Ligand effects associated with the intrinsic selectivity of DNA oxidation promoted by nickel(II) macrocyclic complexes

Ni(ii) ions cleave and inactivate human alpha-1 antitrypsin hydrolytically, implicating nickel exposure as a contributing factor in pathologies related to antitrypsin deficiency

Ni(ii) ions cleave AAT hydrolytically, inactivating the protein.

Self-assembled Cu(ii) and Ni(ii) metallamacrocycles formed from 3,3,3′,3′-tetrabenzyl-1,1′-aroylbis(thiourea) ligands: DNA and protein binding studies, and cytotoxicity of trinuclear complexes

The synthesis and characterization of metallamacrocyclic square planar Ni(ii) and Cu(ii) complexes and the interaction of cytotoxic trinuclear complexes with CT DNA and BSA protein are described.

Mechanism of DNA Strand Cleavage Induced by Hexaaza Macrocyclic Nickel (II) Complex

The hexaaza macrocyclic nickel(II) complex (Ni(II)L-1,8-Dihydroxyethyl-1,3,6,8,10,13-hexaazacyclotetradecane nickle(II) perchlorate monohydrate) was synthesized and purified. The electrochemical character of Ni(II)L was measured, and the interaction of Ni(II)L with calf thymus DNA (CT-DNA) was studied using electrochemical techniques, emission and viscometry, and circular dichroic spectral measurements. All of the experiments suggested that the complex interacted with DNA primarily by partial intercalation. The cyclic voltammetry (CV) showed that the currents of both the reduction peak and the oxidation peak decreased significantly in the presence of DNA, which indicated that Ni(II)L could interact with DNA. The fluorescence intensity of the DNA-ethidium bromide(EB) system decreased distinctly when Ni(II)L was added. The results indicated that Ni(II)L may be completed effectively with EB for the intercalative binding sites. The viscosity of DNA would be decreased slightly by the addition of the complex. Circular dichroic spectral studies revealed that B conformation of CT-DNA became more A-like in structure on interaction with the complex. Noticeably, the complex has been found to cleave plasmid pBR 322 by agarose gel electrophoresis and cleave CT-DNA by high-performance liquid chromatography (HPLC).

Diaqua[(1R,2S,4R,8R,9S,11R)-2,9-dimethyl-1,4,8,11-tetraazacyclotetradecane]nickel(II) dichloride dihydrate

The crystal structure of the title complex, [Ni(C₁₂H₂₈N₄)(H₂O)₂]Cl₂·2H₂O, displays O—H⋯Cl and O—H⋯O hydrogen bonding. The tetra­aza­cyclo­tetra­decane ligand inter­acts with the Ni^II atom in the cis V configuration and the final two ligand binding sites are occupied by water.

One-step synthesis of α/β cyano-aqua cobinamides from vitamin B12 with Zn(II) or Cu(II) salts in methanol

This short communication describes the screening of various metal salts for the preparation of cyano-aqua cobinamides from vitamin B12 in methanol. ZnCl2 and Cu(NO3)2·3H2O have been identified as most active for this purpose and represent useful alternatives to the widely applied Ce(III) method that requires excess cyanide.

Oxidative DNA damage mediated by transition metal ions and their complexes

DNA damage by redox-active metal complexes depends on the interaction of the metal complex with DNA together with the mechanism of oxygen activation. Weak interaction, tight binding, and direct involvement of DNA in the coordination sphere of the metal are described. Metal complexes acting through the production of diffusing radicals and metal complexes oxidizing DNA by metal-centered active species are compared. Metal complexes able to form high-valent metal-oxo species in close contact with DNA and perform DNA oxidation in a way reminiscent of enzymatic chemistry are the most elegant systems.

