Fluorescence quenching of various indoles by nickel complexes

Cysteine-independent CRISPR-Associated Protein Labeling for Presentation and Co-delivery of Molecules Toward Genetic and Epigenetic Regulations

Labeling of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) associated proteins (Cas) remains an immense challenge for their genome engineering applications. To date, cysteine-mediated bioconjugation is the most efficient strategy for labeling Cas proteins. However, introducing a cysteine residue in the protein at the right place might be challenging without perturbing the enzymatic activity. We report a method that does not require cysteine residues for small molecule presentation on the CRISPR-associated protein SpCas9 for in vitro protein detection, probing cellular protein expression, and nuclear co-delivery of molecules in mammalian cells. We repurposed a simple protein purification tag His6 peptide for non-covalent labeling of molecules on the CRISPR enzyme SpCas9. The small molecule labeling enabled us to rapidly detect SpCas9 in a biochemical assay. We demonstrate that small molecule labeling can be utilized for probing bacterial protein expression in realtime. Furthermore, we coupled SpCas9's nuclear-targeting ability in co-delivering the presenting small molecules to the mammalian cell nucleus for prospective genome engineering applications. Furthermore, we demonstrate that the method can be generalized to label oligonucleotides for multiplexing CRISPR-based genome editing and template-mediated DNA repair applications. This work paves the way for genomic loci-specific bioactive small molecule and oligonucleotide co-delivery toward genetic and epigenetic regulations.

The binding of a c-MYC promoter G-quadruplex to neurotransmitters: An analysis of G-quadruplex stabilization using DNA melting, fluorescence spectroscopy, surface-enhanced Raman scattering and molecular docking

The interactions of several neurotransmitter and neural hormone molecules with the c-MYC G-quadruplex DNA sequence were analyzed using a combination of spectroscopic and computational techniques. The interactions between indole, catecholamine, and amino acid neurotransmitters and DNA sequences could potentially add to the understanding of the role of G-quadruplex structures play in various diseases. Also, the interaction of the DNA sequence derived from the nuclear hypersensitivity element (NHE) III1 region of c-MYC oncogene (Pu22), 5'-TGAGGGTGGGTAGGGTGGGTAA-3', has added significance in that these molecules may promote or inhibit the formation of G-quadruplex DNA which could lead to the development of promising drugs for anticancer therapy. The results showed that these molecules did not disrupt G-quadruplex formation even in the absence of quadruplex-stabilizing cations. There was also evidence of concentration-dependent binding and high binding affinities based on the Stern-Volmer model, and thermodynamically favorable interactions in the form of hydrogen-bonding and interactions involving the π system of the aromatic neurotransmitters.

Inhibition of albendazole and 2-(2-aminophenyl)-1H-benzimidazole against tyrosinase: mechanism, structure-activity relationship, and anti-browning effect

BACKGROUND

Tyrosinase is the key enzyme involved in enzymatic browning of plant-derived foods. Inhibition of tyrosinase activity contributes to the control of food browning. Due to safety regulations or other issues, most identified tyrosinase inhibitors are not suitable for practical use. Therefore, it is necessary to search for novel tyrosinase inhibitors. In this study, the anti-tyrosinase activity and mechanism of albendazole and 2-(2-aminophenyl)-1H-benzimidazole (2-2-A-1HB) were investigated through ultraviolet-visible absorption spectroscopy, fluorescence spectra, molecular docking, and molecular dynamic (MD) simulation. The anti-browning effect of albendazole on fresh-cut apples was then elucidated.

RESULTS

Albendazole and 2-2-A-1HB were both efficient tyrosinase inhibitors with IC₅₀ of 51 ± 1.5 and 128 ± 1.3 μmol L^-1 , respectively. Albendazole suppressed tyrosinase non-competitively and formed tyrosinase-albendazole complex statically. Hydrogen bond and hydrophobic interaction were major driving forces in stabilizing the tyrosinase-albendazole complex. While 2-2-A-1HB inhibited the enzyme competitively and quenched its intrinsic fluorescence through a static mechanism, it generated strong binding affinity with tyrosinase through hydrophobic interaction. MD simulations further validated that albendazole/2-2-A-1HB could form stable complexes with tyrosinase and loosened its basic framework structure, leading to a change in secondary structure and conformation. In addition, albendazole could delay the browning of fresh-cut apples by inhibiting the activity of polyphenol oxidase, peroxidase and phenylalanine ammonia-lyase, and reducing the oxidation of phenolic compounds.

CONCLUSION

This research might provide a deep view of tyrosinase inhibition by benzimidazole derivatives and a theoretical basis for developing albendazole as a potential fresh-keeping agent. © 2023 Society of Chemical Industry.

