DNA binding, DNA cleavage, and cytotoxicity studies of two new copper (II) complexes

The DNA binding behavior of [Cu(phen)(phen-dione)Cl]Cl (1) and [Cu(bpy)(phen-dione)Cl]Cl (2) was studied with a series of techniques including UV-vis absorption, circular dichroism spectroscopy, and viscometric methods. Cytotoxicity effect and DNA unwinding properties were also investigated. The results indicate that the Cu(II) complexes interact with calf-thymus DNA by both partially intercalative and hydrogen binding. These findings have been further substantiated by the determination of intrinsic binding constants spectrophotometrically, 12.5?×?10(5) and 5?×?10(5) for 1 and 2, respectively. Our findings suggest that the type of ligands and structure of complexes have marked effect on the binding affinity of complexes involving CT-DNA. Circular dichroism results show that complex 1 causes considerable increase in base stacking of DNA, whereas 2 decreases the base stacking, which is related to more extended aromatic area of 1,10-phenanthroline in 1 rather than bipyridine in 2. Slow decrease in DNA viscosity indicates partially intercalative binding in addition to hydrogen binding on the surface of DNA. The second binding mode was also confirmed by additional tests: interaction in denaturation condition and acidic pH. Also, these new complexes induced cleavage in pUC18 plasmid DNA as indicated in gel electrophoresis and showed excellent antitumor activity against K562 (human chronic myeloid leukemia) cells.     

Synthesis, characterization and DNA-binding of novel chiral complexes delta- and lambda-[Ru(bpy)2L]2+ (L = o-mopip and p-mopip)

Novel chiral Ru(II) complexes [Ru(bpy)2L]2+ (bpy = 2,2-bipyridine; L: o-mopip = 2-(2-methoxylphenyl)imidazo[4,5-f][1,10]phenanthroline, p-mopip = 2-(4-methoxylphenyl)imidazo[4,5-f][1,10]phenanthroline) containing -OCH3 at different positions on the phenyl ring have been synthesized and characterized. The DNA-binding and DNA-photocleavage properties of the complexes were investigated. The theoretical calculations for these complexes were also carried out applying the density functional theory (DFT) method. The experimental results show that: both these two isomer complexes can bind to DNA in an intercalative mode; the DNA-binding affinity of [Ru(bpy)2(p-mopip)] 2 is greater than that of [Ru(bpy)2(o-mopip)] 1; moreover, the DNA-binding affinities of enantiomers delta-1 and delta-2 are all greater than those of lambda-1 and lambda-2, respectively. In addition, a very interesting finding is experimentally obtained, i.e. under a low [DNA]/[Ru] ratio, the emission intensities of delta-1 and lambda-1 are all weaker than those of delta-2 and lambda-2, however, upon a high [DNA]/[Ru] ratio, the emission intensities of both delta-1 and lambda-1 are stronger than those of delta-2 and lambda-2. Such a difference of the emission spectra can be interpreted by the electric effect of substituent on the intercalative ligand. The difference in DNA-binding affinities of these two isomeric complexes can also be reasonably explained by the DFT calculations.     

Interactions of Molecules with Nucleic Acids. X. Covalent Intercalat e Binding of the Carcinogenic BPDE I(+) to Kinked DNA

Abstract

A theoretical model is proposed for the covalent binding of (+) 7 β,8α-dihydroxy-9α, 10α- epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene denoted by BPDE I(+), to N2 on guanine. The DNA must kink a minimum of 39° to allow proper hybrid configurations about the C10 and N2 atoms involved in bond formation and to allow stacking of the pyrene moiety with the non-bonded adjacent base pair. Conservative (same sugar puckers and glycosidic angles as in B-DNA) and non-conservative (alternating sugar puckers as in intercalation sites) conformations are found and they are proposed structures in pathways connecting B-DNA, an intercalation site, and a kink site in the formation of a covalently intercalative bound adduct of BPDE I(+) to N2 on guanine. Stereographic projections are presented for (3′) and (5′) binding in the DNA. Experimental data for bending of DNA by BPDE, orientation of BPDE in DNA and unwinding of superhelical DNA is explained. The structure of a covalent intercalative complex is predicted to result from the reaction. Also, an anti ? syn transition of guanine results in a structure which allows the DNA to resume its overall B-form. The only change is that guanine has been rotated by 200° about its glycosidic bond so that the BPDE I(+) is bound in the major groove. The latter step may allow the DNA to be stored with an adduct which may produce an error in the genetic code.     

