Electron-, Energy-, and Atom-Transfer Reactions Between Metal Complexes and Dna. Elsevier; 1995. pp. 127-77. [DOI: 10.1016/s0898-8838(08)60117-8]

Synthesis, DNA binding, and cleavage studies of Co(III) complexes with fused aromatic NO/NN-containing ligands

Four new Co(III) complexes, namely [Co(cq)(3)](PF(6))(3), [Co(phen)(2)(cq)](PF(6))(3), [Co(bnp)(3)] (PF(6))(3), and [Co(phen)(2)(bnp)](PF(6))(3) (where cq = chromeno[2,3-b]quinoline, phen = 1,10-phenanthroline and bnp = dibenzo[b,g][1,8]naphthyridine), were synthesized and structurally characterized. Spectroscopic data suggested an octahedral geometry for all the complexes. Binding studies of these complexes with double-stranded (ds)DNA were analyzed by absorption spectra, viscosity, and thermal denaturation studies. The results revealed that the metal complex intercalates into the DNA base stack as intercalator. The oxidative cleavage activities of the complexes were studied with supercoiled pUC19 DNA using gel electrophoresis and the results show that the complexes have potent nuclease activity.

Synthesis and structural characterization of ternary Cu (II) complexes of glycine with 2,2'-bipyridine and 2,2'-dipyridylamine. The DNA-binding studies and biological activity

In this study two new complexes [Cu(bpy)(Gly)Cl]·2H(2)O (1) and [Cu(dpa)(Gly)Cl]·2H(2)O (2) (bpy=2,2'-bipyridine; dpa=2,2'-dipyridylamine, Gly=glycine) have been synthesized and characterized by elemental analysis, IR, TGA, UV-vis and magnetic susceptibility measurements. The binding properties of the complexes with CT-DNA were investigated by electronic absorption spectra. The intrinsic binding constants (K(b)) calculated from UV-vis absorption studies were 1.84 × 10(3) M(-1) and 3.1 × 10(3) M(-1) for complexes 1 and 2 respectively. Thermal denaturation has been systematically studied by spectrophotometric method and the calculated ΔT(m) was nearly 5 °C for each complex. All the results suggest that the interaction modes between the complexes and CT-DNA were electrostatic and/or groove binding. The redox behavior of the two complexes was investigated by cyclic voltammetry. Both complexes, in presence and absence of CT-DNA show a quasi-reversible wave corresponding to Cu(II)/Cu(I) redox couple. The change in E(1/2), ΔE and I(pc)/I(pa) ascertain the interaction of complexes 1 and 2 with CT-DNA. Further insight into the binding of complexes with CT-DNA has been made by gel electrophoresis, where the binding of complexes is confirmed through decreasing the mobility and intensity of DNA bands. In addition, the antitumor activity of the complexes was tested on two cancer cell lines; the breast cancer (MCF7) and the human hepatocellular carcinoma (HEPG2), as well as one normal cell line; the human normal melanocytes (HFB4). The results showed that complex 1 was more potent antitumor agent than complex 2. The in-vitro antimicrobial activity of the two complexes was carried out using the disc diffusion method against different species of pathogenic bacteria and fungi. The activity data showed that complex 2 was more active in inhibiting the growth of the tested organisms.

Effect of ancillary ligands on the DNA interaction of [Cr(diimine)3]3+ complexes containing the intercalating dipyridophenazine ligand

The synthesis of photoluminescent Cr(III) complexes of the type [Cr(diimine)(2)(DPPZ)](3+) are described, where DPPZ is the intercalating dipyridophenazine ligand, and diimine corresponds to the ancillary ligands bpy, phen, DMP, and TMP (where bpy = 2,2'-bipyridine, phen = 1,10-phenanthroline, DMP = 5,6-dimethyl-1,10-phenanthroline, and TMP = 3,4,7,8-tetramethyl-1,10-phenanthroline). For TMP, DMP, and phen as ancillary ligands, the complexes have also been resolved into their Lambda and Delta optical isomers. A comparison of the photophysical and electrochemical properties reveal similar (2)E(g) --> (4)A(2g) (O(h)) emission wavelengths and lifetimes, and a variation of 110 mV in the (2)E(g) excited state oxidizing power. A detailed investigation has been undertaken of ancillary ligand effects on the DNA binding of these complexes with a range of polynucleotides. For all four complexes, emission is quenched by the addition of calf thymus B-DNA, with the emission lifetime data yielding bimolecular quenching rate constants close to the diffusion controlled limit. Equilibrium dialysis studies have established a general predilection for AT base binding sites, while companion experiments with added distamycin (a selective minor groove binder) provide evidence for a minor groove binding preference. For the case of [Cr(TMP)(2)(DPPZ)](3+), concomitant equilibrium dialysis and circular dichroism measurements have demonstrated very strong enantioselective binding by the Lambda optical isomer. The thermodynamics of DNA binding have also been explored via isothermal titration calorimetry (ITC). The ITC data establish that the primary binding mode for all four Cr(III) complexes is entropically driven, a result that is attributed to the highly favorable free energy contribution associated with the hydrophobic transfer of the Cr(III) complexes from solution into the DNA binding site.