Comparison of Transition Metal-Mediated Oxidation Reactions of Guanine in Nucleoside and Single-Stranded Oligodeoxynucleotide Contexts

As the most readily oxidized of DNA's four natural bases, guanine is a prime target for attack by reactive oxygen species (ROS) and transition metal-mediated oxidants. The oxidation products of a modified guanosine nucleoside and of a single-stranded oligodeoxynucleotide, 5'-d(TTTTTTTGTTTTTTT)-3' have been studied using oxidants that include Co(II), Ni(II), and Ir(IV) compounds as well as photochemically generated oxidants such as sulphate radical, electron-transfer agents (riboflavin) and singlet oxygen. The oxidized lesions formed include spiroiminodihydantoin (Sp), guanidinohydantoin (Gh), imidazolone (Iz), oxazolone (Z) and 5-carboxamido-5-formamido-2-iminohydantion (2-Ih) nucleosides with a high degree of dependence on the exact oxidation system employed. Interestingly, a nickel(II) macrocyclic complex in conjunction with KHSO(5) leads to the recently reported 2-Ih heterocycle as the major product in both the nucleoside and oligonucleotide contexts.

Specific Recognition of Loop DNA by Dicationic Porphyrins

A series of dicationic porphyrins were found to specifically recognize loop structures of oligodeoxynucleotides, and to selectively oxidize guanine residues upon photo-irradiation at micromolar concentrations. These compounds could, thus, be employed as promising structural probes for specific secondary DNA structures. The production of singlet oxygen ((1)O2) is responsible for the DNA-modification profiles. Both UV-titration and thermal-melting experiments indicate that the strong affinity of the charged porphyrins towards DNA loops is responsible for these molecular-recognition phenomena.

Synthesis, characterization and in vitro biological activity studies of Cu–M (M=Cu2+, Co2+, Ni2+, Mn2+, Zn2+) bimetallic complexes

Six new bimetallic complexes of the type CuCu, CuCo, CuNi, CuZn and CuMn were prepared. The structures of these complexes and the ligand have been proposed on the basis of FAB mass, elemental analysis, UV-vis, IR, EPR and CV studies. All the complexes completely cleave pBS (SK-) DNA at a concentration of 10 microM; however, even at lower concentrations of 2 microM and 0.1 microM, the complexes (I and Ia) showed partial cleavage. The results of the fluorescence binding studies of the metal complexes with CT-DNA showed that the presence of aliphatic ligands added additional binding effects including electrostatic, hydrogen binding and vander Waals interactions. Complexes (I, Ia) showed 50% inhibition of COX-1 and COX-2 activities at as low a concentration as 12.5 microM, 13.5 microM, 14 microM and 14.5 microM. Inhibition assay of top I and top II by different complexes in mutant yeast strains (JN394, JN394 t(-1) and JN394 t(2-5)) with all the complexes showed significant inhibition of topoisomerase at 5 microM concentration. Complexes I and Ia exhibited good anti-microbial activities against all human pathogens tested except Klebsiella pneumoniae. The following studies showed that among the synthesized bimetallic complexes, complexes I and Ia seem to be promising candidates possessing DNA cleavage activities besides anti-microbial and anti-inflammatory properties to serve as chemical nucleases and chemotherapeutic agents.

Synthesis, physico-chemical and DNA interaction studies of homo- and hetero-trinuclear complexes

Synthesis and characterization of three new trinuclear metal complexes of type Cu3, Cu2Zn and Cu2Ni have been achieved by assembling simple mononuclear complexes, namely 2,2'-bipyridyl 3,4-dihydroxo benzaldehyde copper(II) complex and diethylenetriamine complexes of copper(II), nickel(II) and zinc(II) ions, through the reaction of coordinated ligands. The FAB mass spectra for the complexes show fragmentation pattern in accordance with the molecular formula. The frozen electron paramagnetic resonance (EPR) spectrum of tricopper complex shows two sets of parallel lines with approximately 2:1 ratio. The simulation has been carried out by considering dipolar interaction between the two types of copper ions present in the complex. The trimetallic complexes, Cu3, Cu2Ni and Cu2Zn show strong intercalation type of interaction with Calf thymus DNA in 0.02 mol L(-1) of phosphate buffer containing 60 mmol sodium chloride at pH 7.0 at room temperature. The binding constant is found to be in the order Cu3<Cu2Zn<Cu2Ni. The enhanced binding capability of Cu2Ni complex is attributed to the increased symmetry in the overall structure of the complex and the pronounced binding character of positively charged Ni(II) ions with the purines.

