowork with other enzymes (for example, glucose oxidase) to realize cascade sensing.

SIGNIFICANCE

The developed ASBDs can operate at low dosage of substrates with a colorimetric ratio response and can overcome the drawbacks met in DSBDs. We expect that, by designing ASs with fruitful color panel in the future, our work will inspire more interesting in developing environment-benign and low-carbon G4/hemin DNAzymes and desired colorful high-performance sensors.

Synthesis and Structural Studies of Nucleobase Functionalized Hydrogels for Controlled Release of Vitamins

The development of biomolecule-derived biocompatible scaffolds for drug delivery applications is an emerging research area. Herein, we have synthesized a series of nucleobase guanine (G) functionalized amino acid conjugates having different chain lengths to study their molecular self-assembly in the hydrogel state. The gelation properties have been induced by the correct choice of chain lengths of fatty acids present in nucleobase functionalized molecules. The effect of alkali metal cations, pH, and the concentration of nucleobase functionalized amino acid conjugates in the molecular self-assembly process has been explored. The presence of Hoogsteen hydrogen bonding interaction drives the formation of a G-quadruplex functionalized hydrogel. The DOSY nuclear magnetic resonance is also performed to evaluate the self-assembling behavior of the newly formed nucleobase functionalized hydrogel. The nanofibrillar morphology is responsible for the formation of a hydrogel, which has been confirmed by various microscopic experiments. The mechanical behaviors of the hydrogel were evaluated by rheological experiments. The in vitro biostability of the synthesized nucleobase amino acid conjugate is also investigated in the presence of hydrolytic enzymes proteinase K and chymotrypsin. Finally, the nucleobase functionalized hydrogel has been used as a drug delivery platform for the control and sustained pH-responsive release of vitamins B2 and B12. This synthesized nucleobase functionalized hydrogel also exhibits noncytotoxic behavior, which has been evaluated by their in vitro cell viability experiment using HEK 293 and MCF-7 cell lines.

Green Synthesis of Silver Nanoparticles Using Acacia ehrenbergiana Plant Cortex Extract for Efficient Removal of Rhodamine B Cationic Dye from Wastewater and the Evaluation of Antimicrobial Activity

Silver nanoparticles (Ag-NPs) exhibit vast potential in numerous applications, such as wastewater treatment and catalysis. In this study, we report the green synthesis of Ag-NPs using Acacia ehrenbergiana plant cortex extract to reduce cationic Rhodamine B (RhB) dye and for antibacterial and antifungal applications. The green synthesis of Ag-NPs involves three main phases: activation, growth, and termination. The shape and morphologies of the prepared Ag-NPs were studied through different analytical techniques. The results confirmed the successful preparation of Ag-NPs with a particle size distribution ranging from 1 to 40 nm. The Ag-NPs were used as a heterogeneous catalyst to reduce RhB dye from aqueous solutions in the presence of sodium borohydride (NaBH₄). The results showed that 96% of catalytic reduction can be accomplished within 32 min using 20 μL of 0.05% Ag-NPs aqueous suspension in 100 μL of 1 mM RhB solution, 2 mL of deionized water, and 1 mL of 10 mM NaBH₄ solution. The results followed a zero-order chemical kinetic (R² = 0.98) with reaction rate constant k as 0.059 mol L^-1 s^-1. Furthermore, the Ag-NPs were used as antibacterial and antifungal agents against 16 Gram-positive and Gram-negative bacteria as well as 1 fungus. The green synthesis of Ag-NPs is environmentally friendly and inexpensive, as well as yields highly stabilized nanoparticles by phytochemicals. The substantial results of catalytic reductions and antimicrobial activity reflect the novelty of the prepared Ag-NPs. These nanoparticles entrench the dye and effectively remove the microorganisms from polluted water.