Change of the higher order structure of DNA induced by the complexation with intercalating synthetic polymer, as is visualized by fluorescence microscopy.

The electrophoretic movement and Brownian motion of T4DNA, lambda DNA and their complexes with polyacrylamide (PAAm) via intercalative unit from 5-[(4-acryloylamino)phenyl]-3-amino-7-(dimethylamino)-2-methylp henazinium chloride were observed using fluorescence microscopy. It was found that T4DNA/PAAm complex migrates slower than T4DNA alone in gel electrophoresis, although they exhibit similar conformational change during the migration. Quantitative analyses of the translational diffusion of the lambda DNA and its complex in solution demonstrate that the DNA molecules extend due to intercalative binding of PAAm, suggesting the pseudo-grafting structure of the complex.     

Novel 2-aminothiazonaphthalimides as visible light activatable photonucleases: effects of intercalation, heterocyclic-fused area and side chains

A new family of 2-aminothiazonaphthalimides with different side chains as novel intercalative and visible light activatable photonucleases, was designed, synthesized and quantitatively evaluated. The order of their photocleaving abilities was parallel to that of their intercalative properties. The compound with linear heterocyclic-fused chromophore could intercalate into and photocleave DNA more efficiently than the one with angular heterocyclic-fused chromophore. B(2), the most efficient compound, caused obvious DNA damage at 1 microM. Mechanism experiment showed that superoxide anion was involved.     

Synthesis, characterization, structures and DNA-binding properties of complexes [Ru(bpy)2(L)] (L = ptdb, ptda and ptdp) with asymmetric intercalative ligands

A series of Ru(II) polypyridyl complexes [Ru(bpy)₂(ptdb)](ClO₄)₂ (1), [Ru(bpy)₂(ptda)](ClO₄)₂ (2) and [Ru(bpy)₂(ptdp)](ClO₄)₂ (3) with asymmetric intercalative ligands have been synthesized and characterized by EA, mass spectra, ¹H NMR and cyclic voltammetry. The crystal structure of complex 1 has been determined. The DNA-binding properties of the complexes were investigated by absorption titration, luminescence spectroscopy and viscosity measurements. The experimental results suggest that all these complexes bind to DNA in an intercalation mode. The results also show that the order of DNA-binding affinities (A) of this series of complexes is A(1) < A(2) < A(3). It is further confirmed that a ligand planarity of the complexes is a very important factor in affecting the DNA-binding behaviors of such complexes. Theoretical studies for these complexes were also carried out with the density functional theory (DFT) method. The trend in the DNA-binding affinities of this series of complexes can be reasonably explained by the synthetical considerations of the calculated planarity of intercalative ligands, some frontier molecular orbital energies of the complexes and the planarity area (S) of the intercalative ligands.     

Synthesis, crystal structure, magnetic property and nuclease activity of a new binuclear cobalt(II) complex

One new binuclear Co(II) complex of N,N,N',N'-tetrakis(2-benzimidazolylmethyl)-2-hydroxyl-1,3-diaminopropane (HL), [Co(2)L(mu(2)-Cl)](ClO(4))(2) x 3CH(3)CN x C(2)H(5)OC(2)H(5) (1), has been synthesized and its crystal structure and magnetic properties are shown. In 1, each Co(II) atom has a distorted trigonal bipyramidal geometry with a N(3)OCl donor set. The central two Co(II) atoms are bridged by one alkoxo-O atom and one Cl atom with the Co1-Co2 separation of 3.239 A. Susceptibility data of 1 indicate strong intramolecular antiferromagnetic coupling of the high-spin Co(II) atoms. In this paper, the interaction with calf thymus DNA was investigated by UV absorption and fluorescent spectroscopy. Results show the complex binds to ct-DNA with a intercalative mode. The interaction between complex 1 and pBR322 DNA has also been investigated by submarine gel electrophoresis, noticeably, the complex exhibits effective DNA cleavage activity in the absence of any external agents.     