Ternary Nickel(II) Complexes as Hydrolytic DNA-Cleavage Agents

A series of small model complexes made from Ni(II) and the ligands ethylenediamine (en), histamine (hist), and histidylleucine (HisLeu) were prepared and studied as potential hydrolytic DNA-cleavage agents. The stability constants and species-distribution curves for these complexes were determined as a function of pH. The 1 : 1 : 1 ternary complexes [Ni(II)(en)(HisLeu)] (1) and [Ni(II)(hist)(HisLeu)] (2) were the only major species present at the physiologically relevant pH of 6-7, as further corroborated by ESI-MS analysis. The complex geometries of 1 and 2 were analyzed by UV/VIS experiments and molecular dynamics (MD) simulations. Both ternary complexes were found to intercalate with DNA, as shown by UV/VIS, thermal-denaturation, and fluorescence-titration studies with ethidium bromide (EB). The intrinsic binding constants (K(b)) for the bound complexes 1DNA and 2DNA were determined as 150 and 290, resp. Gel-electrophoresis experiments revealed that 1 and 2 cleave supercoiled (type-I) to nicked-circular (type-II) DNA at physiological pH, with rate constants of 0.64 and 0.75 h(-1), resp. A tentative mechanism for this hydrolytic cleavage is proposed.

Synthesis and Structural Characterization of Carborane-Containing Neutral, Self-Assembled Pt-Metallacycles

[structure: see text] We have combined carborane chemistry with the newly developed directional bonding strategy to synthesize neutral macrocycles. The m- and p-carborane dicarboxylates were utilized as the donor linkers in conjunction with 1,8-bis[trans-Pt(PEt3)2NO3]anthracene 3, 2,9-bis[trans-Pt(PEt3)2NO3]phenanthrene 5, and cis-Pt(PEt3)2(NO3)2 unit 6. Three new platinum-based macrocycles, 4, 7, and 8, were thus synthesized. 31P{1H} NMR as well as the X-ray characterization of Pt-metallacycles reveal the formation of single highly symmetrical neutral species.

Coordination-Driven Self-Assemblies with a Carborane Backbone

The design and self-assembly of five new supramolecular complexes (a rectangle, a triangle, a hexagon, and two squares) are described. These assemblies incorporate carborane building blocks and were prepared in excellent yields (>85%). The assemblies and building blocks were characterized with multinuclear NMR spectroscopy, electrospray ionization mass spectrometry, and elemental analysis. Isotopically resolved mass spectrometry data confirm the existence of the rectangle, triangle, and hexagon, and NMR data are consistent with the formation of all five assemblies. The X-ray structures of two linear carborane building blocks, 1,12-(4-CC(C(5)H(4)N)(2)-p-C(2)B(10)H(10) (1) and 1,12-(trans-(Pt(PEt(3))(2)I)CC)(2)-p-C(2)B(10)H(10) (2), are reported: 1 is monoclinic, P2(1)/c, a = 10.6791(4) A, b = 8.0091(14) A, c = 11.6796(4) A, beta = 107.8461(15) degrees , V = 950.89(5) A(3), Z = 2; 2 is monoclinic, C2/c, a = 62.1128(10) A, b = 22.0071(3) A, c = 14.0494(2) A, beta = 89.9411(8) degrees , V = 19204.4(5) A(3), Z = 16. Crystals of the linear linker 1 exhibit close pi-pi pyridine and pyridine-B(carborane) interactions, which are discussed.