Synthesis, DNA binding and cleavage studies of Ni(II) complexes with fused aromatic N-containing ligands

The three Ni(II) complexes of fused aromatic N-containing ligands such as [Ni(bnp)(3)](PF(6))(2) (1), [Ni(phen)(2)(bnp)](PF(6))(2) (2) and [Ni(bpy)(2)(bnp)](PF(6))(2) (3) (where bnp=dibenzo(b)1,8-naphthpyridine, phen=1,10-phenanthroline and bpy=bipyridine) were synthesized and structurally characterized. Elemental analysis, magnetic and spectroscopic data suggested octahedral geometry for all the complexes. Binding of these complexes with (ds)DNA were analyzed by absorption spectra, viscosity and thermal denaturation studies. Detailed analysis revealed that the metal complexes intercalates into the DNA base stack as intercalator. The oxidative cleavage activities of the complexes were studied with supercoiled (SC)pUC19 DNA by using gel electrophoresis, and the results show that complexes have potent nuclease activity.

DNA binding and nuclease activity of a one-dimensional heterometallic nitrosyl complex

The interaction of a structurally characterized Sr-Fe nitrosyl complex with DNA has been studied by UV-vis and fluorescence spectroscopy, viscometric, and gel electrophoresis techniques. From the absorption titration studies the intrinsic binding constant of the complex with DNA was calculated to be 1.6x10(4)M(-1). Fluorimetric studies indicate that the complex compete with EB in binding to DNA. The complex shows nuclease activity on pUC19 supercoiled DNA in presence of H(2)O(2).

DNA-binding studies of mixed-ligand (ethylenediamine)ruthenium(II) complexes

A series of mixed-ligand ruthenium(II) complexes of the type [Ru(en)(2)bpy](2+) (bpy=2,2-bipyridine; 1), [Ru(en)(2)phen](2+) (phen=1,10-phenantroline; 2), [Ru(en)(2)IP](2+) (IP=imidazo[4,5-f][1,10]phenanthroline; 3), and [Ru(en)(2)PIP](2+) (PIP=2-phenylimidazo[4,5-f][1,10]phenanthroline; 4) have been isolated and characterized by UV/VIS, IR, and (1)H-NMR spectral methods. The binding of the complexes with calf thymus DNA has been investigated by absorption, emission spectroscopy, viscosity measurements, DNA melting, and DNA photo-cleavage. The spectroscopic studies together with viscosity measurements and DNA melting studies support that complexes 1 and 2 bind to CT DNA (=calf thymus DNA) by groove mode. Complex 2 binds more avidly to CT DNA than complex 1, complexes 3 and 4 bind to CT DNA by intercalation mode, 4 binds more avidly to CT DNA than 3. Noticeably, the four complexes have been found to be efficient photosensitisers for strand scissions in plasmid DNA.

Mixed-ligand complexes of ruthenium(II) containing new photoactive or electroactive ligands: synthesis, spectral characterization and DNA interactions

