Synthesis, DNA binding of bis-naphthyl ferrocene derivatives and the application as new electroactive indicators for DNA biosensor

A series of bis-naphthyl ferrocene derivatives were synthesized and characterized. Based on the results obtained from UV-visible absorption titration and ethidium bromide (EB) displacement experiments, it was observed that the synthesized compounds exhibited a strong binding ability to dsDNA. In comparison to the viscosity curve of EB, the tested compounds demonstrated a bisintercalation binding mode when interacting with CT-DNA. Differential pulse voltammetry (DPV) was employed to assess the binding specificity of these indicators towards ssDNA and dsDNA. All tested indicators displayed more pronounced signal differences before and after hybridization between probe nucleic acids and target nucleic acids compared to Methylene Blue (MB). Among the evaluated compounds, compound 3j containing an ether chain showed superior performance as an indicator, making it suitable for constructing DNA-based biosensors. Under optimized conditions including probe ssDNA concentration and indicator concentration, this biosensor exhibited good sensitivity, reproducibility, stability, and selectivity. The limit of detection was calculated as 4.53 × 10-11 mol/L. Furthermore, when utilizing 3j as the indicator in serum samples, the biosensor achieved satisfactory recovery rates for detecting the BRCA1 gene.

Bio-inspired nickel nanoparticles of pyrimidine-Schiff base: In vitro anticancer, BSA and DNA interactions, molecular docking and antioxidant studies

In this work, interactions of pyrimidine derivative Schiff base ligand (DMPMM) were studied and its stabilized powder nickel nanoparticles (DMPMM-NiNPs) were synthesized and various biological studies were evaluated. DNA binding studies of CT-DNA with prepared compounds in Tris-HCl/NaCl buffer were carried out by traditional UV-Visible and fluorescence spectroscopic methods, viscosity measurements and cyclic voltammetry. Results showed that the small scale of DMPMM had less activity to interact with biological systems and when it assembled on nickel nanoparticles surface the activity increased. Thermal denaturation and sonochemical denaturation studies of DNA with the presence and the absence of our compounds also were done by UV-Visible spectroscopic method and its results indicated that the synthesized compounds increased the denaturation temperature. BSA binding studies of synthesized compounds were done by UV-Visible and fluorescence spectroscopy. Molecular docking of prepared ligand and its nanoparticles with biomolecules (DNA and BSA) were studied. Antimicrobial studies of the DMPMM and DMPMM-NiNPs were carried out by Agar-Agar well diffusion method. Anticancer studies results evidenced that the synthesized DMPMM-NiNPs had good selectivity to control the growth of cancer cells without damaging the normal cells. Various antioxidant scavenging studies results have shown that DMPMM and DMPMM-NiNPs have significant antioxidant activity. HighlightsStable and solid nickel nanoparticles were prepared.The size of the prepared nickel nanoparticles was nearly 3 to 8 nm.Organic ligand capped nickel nanoparticles interacted with DNA and BSA.Ni nanoparticles increased the denaturation temperature of DNA.It was found to have good anticancer activity with fewer side effects than cisplatin.Communicated by Ramaswamy H. Sarma.

Synthesis, characterization and biological evaluation of novel benzimidazole derivatives