DNA damage induced by sulfite autoxidation catalyzed by copper(ii) tetraglycine complexes

Copper(II)/(III) tetraglycine complexes were investigated for their ability to catalyze the autoxidation of sulfite resulting in oxidative DNA damage. The focus of this work is on DNA damage by Cu(III) and oxysulfur radicals formed by the oxidation of S(IV) oxides by dissolved oxygen in the presence of Cu(II) tetraglycine complexes. The results suggest that sulfite is rapidly oxidized by oxygen in the presence of Cu(II) complexes producing Cu(III) tetraglycine, which can be monitored spectrophotometrically at 365 nm. A synergistic effect of Cu(II) with a second metal ion (Ni(II), Co(II) or Mn(II) traces) was observed.

Analysis of human topoisomerase I inhibition and interaction with the cleavage site +1 deoxyguanosine, via in vitro experiments and molecular modeling studies

Human topoisomerase I (Top1) plays a pivotal role in cell replication and transcription, and therefore is an important anti-cancer target. Homocamptothecin is a lead compound for inhibiting Top1, and is composed of five conjugated planar rings (A-E). The homocamptothecin E-ring beta-hydroxylactone opens slowly to a carboxylate at pH>7.0. We analyzed, which form of homocamptothecin was biochemically relevant in the following ways: (1) the homocamptothecin carboxylate was tested for activity in vitro and found to be inactive; (2) homocamptothecin was incubated with Top1 and dsDNA, and we found that the homocamptothecin beta-hydroxylactone form was stabilized; (3) the homocamptothecin E-ring beta-hydroxylactone was modified to prevent opening, and the derivatives were either inactive or had low activity. These results indicated that the homocamptothecin beta-hydroxylactone was the active form, and that an E-ring carbonyl oxygen and adjacent unsubstituted/unprotonated ring atom were required for full activity. Homocamptothecin and derivatives were docked into a Top1/DNA active site model, in which the +1 deoxyguanosine was rotated out of the helix, in order to compare the interaction energies between the ligands and the Top1/DNA active site with the in vitro activities of the ligands. It was found that the ligand interaction energies and in vitro activities were correlated, while the orientations of the ligands in the Top1/DNA active site explained the importance of the E-ring beta-hydroxylactone independently of E-ring opening. An essential component of this Top1/DNA active site model is the rotated +1 deoxyguanosine, and in vitro experiments and molecular modeling studies supported rotation of the +1 deoxyguanosine out of the helix. These results allow for the rational design of more potent Top1 inhibitors through engineered interactions with as yet unutilized Top1 active-site residues including: Glu356, Asn430, and Lys751.

Mechanism of two-electron oxidation of deoxyguanosine 5'-monophosphate by a platinum(IV) complex

Many transition metal complexes mediate DNA oxidation in the presence of oxidizing radiation, photosensitizers, or oxidants. The final DNA oxidation products vary depending on the nature of metal complexes and the structure of DNA. Here we propose a mechanism of oxidation of a nucleotide, deoxyguanosine 5'-monophosphate (dGMP) by trans-d,l-1,2-diaminocyclohexanetetrachloroplatinum (trans-Pt(d,l)(1,2-(NH(2))(2)C(6)H(10))Cl(4), [Pt(IV)Cl(4)(dach)]; dach = diaminocyclohexane) to produce 7,8-dihydro-8-oxo-2'-deoxyguanosine 5'-monophosphate (8-oxo-dGMP) stoichiometrically. The reaction was studied by high-performance liquid chromatography (HPLC), (1)H and (31)P nuclear magnetic resonance (NMR), and electrospray ionization mass spectrometry (ESI-MS). The proposed mechanism involves Pt(IV) binding to N7 of dGMP followed by cyclization via nucleophilic attack of a phosphate oxygen at C8 of dGMP. The next step is an inner-sphere, two-electron transfer to produce a cyclic phosphodiester intermediate, 8-hydroxyguanosine cyclic 5',8-(hydrogen phosphate). This intermediate slowly converts to 8-oxo-dGMP by reacting with solvent H(2)O.