Mixed-ligand ruthenium(II) complexes of three photoactive ligands, viz., (E)-1-[2-(4-methyl-2-pyridyl)-4-pyridyl]-2-(1-naphthyl)-1-ethene (mppne), (E)-1-(9-anthryl)-2-[2-(4-methyl-2-pyridyl)-4-pyridyl]-1-ethene (mppae) and (E)-1-[2-(4-methyl-2-pyridyl)-4-pyridyl]-2-(1-pyrenyl)-1-ethene (mpppe), in which a 2,2'-bipyridyl unit is linked via an ethylinic linkage to either a naphthalene, an anthracene or a pyrene chromophore and three electroactive ligands, viz., 4-(4-pyridyl)-1,2-benzenediol (catpy), 5,6-dihydroxy-1,10-phenanthroline (catphen) and 1,2-benzenediol (cat), were synthesized in good to moderate yields. Complexes [Ru(bpy)(2)(mppne)](2+) (bpy is 2, 2'-bipyridyl), [Ru(bpy)(2)(mppae)](2+), [Ru(bpy)(2)(mpppe)](2+), [Ru(bpy)(2)(sq-py)](+), [Ru(bpy)(2)(sq-phen)](+) and [Ru(phen)(2)(bsq)](+) (phen is 1,10-phenanthroline) were fully characterized by elemental analysis, IR, (1)H NMR, fast-atom bombardment or electron-impact mass, UV-vis and cyclic voltammetric methods. In the latter three complexes, the ligands catpy, catphen and cat are actually bound to the metal center as the corresponding semiquinone species, viz., 4-(4-pyridyl)-1,2-benzenedioleto(+I) (sq-py), 1,10-phenanthroline-5,6-dioleto(+I) (sq-phen) and 1,2-benzenedioleto(+I) (bsq), thus making the overall charge of the complexes formally equal to + 1 in each case. These three complexes are electron paramagnetic resonance active and exhibit an intense absorption band between 941 and 958 nm owing to metal-to-ligand charge transfer (MLCT, d (Ru)-->pi*(sq)) transitions. The other three ruthenium(II) complexes containing three photoactive ligands, mppne, mppae and mpppe, exhibit MLCT (d (Ru)-->pi*(bpy) ) bands in the 454-461-nm region and are diamagnetic. These can be characterized by the (1)H NMR method. [Ru(bpy)(2)(mppne)](2+), [Ru(bpy)(2)(mppae)](2+) and [Ru(bpy)(2)(mpppe)](2+) exhibit redox waves corresponding to the Ru(III)/Ru(II) couple along with the expected ligand (bpy and substituted bpy) based ones in their cyclic and differential pulse voltammograms (CH(3)CN, 0.1 M tetrabutylammonium hexafluorophosphate)-corresponding voltammograms of [Ru(bpy)(2)(sq-py)](+), [Ru(bpy)(2)(sq-phen)](+) and [Ru(phen)(2)(bsq)](+) are mainly characterized by waves corresponding to the quinone/semiquinone (q/sq) and semiquinone/1,2-diol (sq/cat) redox processes. The results of absorption and fluorescence titration as well as thermal denaturation studies reveal that [Ru(bpy)(2)(mppne)](2+) and [Ru(bpy)(2)(mppae)](2+) are moderate-to-strong binders of calf thymus DNA with binding constants ranging from 10(5) to 10(6) M(-1). Under the identical conditions of drug and light dose, the DNA (supercoiled pBR 322) photocleavage activities of these two complexes follow the order:[Ru(bpy)(2)(mppne)](2+)>[Ru(bpy)(2)(mppae)](2+), although the emission quantum yields follow the reverse order. The other ruthenium(II) complexes containing the semiquinone-based ligands are found to be nonluminescent and inefficient photocleavage agents of DNA. However, experiments shows that [Ru(bpy)(2)(sq)](+)-based complexes oxidize the sugar unit and could be used as mild oxidants for the sugar moiety of DNA. Possible explanations for these observations are presented.

Recognition of guanines at a double helix–coil junction in DNA by a trinuclear copper complex

Coordination between guanine N7 and a trinuclear copper complex appears critical for selective and efficient strand scission of DNA at a helix-coil junction as indicated by the lack of reactivity of comparable DNA containing 7-deazaguanine in place of guanine; both the base pair at the junction and coil flexibility also modulate the specificity of DNA oxidation.

DNA interactions of new mixed-ligand complexes of cobalt(III) and nickel(II) that incorporate modified phenanthroline ligands

Four new mixed-ligand complexes, namely [Co(phen)(2)(qdppz)](3+), [Ni(phen)(2)(qdppz)](2+), [Co(phen)(2)(dicnq)](3+) and [Ni(phen)(2)(dicnq)](2+) (phen=1,10-phenanthroline, qdppz=naptho[2,3-a]dipyrido[3,2-H:2',3'-f]phenazine-5,18-dione and dicnq=dicyanodipyrido quinoxaline), were synthesized and characterized by FAB-MS, UV/Vis, IR, 1H NMR, cyclic voltammetry and magnetic susceptibility methods. Absorption and viscometric titration as well as thermal denaturation studies revealed that each of these octahedral complexes is an avid binder of calf-thymus DNA. The apparent binding constants for the dicnq- and qdppz-bearing complexes are in the order of 10(4) and >10(6) M(-1), respectively. Based on the data obtained, an intercalative mode of DNA binding is suggested for these complexes. While both the investigated cobalt(III) complexes and also [Ni(phen)(2)(qdppz)](2+) affected the photocleavage of DNA (supercoiled pBR 322) upon irradiation by 360 nm light, the corresponding dicnq complex of nickel(II) was found to be ineffective under a similar set of experimental conditions. The physico-chemical properties as well as salient features involved in the DNA interactions of the cobalt(III) and nickel(II) complexes investigated here were compared with each other and also with the corresponding properties of the previously reported ruthenium(II) analogues.

