DNA Binding Behavior Research Articles

DNA-binding and photocleavage of fluorescein-porphyrinatozinc complexes

Three fluorescein-porphyrinatozinc(II) complexes, Zn(Fl-HPTTP) (1) (Fl-HPTTP = 5-(4-fluoresceinhexyloxy)phenyl-10,15,20-tritolylporphyrin), Zn(Fl-HPTPP) (2) (Fl-HPTPP = 5-(4-fluoresceinhexyloxy)phenyl-10,15,20-triphenylporphyrin), and Zn(Fl-HPTCPP) (3) (Fl-HPTCPP = 5-(4-fluoresceinhexyloxy)phenyl-10,15,20-tri(4-chloro)phenylporphyrin), have been synthesized and characterized by elemental analysis, IR, UV-Vis, ES-MS, and 1H NMR. The DNA-binding behaviors of these complexes with calf-thymus DNA (ct-DNA) were investigated by UV-Vis absorption titration, fluorescence spectra, viscosity measurements, thermal denaturation, and circular dichroism. The results suggest that 1, 2, and 3 interact with ct-DNA by intercalation and the DNA-binding affinities of these fluorescein-porphyrinatozinc(II) complexes may be closely associated with electronic effects of the substituent group introduced on the porphyrin ring of the ligands. The DNA-binding affinity (K b values) follows the order 1 > 2 > 3. In addition, their photocleavage reactions with pBR322 supercoiled plasmid DNA were investigated by gel electrophoresis experiments. All complexes exhibit significant DNA cleavage activity. The cleavage ability of the fluorescein-porphyrinatozinc(II) complexes follows the order 1 > 2 > 3, in parallel to the magnitude of their intrinsic binding constants.

DNA-binding and photocleavage studies of metallofluorescein–porphyrin complexes of zinc(II) and copper(II)

The DNA-binding behaviors of the fluorescein–porphyrinatozinc(II) complex Zn(Fl-PPTPP) (Fl-PPTPP = 5-(4-fluoresceinpropyloxy)phenyl-10,15,20-triphenylporphyrin) and fluorescein–porphyrinatocopper(II) complex Cu(Fl-PPTPP) with calf thymus DNA (CT-DNA) were investigated by UV–Vis absorption titrations, fluorescence spectra, viscosity measurements, thermal denaturation and circular dichroism. The results suggest that both complexes interact with CT-DNA by intercalation. In addition, their photocleavage reactions with pBR322 supercoiled plasmid DNA were investigated. Both complexes exhibit significant DNA cleavage activity, and singlet oxygen may play an important role in these reactions.

DNA-Binding Studies of Fluoxetine Antidepressant

Fluoxetine is a selective serotonin reuptake inhibitor (SSRI) antidepressant that is widely prescribed. The DNA-binding behavior of fluoxetine antidepressant and calf thymus DNA was investigated in Tris-HCl buffer at physiological pH 7.4 with a series of techniques, including UV-Vis and circular dichroism spectroscopies, competitive study with Hoechst 33258, viscometry, and cyclic voltammetry. Fluoxetine molecules bind to DNA via groove mode as illustrated by hypochromism with no red shift in the UV absorption band of fluoxetine, decrease in Hoechst-DNA solution fluorescence, and no significant changes in viscosity of DNA. The CD spectra of DNA molecules show a little change in stacking mode of base pair but no modification changes in DNA conformation, for example, from B-DNA to A or C-DNA. The binding constant (K(b)) of DNA with fluoxetine was calculated to be 6.7 × 10(4) M(-1), which is in the range of reported and known groove binders, such as distamycin. All results showed the groove-binding mode of interaction of fluoxetine with DNA.

Synthesis, Characterization, DNA Binding, and Cleavage Activity of New Co(III) and Ru(II) Complexes of Substituted Quinolines

The cobalt(III) and ruthenium(II) complexes of the type [M(L)2]n+ (M = Co(III) or Ru(II) ion, n = 3 for Co and 2 for Ru, L = 2-thiol/seleno 4-methylquinoline) were synthesized and structurally characterized. The spectral and magnetic data suggested octahedral geometry for all the complexes. DNA binding behaviors of these complexes with calf thymus DNA (CT-DNA) have been investigated by absorption spectra, viscosity, and thermal denaturation methods. The metal complexes intercalates into the DNA base stack. The oxidative cleavage activities of the complexes shows that the complexes act as potent nucleases.