Synthesis of 5,12-dioxocyclam nickel (II) complexes having quinoxaline substituents at the 6 and 13 positions as potential DNA bis-intercalating and cleaving agents

Several dioxocyclams containing quinoxaline moieties, as well as their nickel(II) complexes were synthesized and studied for their ability to bind and oxidatively cleave DNA. Although no evidence for binding by intercalation was found, the ability of the Ni(II) complexes to cleave DNA in the presence of Oxone was strongly dependent on both the nature and the spatial orientation of the quinoxaline moieties, suggesting at least transient association of these complexes with DNA.

Metal-ligand charge-transfer-promoted photoelectronic Bergman cyclization of copper metalloenediynes: photochemical DNA cleavage via C-4' H-atom abstraction

Metal-to-ligand charge-transfer (MLCT) photolyses (lambda > or = 395 nm) of copper complexes of cis-1,8-bis(pyridin-3-oxy)oct-4-ene-2,6-diyne (bpod, 1), [Cu(bpod)(2)]PF(6) (2), and [Cu(bpod)(2)](NO(3))(2) (3) yield Bergman cyclization of the bound ligands. In contrast, the uncomplexed ligand 1 and Zn(bpod)(2)(CH(3)COO)(2) compound (4) are photochemically inert under the same conditions. In the case of 4, sensitized photochemical generation of the lowest energy (3)pi-pi state, which is localized on the enediyne unit, leads to production of the trans-bpod ligand bound to the Zn(II) cation by photoisomerization. Electrochemical studies show that 1, both the uncomplexed and complexed, exhibits two irreversible waves between E(p) values of -1.75 and -1.93 V (vs SCE), corresponding to reductions of the alkyne units. Irreversible, ligand-based one-electron oxidation waves are also observed at +1.94 and +2.15 V (vs SCE) for 1 and 3. Copper-centered oxidation of 2 and reduction of 3 occur at E(1/2) = +0.15 and +0.38 V, respectively. Combined with the observed Cu(I)-to-pyridine(pi) MLCT and pyridine(pi)-to-Cu(II) ligand-to-metal charge transfer (LMCT) absorption centered near approximately 315 nm, the results suggest a mechanism for photo-Bergman cyclization that is derived from energy transfer to the enediyne unit upon charge-transfer excitation. The intermediates produced upon photolysis degrade both pUC19 bacterial plasmid DNA, as well as a 25-base-pair, double-stranded oligonucleotide. Detailed analyses of the cleavage reactions reveal 5'-phosphate and 3'-phosphoglycolate termini that are derived from H-atom abstraction from the 4'-position of the deoxyribose ring rather than redox-induced base oxidation.

Influence of carbocation stability in the gas phase on solvolytic reactivity: beyond bridgehead derivatives

The intrinsic gas-phase stability of bicyclic secondary carbocations has been determined by Dissociative Proton Attachment of chlorides and alcohols, respectively. From these data, Gibbs free energies for hydride transfer relative to 1-adamantyl (Delta(r)G degrees (8,exp)) are derived after application of appropriate leaving group corrections, and good agreement with theoretical values, (Delta(r)G degrees (8,comp)), calculated at the G2(MP2) or MP2/6-311G(d,p) level, is reached (Table 1). The relative rate constants for solvolysis (log(k/k(0))) of the bicyclic secondary derivatives correlate with the stabilities of the respective carbocations in the same manner as tertiary bridgehead derivatives, but simple monoderivatives and acyclic derivatives solvolyze faster than predicted on the grounds of the ion stabilities. The corresponding stabilities of cyclopropyl- and benzyl-substituted carbocations have been obtained by a combination of experimental and computational data available in the literature with computational methods. Correlation of the rate constants for solvolysis vs ion stabilities for these compounds reveals a trend similar to that observed for bridgehead derivatives, but with much more scatter, which is attributed to nucleophilic solvent participation and/or nucleophilic solvation.