Synthesis, characterization, DNA-binding and photocleavage of complexes [Ru(phen)2(6-OH-dppz)]2+ and [Ru(phen)2(6-NO2-dppz)]2+

Two new complexes, ([Ru(phen)(2)(6-OH-dppz)](2+)) (1) and ([Ru(phen)(2)(6-NO(2)-dppz)](2+)) (2) (phen=1,10-phenanthroline; 6-OH-dppz=6-hydroxyl-dipyrido[3,2-a:2',3'-c]phenazine; 6-NO(2)-dppz=6-nitro-dipyrido[3,2-a:2',3'-c]phenazine), have been synthesized and characterized by elemental analysis, ES-MS (electrospray mass spectra), (1)H NMR, UV-Vis (UV-visible) and CV (cyclic voltammetry). The DNA-binding behaviors of both complexes have been studied by spectroscopic methods and viscosity measurements. The results indicate that the two complexes all bind to calf thymus DNA (CT-DNA) in an intercalative mode, and the DNA-binding affinity of complex 2 is greater than that of complex 1. In addition, complex 1 can promote photocleavage of pBR322 DNA upon irradiation, whereas complex 2 can promote cleavage of pBR322 DNA both upon irradiation and in the dark, with more efficient cleavage occurring upon irradiation. Theoretical studies for these complexes have been also carried out with the density functional theory (DFT) method. The difference in the DNA-binding behaviors of the two complexes can be reasonably explained by the DFT calculations.     

Probing the Site-Selective Binding of an Antiretroviral Drug,Stavudine to Calf Thymus Dna

The interaction of an anti-HIV drug, stavudine (STV) with calf thymus deoxyribonucleic acid (DNA) was investigated employing acridine orange (AO) as a fluorescence probe. Spectroscopic investigations revealed the intercalative mode of binding of STV to DNA. The analysis of fluorescence data indicated the presence of static quenching mechanism between STV and DNA. Thermodynamic parameters indicated the presence of van der Waals forces in addition to intercalative mode of binding. CD data revealed the partial B→A conformational transition of DNA upon intercalative mode of binding with STV.     

Interaction of (+/-)-7r,8t-dihydroxy-9t,10t-epoxy-7,8,9,10-tetrahydrobenzo(a)pyrene with relaxed circular pBR322 DNA

The interaction of (+/-)-BPDE (1) with DNA at neutral pH was investigated by the application of relaxed circular pBR322 DNA. (+/-)-BPDE causes a rapid positive supercoiling of this DNA followed by a slower spontaneous relaxation. The results indicate that there are two clearly discernible types of chemical interactions between 1 and DNA, a rapid intercalative covalent binding and a slower strand breakage. The implications of these findings are discussed.     

Oxidative DNA cleavage mediated by a new copper (II) terpyridine complex: crystal structure and DNA binding studies

The copper (II) complex [Cu(Itpy)(2)](ClO(4))(2) (1), (Itpy=imidazole terpyridine) has been synthesized and structurally characterized. Crystal structure of the complex shows the complex to be a monomeric copper (II) species with two Itpy ligands coordinated to the metal ion to give a six coordinate complex. The complex has a distorted octahedral geometry with axial elongation. Variable temperature crystal structure data shows dynamic nature of the Jahn-Teller distortion. The complex is an avid DNA binder with a binding constant of 4.26+/-0.20x10(3)M(-1). Observed changes in the viscosity and circular dichroic spectrum of calf thymus DNA solution in the presence of complex 1 suggests intercalative binding of complex 1 to DNA. The complex cleaves supercoiled pBR322 DNA oxidatively in the presence of hydrogen peroxide.     

Conformational flexibility in DNA structure and its implications in understanding the organization of DNA in chromatin.

X-ray crystallographic studies of drug-nucleic acid crystalline complexes have suggested that DNA first bends or 'kinks' before accepting an intercalative drug or dye. This flexibility in DNA structure is made possible by altering the normal C2' endo deoxyribose sugar puckering in B DNA to a mixed sugar puckering pattern of the type C3' endo (3'-5') C2' endo and partially unstacking base pairs. A kinking scheme such as this would require minimal sterochemical rearrangement and would also involve small energies. This has prompted us to ask more generally if a conformational change such as this could be used by proteins in their interactions with DNA. Here we describe an interesting superhelical DNA structure formed by kinking DNA every ten base pairs. This structure may be used in the organization of DNA within the nucleosome structure in chromatin.     