Synthesis, characterization, DNA-binding and cytotoxic properties of Ru(II) complexes: [Ru(MeIm)4L]2+ (MeIm = 1-methylimidazole, L = phen, ip and pip)

Three new ruthenium(II) complexes, [Ru(MeIm)4phen]2+ (1), [Ru(MeIm)4ip]2+ (2) and [Ru(MeIm)4pip]2+ (3), have been synthesized and characterized. The binding properties of the three complexes towards calf-thymus DNA were investigated by different spectrophotometric methods and viscosity measurements. In addition, the cytotoxicity of these complexes has been evaluated by MTT method and Giemsa staining experiment. The main results reveal that the plane area and hydrophobicity of intercalative ligands have a significant effect on the DNA-binding behaviors and the IC50 value of complex 2 against MCF-7 cells is close to that of cis-Pt(NH3)2Cl2.

Studies on DNA binding behaviour of biologically active transition metal complexes of new tetradentate N2O2 donor Schiff bases: Inhibitory activity against bacteria

A series of Cu(II), Ni(II) and Zn(II) complexes of the type ML have been synthesized with Schiff bases derived from o-acetoacetotoluidide, 2-hydroxybenzaldehyde and o-phenylenediamine/1,4-diaminobutane. The complexes are insoluble in common organic solvents but soluble in DMF and DMSO. The measured molar conductance values in DMSO indicate that the complexes are non-electrolytic in nature. All the six metal complexes have been fully characterized with the help of elemental analyses, molecular weights, molar conductance values, magnetic moments and spectroscopic data. The analytical data helped to elucidate the structure of the metal complexes. The Schiff bases are found to act as tetradentate ligands using N2O2 donor set of atoms leading to a square-planar geometry for the complexes around all the metal ions. The binding properties of metal complexes with DNA were investigated by absorption spectra, viscosity measurements and cyclic voltammetry. Detailed analysis reveals that the metal complexes intercalate into the DNA base stack as intercalators. All the metal complexes cleave the pUC19 DNA in presence of H2O2. The Schiff bases and their complexes have been screened for their antibacterial activity against five bacterial strains (Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli, Staphylococcus epidermidis, Klebsiella pneumoniae) by disk diffusion method. All the metal complexes have potent biocidal activity than the free ligands.

Probing the DNA-binding behavior of tryptophan incorporating mixed-ligand complexes

Mixed-ligand Cu(II), Ni(II), Co(II), and Zn(II) complexes using a tryptophan-derived Schiff base (obtained by the condensation of tryptophan and benzaldehyde) as the primary ligand and 1,10-phenanthroline as the co-ligand were synthesized and characterized analytically and spectroscopically by performing elemental analyses, magnetic susceptibility and molar conductance measurements, UV-Vis, IR, NMR, and FAB-MS. The binding properties of metal complexes with DNA were investigated by electronic absorption spectroscopy, cyclic voltammetry, and by performing viscosity measurements, and the results showed that these complexes have the ability to interact with DNA via an intercalative mode. The DNA cleavage efficiencies of these complexes with pUC19 DNA were investigated by gel electrophoresis. The complexes were found to promote the cleavage of pUC19 DNA from the supercoiled form I to the open circular form II and the linear form III in the presence of ascorbic acid. Finally, the in vitro antibacterial activities of the Schiff base and its mixed-ligand metal complexes were screened against the bacteria Staphylococcus aureus, Bacillus subtilis, Pseudomonas aeruginosa, Escherichia coli, and Salmonella typhi. The antibacterial screening data revealed that the complexes show growth inhibitory activity against bacteria.

Solid and solution structures and DNA binding properties of [MII(4-CNpy)2(SO4)(H2O)3]·H2O for M = Cu, Co, Ni

Compounds of the type [M(H2O)3(SO4)(4-CNpy)2]·H2O, with M=Co and Ni, display an interesting hydrogen bonded layered structure in the solid state. The copper analog of the above species, [Cu(H2O)3(SO4)(4-CNpy)2]·H2O (1), has now been synthesized as well and is found to be isostructural in the crystallographic sense to the Co (2) and Ni (3) species. The solid and solution phase UV–Vis–NIR spectra of 1, 2, and 3 indicate that species of the type [M(H2O)4(4-CNpy)2]2+ may be present in aqueous solutions of 1, 2, and 3. The DNA binding behavior of the above water-soluble complexes with Calf-Thymus (CT) DNA has been investigated by isothermal titration calorimetry (ITC) to find that the nature and extent of interaction are dependent on the identity of the metal.