Interaction between macrocyclic nickel complexes and the nucleotides GMP, AMP and ApG

Reactions between the nucleotides GMP, AMP and ApG and the complexes Ni(tren), Ni(cyclam) and NiCR in aqueous solution have been monitored by (1)H, (15)N NMR and UV spectroscopy. The three nickel complexes display different properties in reactions with nucleotides. Ni(tren) which has a pseudo-octahedral coordination geometry was shown to bind to all three nucleotides. Ni(cyclam) and NiCR, both with four nitrogen atoms in a square planar arrangement are not able to bind to nucleotides efficiently because of steric hindrance. Oxidation of Ni(cyclam) by KHSO(5) to produce trivalent Ni(III)(cyclam) improves the coordination capacity, while oxidation of NiCR does not produce a similar effect. The nucleotides interact with trivalent nickel complexes to different extent. Ni(III)CR is seen to oxidize GMP gradually but does not affect AMP significantly. Ni(III)(cyclam), on the other hand, does not oxidize either GMP or AMP at the 1:1 concentration of oxidant used. This result is probably due to the lower redox potential of Ni(cyclam). ApG binds less efficiently to the Ni complexes but is easier oxidized than the mononucleotides.

Intrinsic (gas phase) thermodynamic stability of 2-adamantyl cation. Its bearing on the solvolysis rates of 2-adamantyl derivatives

The standard enthalpy of formation of gaseous 2-adamantyl chloride(2-Ad-Cl) was determined by calorimetric techniques. The standard Gibbs energy change for the chloride anion exchange between 1-adamantyl (1-Ad+) and 2-adamantyl (2-Ad+) cations in the gas phase was obtained by Fourier transform ion cyclotron resonance spectroscopy (FT ICR). Theoretical calculations at the G2(MP2) level were performed on these and other relevant species. This and data from the literature provided three highly consistent independent estimates of the relative stabilities of 2-Ad+ and 1-Ad+. This difference in gas-phase stability was compared to the differential structural effects on the rates of solvolysis of the corresponding chlorides and tosylates, and it was shown that the thermodynamic stability of the secondary cation is the leading factor determining the solvolytic reactivity of the precursors in the absence of solvent effects. Thus, under these conditions, the previously established linear free energy correlation between carbenium ion stability and solvolytic reactivity of bridgehead derivatives applies also to secondary derivatives.

Carborane-containing liquid crystals: synthesis and structural, conformational, thermal, and spectroscopic characterization of diheptyl and diheptynyl derivatives of p-carboranes

Molecular and electronic structures for four p-carborane derivatives were studied in the context of their liquid crystalline properties. Thus molecular and crystal structures of diheptyl and diheptynyl derivatives of 10- and 12-vertex bi-p-carboranes were determined by X-ray crystallography and compared to the results of ab initio calculations at the HF/6-31G level of theory. Experimentally observed significant positional disorder of one of the substituents in the 10-vertex derivatives, 2[2]a and 2[2]b, was related to conformational properties of the alkyl-carborane bond. Experimental and theoretical studies of the electronic structures were conducted for the four compounds using UV and NMR spectroscopies. The nature of the unique long wavelength absorption band at 232 nm in the diheptynyl derivative 2[2]b was explained using INDO/2//HF/6-31G analysis. The complete assignment of the (13)C signals was accomplished using a long-range coupling technique and was supported by the calculated (HF/6-31G) isotropic shielding tensors. Analysis of absorption spectra, NMR substituent effects, and trends in bond lengths shows generally strong cage-acetylene electronic interactions for the 10-vertex p-carborane, while the 12-vertex p-carborane remains largely electronically isolated. Ab initio calculations revealed that 12-vertex p-carborane has significantly larger electronic polarizability and quadrupole moments than the 10-vertex analogues, which are larger than those for bicyclo[2.2.2]octane compounds. All these results on packing, conformational, and electronic properties form the basis for the discussion of thermal behavior of the four carborane compounds, bicyclo[2.2.2]octane analogues, and some related compounds.