In search of achieving less toxic and more potent chemotherapeutics, three novel heterocyclic benzimidazole derivatives: 2-(1H-benzo[d]imidazol-2-yl)-4-chlorophenol (BM1), 4-chloro-2-(6-methyl-1H-benzo[d]imidazol-2-yl)phenol (BM2) and 4-chloro-2-(6-nitro-1H-benzo[d]imidazol-2-yl)phenol (BM3) with DNA-targeting properties, were synthesized and fully characterized by important physicochemical techniques. The DNA binding properties of the compounds were investigated by UV-Visible absorption titrations and thermal denaturation experiments. These molecules exhibited a good binding propensity to fish sperm DNA (FS-DNA), as evident from the high binding constants (K_b) values: 1.9 × 10⁵, 1.39 × 10⁵ and 1.8 × 10⁴ M^‒1 for BM1, BM2 and BM3, respectively. Thermal melting studies of DNA further validated the absorption titration results and best interaction was manifested by BM1 with ΔT_m = 4.96 °C. The experimental DNA binding results were further validated theoretically by molecular docking study. It was confirmed that the molecules (BM1-BM3) bind to DNA via an intercalative and groove binding mode. The investigations showed a correlation between binding constants and energies obtained experimentally and through molecular docking, indicating a binding preference of benzimidazole derivatives with the minor groove of DNA. BM1 was the preferential candidate for DNA binding because of its flat structure, π-π interactions and less steric hindrance. To complement the DNA interaction, antimicrobial assays (antibacterial & antifungal) were performed. It was observed that compound BM2 showed promising activity against all bacterial strains (Micrococcus luteus, Staphylococcus aureus, Enterobacter aerogenes and Escherichia coli) and fungi (Aspergillus flavus, Aspergillus fumigatus and Fusarium solani), while rest of the compounds were active against selective strains. The MIC values of BM2 were found to be in the range of 12.5 ± 2.2-25 ± 1.5 µg/mL. Thus, the compound BM2 was found to be the effective DNA binding antimicrobial agent. Furthermore, the preliminary cytotoxic properties of synthesized compounds were evaluated by brine shrimps lethality assay to check their nontoxic nature towards healthy normal cells.Communicated by Ramaswamy H. Sarma.

A new class of Ru(II) polyazine agents with potential for photodynamic therapy

Appending anthracene units to [(bpy)2Ru(dpp)](2+) results in Ru(II) agents that exhibit dynamic photoreactivity towards DNA and protein. [(Anthbpy)(bpy)Ru(dpp)](2+) and [(Anthbpy)2Ru(dpp)](2+) are the first metal-organic Ru(II) agent with dpp ligands shown to photomodify DNA in the presence or absence of oxygen, while also binding protein in an oxygen-dependent manner.

Interactions of a biocompatible water-soluble anthracenyl polymer derivative with double-stranded DNA

We have studied the interaction of a polymeric water soluble anthracenyl derivative () with salmon testes DNA. The results from UV-Vis, fluorescence, Fourier transform infrared (FT-IR) and circular dichroism spectroscopies indicate that the groove binding process regulates the interaction between and DNA. The binding constants, calculated by absorption spectroscopy at 298, 304 and 310 K, were equal to 3.2 × 10(5) M(-1), 4.7 × 10(5) M(-1), and 6.6 × 10(5) M(-1) respectively, proving a relatively high affinity of for salmon testes DNA. Results of Hoechst 33258 displacement assays strongly support the groove binding mode of to DNA. The association stoichiometry of the :DNA adduct was found to be 1 for every 5 base pairs. FT-IR spectra, recorded at different /DNA molar ratios, indicate the involvement of the phosphate groups and adenine and thymine DNA bases in the association process. Thermodynamic results suggest that hydrophobic forces regulate the binding of with DNA without excluding some extent of involvement of van der Waals forces and hydrogen bonding arising due to surface binding between the hydrophilic polymeric arms of the ligand and the functional groups positioned on the edge of the groove. The resulting composite biomaterial could constitute a valuable candidate for future biological and/or photonic applications.

DNA Cleavage and Condensation Activities of Mono- and Binuclear Hybrid Complexes and Regulation by Graphene Oxide

Hybrid complexes with N,N'-bis(2-benzimidazolylmethyl)amine and cyclen moieties are novel enzyme mimics and controlled DNA release materials, which could interact with DNA through three models under different conditions. In this paper, the interactions between plasmid DNA and seven different complexes were investigated, and the methods to change the interaction patterns by graphene oxide (GO) or concentrations were also investigated. The cleavage of pUC19 DNA promoted by target complexes were via hydrolytic or oxidative mechanisms at low concentrations ranging from 3.13 × 10(-7) to 6.25 × 10(-5) mol/L. Dinuclear complexes 2a and 2b can promote the cleavage of plasmid pUC19 DNA to a linear form at pH values below 7.0. Furthermore, binuclear hybrid complexes could condense DNA as nanoparticles above 3.13 × 10(-5) mol/L and partly release DNA by graphene oxide with π-π stacking. Meanwhile, the results also reflected that graphene oxide could prevent DNA from breaking down. Cell viability assays showed dinuclear complexes were safe to normal human hepatic cells at relative high concentrations. The present work might help to develop novel strategies for the design and synthesis of DNA controllable releasing agents, which may be applied to gene delivery and also to exploit the new application for GO.