Cellular accumulation and DNA interaction studies of cytotoxic trans-platinum anticancer compounds

Fortyyears after the discovery of the anticancer effects of cisplatin, scientists are still pursuing the development of platinum complexes with improved properties regarding side effects and resistance, which are two main problems in cisplatin treatment. Among these compounds, trans-configured platinum complexes with oxime ligands emerged as a new class with features distinct from those of established anticancer agents, including different DNA binding behavior, increased cellular accumulation, and a different pattern of protein interaction. We report herein on the reactivity with biomolecules of three novel pairs of cis- and trans-configured acetone oxime platinum(II) complexes and one pair of 3-pentanone oxime platinum(II) complexes. Cellular accumulation experiments and in vitro DNA platination studies were performed and platinum contents were determined by inductively coupled plasma mass spectrometry. The trans-configured complexes were accumulated in SW480 cells in up to 100 times higher amounts than cisplatin and up to 50 times higher amounts than their cis-configured counterparts; r (b) values (number of platinum atoms per nucleotide) were more than tenfold increased in cells treated with trans complexes compared with cells treated with cisplatin. The interaction of the complexes with DNA was studied in cell-free experiments with plasmid DNA (pUC19), in capillary zone electrophoresis with the DNA model 2-deoxyguanosine 5'-monophosphate, and in in vitro experiments showing the degree of DNA damage in the comet assay. Whereas incubation with cis compounds did not induce degradation of DNA, the trans complexes led to pronounced strand cleavage.

Spectral characteristics, DNA-binding and cytotoxicity of two functional Ru(ii) mixed-ligand complexes

Two functional Ru(II) mixed-ligand complexes, [Ru(phen)(2)(ttbd)](2+) (1) (ttbd = 4-(6-propenyl-pyrido[3,2-a]phenzain-10-yl-benzene-1,2-diamine, phen = 1,10-phenanthroline) and [Ru(bpy)(2)(ttbd)](2+) (2) (bpy = 2,2'-bipyridine), have been synthesized and characterized. The spectral characteristics of complexes 1 and 2 were investigated using fluorescence spectroscopy and revealed that both complexes were very sensitive to solvent polarity and oxygen molecules in nonaqueous solvents. The binding properties of the two complexes towards calf thymus DNA (CT-DNA) were investigated with different spectrophotometric methods, viscosity measurements and quantum chemistry calculations, indicating that both complexes could enantioselectively bind to CT-DNA by means of intercalation, but with different binding strengths and discrimination. On the other hand, the cytotoxicity of both complexes have been evaluated by MTT assays and Giemsa staining experiments. The main results reveal that the hydrophobicity and surface area of the ancillary ligands have a significant effect on their DNA binding behavior and both complexes are likely to be useful for optically probing nonaqueous and oxygen-free environments.

Enantiomeric recognition of chiral L– and D–penicillamine Zinc(ii) complexes: DNA binding behavior and cleavage studies

Two designed L–/D–penicillamine based enantiomeric Zn(II) complexes 1a and 1b of 1,10–phenanthroline were synthesized and structurally characterized. The interactions of the complexes with CT DNA have been explored by absorption, fluorescence and CD measurements, revealing that both the complexes interact with DNA via electrostatic binding. All the corroborative results indicated the enantiopreferential selective binding of L–form of the complex over the D–form. A gel electrophoretic pictogram of the complexes 1a and 1b demonstrates their ability to cleave pBR322 DNA through hydrolytic process; validated by T4 religation assays; furthermore, the L–form of the complex exhibited more pronounced cleavage than the D–form. However, both complexes preferred the minor groove of the DNA double helix. Interaction studies with mononucleotides revealed that both the enantiomers possess high affinity towards the A–T base pairs of DNA, consistent with the previous reports on stereospecific selectivity of Zn(II) complexes. These studies were further supported by molecular docking studies and the resulting binding energy of docked metal complexes 1a and 1b were found to be −306.4 and −289.1 KJ mol−1, respectively. The more negative relative binding energy of L–form of complex suggests greater propensity for DNA than the D–enantiomer.

The importance of cellular localisation of probes: synthesis, photophysical properties, DNA interactions and cellular imaging properties of rhenium dppz complexes with known cellular localisation vectors

The synthesis, photophysical properties, DNA binding, DNA cleavage and cellular imaging behaviour of a range of complexes of the type [Re(CO)3(dppz)(PyR)]+ are reported, where PyR represents a range of substituted pyridines which have previously been studied for cellular localisation of related complexes. Confocal imaging experiments confirm that the complexes retain the variety of cellular localisation behaviour associated with the PyR units in other complexes, and suggest applications as probes for oligonucleotides in specific cellular compartments (e.g. mitochondrial DNA). This study illustrates the importance of considering cellular localisation as a prime consideration in the design of probes for in vivo application.