Characterization of the Ni(III) intermediate in the reaction of (1,4,8,11-tetraazacyclotetradecane)nickel(II) perchlorate with KHSO5: implications to the mechanism of oxidative DNA modification

We report the detection and characterization of the Ni(III) intermediates generated by reaction of (1,4,8,11-tetraazacyclotetradecane)nickel(II) perchlorate with KHSO5. Four Ni(III) intermediates can be trapped or detected through variation in Cl- or KHSO5 concentrations. Upon oxidation of [Ni(cyclam)]2+ by 2.5 equiv of KHSO5, deprotonation of the cyclam ligand generates two red Ni(III) species with lambda max = 530 nm and g perpendicular = 2.20 and g parallel = 2.02 or g perpendicular = 2.16 and g parallel = 2.01 for the axial 4-coordinate or 6-coordinate dichloride species, respectively. These forms decay to Ni(II) products via complex ligand oxidation mechanisms. The Ni(III) dichloride species can be reprotonated and subsequently binds to DNA via an outer-sphere interaction as evidenced by the inverted sign of the CD signal near 400 nm. Cumulatively, the results indicate that the Ni(III) center is coordinately saturated under excess chloride conditions but is still able to interact with DNA substrates. This suggests alternative mechanistic pathways for DNA modification by reaction of [Ni(cyclam)]2+ with KHSO5 and possibly other Ni(II) complexes as well.

Nickel and cobalt reagents promote selective oxidation of Z-DNA

The structural characteristics of Z-DNA were used to challenge the selectivity of guanine oxidation promoted by nickel and cobalt reagents. Base pairing and stacking within all helical structures studied previously had hindered access to guanine and limited its reaction. However, the Z-helix uniquely retains high exposure of guanine N7. This exposure was sufficient to direct oxidation specifically to a plasmid insert -(CG)(13)AATT(CG)(13)- that adopted a Z-conformation under native supercoiling. An alternative insert -(CG)(7)- retained its B-conformation and demonstrated the expected lack of reactivity. For a nickel salen complex made from a particularly bulky ligand, preferential reaction shifted to the junctions within the Z-DNA insert as is common for large reagents. Inactivation of the nickel reagents by high-salt concentrations prevented parallel investigations of Z-DNA, formed by oligonucleotides. However, the activity of Co(2+) was minimally affected by salt and consequently confirmed the high reactivity of 5'-p(CG)(4) in its Z-conformation. These reagents may now be applied to a broad array of targets, since their structural specificity remains predictable for both complex and helical assemblies of nucleic acids.

Selective association between a macrocyclic nickel complex and extrahelical guanine residues

Nickel-dependent recognition and oxidation of guanine have been linked in part through the paramagnetic effects of nickel on the NMR of model oligonucleotide duplexes. Direct interaction between nickel and guanine N7 had originally been postulated from correlations between the efficiency of guanine oxidation and the environment surrounding its N7 position. (1)H and (31)P NMR spectra of DNA containing a single, isolated extrahelical guanine are consistent with selective binding of nickel to the N7 of this unique base over a background of nonspecific association to the phosphate backbone. The presence of a macrocyclic complex or simple salt of nickel did not detectably alter the structure of the duplex or extrahelical residue. Accordingly, nickel appeared to bind the extrahelical guanine N7 within the major groove as indicated by paramagnetic effects on the proton signals of nucleotides on the 5' but not 3' side of the nickel binding site. Similar (1)H NMR analysis of DNA containing a dynamic equilibrium of extrahelical guanine residues also suggested that the nickel complex did not affect the native distribution of structures. Oxidation of these sites by a nickel-mediated pathway consequently reflected their solvent accessibility in a general and metal-independent manner. The close proximity of the extrahelical guanines produced a composite of paramagnetic effects on each adjacent nucleotide resulting from both direct and proximal coordination of nickel.