DNA interaction studies of a platinum(II) complex containing L-histidine and 1,10-phenanthroline ligands

The aim of this study was developing coordination complexes that can be used as inorganic medicinal agents. The water soluble [Pt(phen)(His)]NO(3)·3H(2)O complex in which phen=1,10-phenantheroline and His=L-histidine was synthesized and characterized using physicochemical methods. Binding interaction of this complex with calf thymus (CT) DNA was investigated by emission, absorption, circular dichroism, and viscosity measurement techniques. Upon addition of CT-DNA, changes were observed in the characteristic ultraviolet-visible (UV-Vis) bands (hypochromism) of the complex. The complex binds to CT-DNA in an intercalative mode. The calculated binding constant, K(b), was 8 ± 0.2 × 10(4) M(-1). In addition, circular dichroism (CD) study showed that the phenanthroline ligand was inserted between the base pair stack of the double-helical structure of DNA. Also, the fluorescence spectral characteristics showed an increase in fluorescence intensity of the platinum complex in the presence of increasing amounts of DNA solution. The experimental results showed that the platinum complex binds to DNA via intercalative and hydrogen bonding mode.     

A novel binuclear palladium complex with benzothiazole-2-thiolate: synthesis, crystal structure and interaction with DNA

The novel Pd(II) complex, [Pd(2)(micro-bzta)(4)].1.5DMSO (where bzta=benzothiazole-2-thiolate) has been synthesized and structurally characterized by element analysis, IR and single-crystal X-ray diffractometry. In the binuclear complex, two palladium(II) are bridged by four deprotonated benzothiazole-2-thialate in a head to tail disposition and the distance of the two Pd(II) is 2.747 A. Three-dimensional structure of the complex was constructed though S...S (3.339 A) weak interaction and pi...pi stack. The binding of the title complex with fish sperm DNA (FS-DNA) has been investigated by absorption and fluorescence spectra. The results indicate that the complex bind to FS-DNA in an intercalative mode and the intrinsic binding constant K of the title complex with FS-DNA is about 1.2 x 10(4)M(-1). Gel electrophoresis assay demonstrates the ability of the complex to cleave the pUC19 plasmid DNA.     

Synthesis, characterization, and DNA binding and cleavage properties of copper(II)-tryptophanphenyl-alanine-1,10-phenanthroline/2,2'-bipyridine complexes

The mononuclear dipeptide‐based Cu^II complexes [Cu^II(trp‐phe)(phen)(H₂O)] ⋅ ClO₄ ( 1 ) and [Cu^II(trp‐phe)(bpy)(H₂O)] ⋅ ClO₄ ( 2 ) (trp‐phe=tryptophanphenylalanine, phen=1,10‐phenanthroline, bpy=2,2′‐bipyridine) were isolated, and their interaction with DNA was studied. They exhibit intercalative mode of interaction with DNA. The intercalative interaction was quantified by Stern Volmer quenching constant (K_sq=0.14 for 1 and 0.08 for 2 ). The Cu^II complexes convert supercoiled plasmid DNA into its nicked circular form hydrolytically at physiological conditions at a concentration as low as 5 μM (for 1 ) and 10 μM (for 2 ). The DNA hydrolysis rates at a complex concentration of 50 μM were determined as 1.74 h⁻¹ (R=0.985) for 1 and 0.65 h⁻¹ (R=0.965) for 2 . The rate enhancement in the range of 2.40–4.10×10⁷‐fold compared to non‐catalyzed double‐stranded DNA is significant. This was attributed to the presence of a H₂O molecule in the axial position of the Cu complexes.     

Synthesis, characterization, DNA-binding and photocleavage studies of [Ru(bpy)2(PPIP)]2+ and [Ru(phen)2(PPIP)]2+

A novel ligand 2-(4'-phenoxy-phenyl)imidazo[4,5-f][1,10]phenanthroline (PPIP) and its complexes [Ru(bpy)(2)(PPIP)](2+) (1) (bpy = 2,2'-bipyridine) and [Ru(phen)(2)(PPIP)](2+) (2) (phen = 1,10-phenanthroline) have been synthesized and characterized by mass spectroscopy, (1)H NMR and cyclic voltammetry. The interaction of two complexes with calf thymus DNA (CT-DNA) was investigated by spectroscopic and viscosity measurements. The results suggest that both complexes bind to DNA via an intercalative mode. Both complexes have also been found to promote the photocleavage of plasmid pBR 322 DNA under irradiated.     