Synthesis, characterization, and DNA damaging of bivalent metal complexes incorporating tetradentate dinitrogen–dioxygen ligand as potential biocidal agents

A new symmetrical tetradentate Schiff base was prepared by the condensation of 5-nitro-o-vanillin and diaminoethane. Its complexes were synthesized and characterized by elemental analysis, magnetic moment, molar conductance, UV-Vis, IR, 1H NMR, ESI-mass, and EPR spectra. The DNA-binding behavior of these complexes was investigated by absorption spectra, cyclic voltammetry, and viscosity measurements. The DNA-binding constants for Co(II), Ni(II), Cu(II), and Zn(II) complexes were 1.58 × 104, 1.65 × 104, 2.71 × 104, and 1.83 × 104 (mol L−1)−1, respectively. The results suggest that the complexes intercalate between DNA base pairs. Further, all these complexes exhibit moderate to high ability to cleave pUC19 DNA. The ligand and its complexes have been screened for antimicrobial activities using the disc diffusion method against selected bacteria and fungi. Antibacterial activity was greater against Gram-positive than Gram-negative bacteria for Cu(II) complex and antifungal activity was greater against Aspergillus niger and Candida albicans for the Cu(II) complex.

Synthesis, DNA-binding, and photocleavage studies of ruthenium(II) complexes with an asymmetric ligand

An asymmetric ligand (pdpiq = 2-(pyridine-2-yl)-6,7-diphenyl-1-H-imidazo[4,5-g]quinoxaline) and its ruthenium complexes with [Ru(L)2pdpiq]2+ (L = bpy (2,2′-bipyridine) or phen (1,10-phenanthroline)) have been synthesized and characterized by elemental analysis, ES-MS, and 1H NMR. The DNA-binding behaviors of these complexes were studied by spectroscopic methods and viscosity measurements. The results indicate that the complexes can intercalate into DNA base pairs. When irradiated at 365 nm, the two complexes promote the cleavage of plasmid pBR322DNA. The mechanism of DNA cleavage is an oxidative process by generating singlet oxygen.

Ruthenium(II) complexes: structure, DNA-binding, photocleavage, antioxidant activity, and theoretical studies

Two triazine-containing ruthenium(II) complexes, [Ru(dmb)2(pdpt)](ClO4)2 (dmb = 4,4′-dimethyl-2,2′-bipyridine, pdpt = 3-(pyridine-2-yl)-5,6-diphenyl-as-triazine) (1) and [Ru(dmb)2(pdtp)](ClO4)2 (pdtp = 3-(pyridine-2-yl)-as-triazino[5,6-f]phenanthrene) (2), were synthesized and characterized by elemental analysis, ES-MS, 1H NMR, UV-Vis spectra, and cyclic voltammetry; the crystal structure of 2 was determined by X-ray diffraction. DNA-binding behaviors of both complexes were studied by absorption titration, thermal denaturation, and viscosity measurements. The photoactivated DNA cleavage of plasmid pBR322 in the presence of 1 and 2 was explored through gel electrophoresis. Antioxidant activities of the two complexes against hydroxyl radical (•OH) were also investigated. The results indicate that the DNA-binding affinity of 2 is much greater than that of 1, and that 2 binds to calf thymus DNA by intercalation, but 1 binds in partial intercalation, with π–π stacking on the DNA surface. Experimental findings made through analysis of the CV, absorption spectra, X-ray crystal structure, and the DNA-binding properties were compared with those of theoretical studies using density functional calculations.

A sequence-specific threading tetra-intercalator with an extremely slow dissociation rate constant

A long-lived and sequence specific ligand-DNA complex would make possible the modulation of biological processes for extended periods. We have been investigating the threading polyintercalation approach to DNA recognition in which chains of aromatic units thread back and forth repeatedly through the double helix. Here we report the preliminary sequence specificity and detailed kinetic analysis of a structurally characterized threading tetraintercalator. Specific binding on a relatively long DNA strand was observed, strongly favoring a predicted 14-base pair sequence. Kinetic studies revealed a multi-step association process and specificity was found to derive primarily from large differences in dissociation rates. Importantly, the rate-limiting dissociation rate constant of the tetraintercalator complex dissociating from its preferred binding site was extremely slow, corresponding to a 16 day half-life, making it one of the longer non-covalent complex half-lives yet measured, and, to the best of our knowledge, the longest for a DNA binding molecule.