The importance of being r: greater oxidative stability of RNA compared with DNA

The 2'-hydroxyl group of ribose imparts hydrolytic lability on RNA, which provides a mechanism for numerous biological functions. Recent evidence from chemical cleavage studies shows that this hydroxyl group also stabilizes the sugar moiety in RNA towards oxidation relative to DNA. Is this just because RNA needs to be distinguishable from DNA or does it have other evolutionary significance?

Insertion of dGMP and dAMP during in vitro DNA synthesis opposite an oxidized form of 7,8-dihydro-8-oxoguanine

Oxidative damage to DNA bases commonly resultsin the formation of oxidized purines, particularly 7,8-dihydro-8-oxoguanine (8-oxoG) and 7,8-dihydro-8-oxoadenine (8-oxoA), the former being a well-known mutagenic lesion. Since 8-oxoG is readily subject to further oxidation compared with normal bases, the insertion of a base during DNA synthesis opposite an oxidized form of 8-oxoG was investigated in vitro. A synthetic template containing a single 8-oxoG lesion was first treated with different one-electron oxidants or under singlet oxygen conditions and then subjected to primer extension catalyzed by Klenow fragment exo- (Kf exo-), calf thymus DNA polymerase alpha (pol alpha) or human DNA polymerase beta (pol beta). Consistent with previous reports, dAMP and dCMP are inserted selectively opposite 8-oxoG with all three DNA polymerases. Interestingly, oxidation of 8-oxoG was found to induce dAMP and dGMP insertion opposite the lesion by Kf exo- with transient inhibition of primer extension occurring at the site of the modified base. Furthermore, the lesion constitutes a block during DNA synthesis by pol alpha and pol beta. Experiments with an 8-oxoA-modified template oligonucleotide show that both 8-oxoA and an oxidized form of 8-oxoA direct insertion of dTMP by Kf exo-. Mass spectrometric analysis of 8-oxoG-containing oligonucleotides before and after oxidation with IrCl62-are consistent with oxidation of primarily the 8-oxoG site, resulting in formation of a guanidinohydantoin moiety as the major product. No evidence for formation of abasic sites was obtained. These results demonstrate that an oxidized form of 8-oxoG, possibly guanidinohydantoin, may direct misreading and misinsertion of dNTPs during DNA synthesis. If such a process occurred in vivo, it would represent a point mutagenic lesion leading to G-->T and G-->C transversions. However, the corresponding oxidized form of 8-oxoA primarily shows correct insertion of T during DNA synthesis with Kf exo-.

Oxidation of guanines in the iron-responsive element RNA: similar structures from chemical modification and recent NMR studies

BACKGROUND

The translation or stability of the mRNAs from ferritin, maconitase, erythroid aminoevulinate synthase and the transferrin receptor is controlled by the binding of two iron regulatory proteins to a family of hairpin-forming RNA sequences called iron-responsive elements (IREs). The determination of high-resolution nuclear magnetic resonance (NMR) structures of IRE variants suggests an unusual hexaloop structure, leading to an intra-loop G-C base pair and a highly exposed loop guanine, and a special internal loop/bulge in the ferritin IRE involving a shift in base pairing not predicted with standard algorithms.

RESULTS

Cleavage of synthetic 55- and 30-mer RNA oligonucleotides corresponding to the ferritin IRE with complexes based on oxoruthenium(IV) shows enhanced reactivity at a hexaloop guanine and at a guanine adjacent to the internal loop/bulge with strong protection at a guanine in the internal loop/bulge. These results are consistent with the recent NMR structures. The synthetic 55-mer RNA binds the iron-regulatory protein from rabbit reticulocyte lysates. The DNA analogs of the 55- and 30-mers do not show the same reactivity pattern.

CONCLUSIONS

The chemical reactivity of the guanines in the ferritin IRE towards oxoruthenium(IV) supports the published NMR structures and the known oxidation chemistry of the metal complexes. The results constitute progress towards developing stand-alone chemical nucleases that reveal significant structural properties and provide results that can ultimately be used to constrain molecular modeling.