Binding of Enantiomers of Trans-7, 8-dihydroxy-anti-9,10-epoxy-7,8,9,10- tetrahydro-benzo [a]pyrene to Polynucleotides

Abstract

DNA covalent binding studies with enantiomers of trans-7,8-dihydroxy- anti-9,10-epoxy- 7,8,9,10-tetrahydro-benzo [a] pyrene (anti-BPDE) have been carried out by means of spectroscopic techniques (UV, CD, and fluorescence). Synthetic polynucleotides are employed to investigate binding differences between the G · C and A · T base pairs and to elucidate the bases for the stereoselective covalent binding of DNA toward anti-BPDE. The results indicate that of all the polynucleotides studied, only poly(dA-dT) · poly(dA-dT) exhibits predominant intercalative covalent binding towards (+)-anti-BPDE and suffers the least covalent modification. Only minor intercalative covalent contributions are found in alternating polymer poly(dA-dC) · poly(dG-dT). These observations parallel the DNA physical binding results of anti-BPDE and its hydrolysis products. They support the hypothesis that intercalative covalent adducts derive from intercalative physical binding while the external covalent adducts derive from external bimolecular associations. In contrast to the A · T polymers, the guanine containing polymers exhibit pronounced reduction in covalent modification by (-)-anti-BPDE. The intercalative covalent binding mode becomes relatively more important in the adducts formed by the (-) enantiomer as a consequence of decreased external guanine binding. These findings are consistent with the guanine specificity, stereoselective covalent binding at dG, the absence of stereoselectivity at dA for anti-BPDE, and the enhanced binding heterogeneity for the (-) enantiomer as found in the native DNA studies. The possible sequence and/or conformational dependence of such stereoselective covalent binding is indicated by the opposite pyrenyl CD sign exhibited by (+)-anti-BPDE bound to polynucleotides with pyrimidine on one strand and purine on another vs. that bound to polymers containing alternating purine-pyrimidine sequences.     

Mixed-ligand copper(II)-phenanthroline-dipeptide complexes: synthesis, characterization, and DNA-cleavage properties

The mixed-ligand complexes [Cu(II)(HisLeu)(phen)](+) (1) and [Cu(II)(HisSer)(phen)](+) (2; phen=1,10-phenanthroline) were synthesized and characterized. The intercalative interaction of the Cu(II) complexes with calf-thymus DNA (CT-DNA) was probed by UV/VIS and fluorescence titration, as well as by thermal-denaturation experiments, and the intrinsic binding constants (K(b)) for the complexes with 1 and 2 were 4.2x10(3) and 4.9x10(3) M(-1), resp. Both complexes were found to be efficient catalysts for the hydrolytic cleavage of plasmid pUC19 DNA, as tested by gel electrophoresis, converting the DNA from the supercoiled to the nicked-circular form at rate constants of 1.32 and 1.40 h(-1) for 1 and 2, resp.     

An intercalative and minor groove binding model for the DNA cleavage reagent, copper(I) (1,10-phenanthroline)2

On account of the stereochemical structure and interaction characteristics of the DNA cleavage reagent copper(I) (1,10-phenanthroline)2, both intercalative and minor groove binding modes to B-DNA could be expected to occur. In the proposed model, the suitable dihedral angle between phenanthrolines allows that one of the two planar ligands partially intercalates between base pairs, and meanwhile the other ligand locates along the minor groove.     

DNA intercalation and photosensitization by cationic meso substituted porphyrins.

Several cationic porphyrins are known to bind to DNA by intercalative and outside binding modes. This study identifies the cis and trans isomers of bis(N-methyl-4-phridiniumyl)diphenyl porphyrin as DNA intercalators based on evidence from a DNA topoisomerase I assay. Moreover, both isomers are shown to be potent photosensitizers of DNA, inducing multiple S1 nuclease sensitive breaks in the phosphodiester backbone. Porphyrin-induced photodamage in DNA was also shown to be quantitatively dependent upon ionic strength and to inhibit the action of restriction endonucleases. The results indicate that these porphyrins can be useful probes of DNA structure and have potential as DNA-targeted photosensitizers.