DNA binding behaviors and cleavage properties of a Ru(II) polypyridyl complex

A novel complex, [Ru(phen) 2pzip] 2+ 1 (phen = 1,10-phenanthroline; pzip = 2-(pyrazine-2-yl)imidazo-[4,5- f][1,10]phenanthroline]), has been synthesized and characterized by elemental analysis, ES-MS, 1H NMR. The DNA-binding behaviors of this complex were studied by spectroscopic methods and viscosity measurements. The results indicate that the complex can bind to CT-DNA in an intercalative mode. When irradiated at 365 nm, complex 1 can promote the cleavage of plasmid pBR322DNA. Furthermore, Zn 2+ can trigger the DNA cleavage of complex 1 without irradiation. The mechanism studies revealed that the DNA cleavage by complex 1 in the presence of Zn 2+ is likely to proceed via a hydrolytic cleavage process.

Metal ion and DNA binding by single-chain PvuII endonuclease: lessons from the linker

Understanding the roles of metal ions in restriction enzymes has been complicated by both the presence of two metal ions in many active sites and their homodimeric structure. Using a single-chain form of the wild-type restriction enzyme PvuII (scWT) in which subunits are fused with a short polypeptide linker (Simoncsits et al. in J. Mol. Biol. 309:89-97, 2001), we have characterized metal ion and DNA binding behavior in one subunit and examined the effects of the linker on dimer behavior. scWT exhibits heteronuclear single quantum coherence NMR spectra similar to those of native wild-type PvuII (WT). For scWT, isothermal titration calorimetry data fit to two Ca(II) sites per subunit with low-millimolar K (d)s. The variant scWT|E68A, in which metal ion binding in one subunit is abolished by mutation, also binds two Ca(II) ions in the WT subunit with low-millimolar K (d)s. When there are no added metal ions, DNA binding affinity for scWT is tenfold stronger than that of the native WT, but tenfold weaker at saturating Ca(II) concentration. In the presence of Ca(II), scWT|E68A binds target DNA similarly to scWT, indicating that high-affinity substrate binding can be carried energetically by one metal-ion-binding subunit. Global analysis of DNA binding data for scWT|E68A suggests that the metal-ion-dependent behaviors observed for WT are reflective of independent subunit behavior. This characterization provides an understanding of subunit contributions in a homodimeric context.

Ruthenium(II) complexes: Cellular uptake, cytotoxicity, DNA-binding, photocleavage and antioxidant activity studies

Two new ruthenium(II) complexes [Ru(dmp) 2(DNPIP)] 2+ 1 and [Ru(dmp) 2(DAPIP)] 2+ 2 were synthesized and characterized. The DNA-binding behaviors of these complexes were investigated by absorption spectra, viscosity measurements and photocleavage. The DNA-binding constants for complexes 1 and 2 have been determined to be 6.24 (±0.11) × 10 4 and 1.64 (±0.49) × 10 4 M −1. The results suggest that complexes 1 and 2 intercalate between the DNA base pairs. Binding stoichiometries were studied through a luminescence-based Job plot. The major inflection points for complexes 1 and 2 at χ = 0.31 and χ = 0.51 were observed. The data were consistent with 2:1 and 1:1 bp [complex]/[DNA] binding mode. Complex 1 shows higher activity than complex 2 against the selected tumor cell lines. In addition, the cellular uptake and antioxidant activity on hydroxyl radical were also explored.

Synthesis, characterization, DNA interaction and antibacterial activities of two tetranuclear cobalt(II) and nickel(II) complexes with salicylaldehyde 2-phenylquinoline-4-carboylhydrazone

Abstract Salicylaldehyde 2-phenylquinoline-4-carboylhydrazone (H 2 L), and its novel tetranuclear cobalt(II), nickel(II) complexes have been synthesized and characterized. The crystal structure of (NiL) 2 ·[NiL(H 2 O)(DMF)] 2 ·H 2 O·DMF obtained from DMF solutions of compound 2 was determined by X-ray diffraction analysis. The DNA-binding investigation suggests that the two complexes bind to DNA via groove binding mode. The in vitro antibacterial activity of complexes against Escherichia coli , Staphylococcus aureus , Bacillus subtilis was screened and compared to the activity of the free ligand, the antibacterial activity of complex 1 is active than complex 2 which is in consistent with their DNA-binding behaviors.