Synthesis, DNA interaction and anticancer activity of 2-anthryl substituted benzimidazole derivatives

2-Anthryl substituted benzimidazole derivatives were synthesized and anticancer activity, cellular uptake, DNA interaction and molecular docking studies have been accomplished.

Physiologically relevant concentrations of NaCl and KCl increase DNA photocleavage by an N-substituted 9-aminomethylanthracene dye

This paper describes the synthesis of a new 9-aminomethylanthracene dye N-substituted with a pyridinylpolyamine side chain (4). The effects of NaCl and KCl on anthracene/DNA interactions were then studied, with the goal of simulating the conditions of high ionic strength that a DNA photosensitizer might encounter in the cell nucleus (~150 mM of NaCl and 260 mM of KCl). As exemplified by methylene blue (5), the expected effect of increasing ionic strength is to decrease DNA binding and photocleavage yields. In contrast, the addition of 150 mM of NaCl in combination with 260 mM of KCl to photocleavage reactions containing micromolar concentrations of 4 triggers the conversion of supercoiled, nicked, and linear forms of pUC19 plasmid into a highly degraded band of DNA fragments (350 nm hν, pH 7.0). Circular dichroism spectra point to a correlation between salt-induced unwinding of the DNA helix and the increase in DNA photocleavage yields. The results of circular dichroism, UV-vis absorption, fluorescence emission, thermal denaturation, and photocleavage inhibition experiments suggest that the combination of salts causes a change in the DNA binding mode of 4 from intercalation to an external interaction. This in turn leads to an increase in the anthracene-sensitized production of DNA-damaging reactive oxygen species.

Metal-free cleavage efficiency toward DNA by a novel PNA analog-bridged macrocyclic polyamine

In this report we describe the synthesis of a new class of cyclen-contained compounds with novel peptide nucleic acid (PNA) analog motif. Target bis-cyclen derivative B was prepared and characterized by ESI-MS, NMR and HPLC. Interactions between compound B and calf thymus DNA were studied by thermal denaturation. Results indicate that the DNA binding affinity of B is stronger than that of mono-cyclen compound A, and the binding ability is little affected by the change of ionic strength. Agarose and denaturing polyacrylamide gel electrophoresis were used to assess the DNA cleavage activities. The macrocyclic polyamine-PNA analog conjugate B as a nuclease model can effectively cleave DNA via an oxidative pathway at micromolar concentration (10 μM) without the use of any additional metal ions. Meanwhile, the mono-cyclen compound A shows nearly no DNA cleavage effect under the same conditions.

Cationic lipids containing protonated cyclen and different hydrophobic groups linked by uracil-PNA monomer: synthesis and application for gene delivery

In this report, as candidates for non-viral gene vectors, cationic lipids L1, L2 and L3 based on protonated cyclen and different hydrophobic groups (cholesterol, dodecanol or diosgenin) linked by PNA monomer were designed and synthesized. Their liposomes were easily prepared by mixing the synthesized lipids with dioleoylphosphatidyl ethanolamine (DOPE) under appropriate mole ratios. Agarose gel retardation and fluorescent titration by ethidium bromide (EB) showed the strong DNA-binding ability with the K(sv) values of 1.21 × 10(7), 3.76 × 10(6) and 2.90 × 10(6) M(-1) for the liposomes formed from L1-L3, respectively. These liposomes could retard pDNA at an N/P ratio of 3 and form lipoplexes with sizes around 200-300 nm and zeta-potential values of +20-50 mV at N/P ratio from 4 to 10. Besides, the cytotoxicity of the three lipoplexes assayed by MTT is quite different. The results from in vitro transfection in HEK 293T and A549 cell lines showed that the transfection efficiency of L3/DOPE/DNA lipoplex at an N/P ratio of 6 and lipid/DOPE mole ratio of 1:2 is slightly higher than that of Lipofectamine 2000™, indicating that the title PNA monomer-based cationic lipids have great potential to be efficient non-viral gene vector.