Efficient detection for Nitrofurazone based on novel Ag2S QDs/g-C3N4 fluorescent probe

In the paper, a novel fluorescent probe based on Ag₂S QDs/g-C₃N₄ composite was synthesized by loading Ag₂S quantum dots (Ag₂S QDs) on the surface of g-C₃N₄ through in-situ synthesis method and developed to detect Nitrofurazone (NFZ) sensitively. The results showed that the linear detection range of Ag₂S QDs/g-C₃N₄ to NFZ was 0-30 μM, with a low detection limit of 0.054 μM. The results of time-fluorescence-resolved spectroscopy and UV-vis absorption spectroscopy exhibited that the possible detection mechanism of Ag₂S QDs/g-C₃N₄ to NFZ was proposed to be Internal Filtration Effect (IFE). Moreover, Multiwfn wavefunction analysis was employed to uncover the possible interaction between the Ag₂S QDs/g-C₃N₄ and NFZ, thereby further revealing the fluorescence detection mechanism from the scale of atoms. Combining experiments and theoretical calculations, we proposed the sensing mechanism of the formation of non-fluorescent ground state complex linked by hydrogen bonds. This work indicated that the Ag₂S QDs/g-C₃N₄ composite processed the ability to detect NFZ efficiently and sensitively.

The interaction between bovine serum albumin and [6]-,[8]- and [10]-gingerol: An effective strategy to improve the solubility and stability of gingerol

In this study, the binding mechanism between bovine serum albumin (BSA) and three gingerols ([6]-, [8]- and [10]-gingerol) was evaluated to explore an effective strategy for improving solubility and stability of gingerols. The fluorescence analysis suggested gingerols could bind with BSA to form a stable BSA/gingerols complex and [10]-gingerol had the strongest binding affinity (K_a = 4.016 × 10⁴ L/mol) at 298 K. Thermodynamic parameters and molecular modeling validated that hydrophobic interaction and hydrogen bonds were the main driving force for the interaction of BSA/gingerols. Gingerols bound to BSA at site I (subdomain IIA) resulted in a conformational change of BSA with a structure shrinkage, which was responsible for the decrease of surface hydrophobicity. The formation of BSA/gingerols complexes promoted the solubility of [6]-, [8]- and [10]-gingerol increasing by 1.50, 6.04 and 23.50 times, respectively. In addition, the stability and antioxidant capacity of gingerols was significantly improved after binding with BSA.

Malachite Green, the hazardous materials that can bind to Apo-transferrin and change the iron transfer

Different groups of synthetic dyes might lead to environmental pollution. The binding affinity among hazardous materials with biomolecules necessitates a detailed understanding of their binding properties. Malachite Green might induce a change in the iron transfer by Apo-transferrin. Spectroscopic studies showed malachite green oxalate (MGO) could form the apo-transferrin-MGO complex and change the Accessible Surface Area (ASA) of the key amino acids for iron transfer. According to the ASA results the accessible surface area of Tyrosine, Aspartate, and Histidine of apo-transferrin significantly were changed, which can be considered as a convincing reason for changing the iron transfer. Moreover, based on the fluorescence data MGO could quench the fluorescence intensity of apo-transferrin in a static quenching mechanism. The experimental and Molecular Dynamic simulation results represented that the binding process led to micro environmental changes, around tryptophan residues and altered the tertiary structure of apo-transferrin. The Circular Dichroism (CD) spectra result represented a decrease in the amount of the α-Helix, as well as, increase in the β-sheet volumes of the apo-transferrin structure. Moreover, FTIR spectroscopy results showed a hypochromic shift in the peaks of amide I and II. Molecular docking and MD simulation confirmed all the computational findings.

Fluorescent DNA-templated silver nanoclusters for highly sensitive detection of D-penicillamine

Herein, fluorescent DNA-templated silver nanoclusters (DNA-AgNCs) with red emission were synthesized and utilized as novel probe to detect D-penicillamine (D-Pen) for the first time. D-Pen molecules contain a thiol which can combine with Ag to form a non-fluorescent ground state complex, inducing the aggregation of DNA-AgNCs followed by the fluorescence quenching. The quenching mechanism is well-studied and found to be a static quenching process. This method can detect D-Pen in the range of 0.025-0.7 μM with the detection limit as low as 8 nM, which is 1-3 orders of magnitude more sensitive than those based on other fluorescent nanoprobes. More importantly, the preparation procedure for DNA-AgNCs is fast and without the requirement of heavy metal ions. Thus, this detection strategy is time-saving and eco-friendly. Satisfactory recoveries have been acquired for monitoring D-Pen in human serum samples and pharmaceutical samples owing to the high sensitivity.

Comparing the inhibitory abilities of epigallocatechin-3-gallate and gallocatechin gallate against tyrosinase and their combined effects with kojic acid

Inhibition of tyrosinase activity contributes to the control of food browning and skin pigmentation diseases. Herein, the inhibitory mechanism of epigallocatechin-3-gallate (EGCG) and gallocatechin gallate (GCG) on tyrosinase were investigated. Both EGCG and GCG inhibited tyrosinase in a mixed manner with the IC₅₀ values of 39.4 ± 0.54 μM and 36.8 ± 0.21 μM, and showed a synergism with their combination, while EGCG and GCG combined with kojic acid (IC₅₀ = 19.2 ± 0.26 μM) exhibited antagonism and additive effect, respectively. EGCG and GCG interacted with tyrosinase mainly by hydrogen bonding and hydrophobic interactions and induced a looser conformation of tyrosinase. Molecular docking indicated that EGCG and GCG bound to the active center of tyrosinase and interacted with copper ions and key amino acid residues. Molecular dynamics simulation further characterized the structure and property of EGCG/GCG-tyrosinase complex. This study provides novel insights into the mechanism of catechins as tyrosinase inhibitors.