Structural basis for stabilization of Z-DNA by cobalt hexaammine and magnesium cations

In the equilibrium between B-DNA and Z-DNA in poly(dC-dG), the [Co(NH3)6]3+ ion stabilizes the Z form 4 orders of magnitude more effectively than the Mg2+ ion. The structural basis of this difference is revealed in Z-DNA crystal structures of d(CpGpCpGpCpG) stabilized by either Na+/Mg2+ or Na+/Mg2+ plus [Co(NH3)6]3+. The crystals diffract X-rays to high resolution, and the structures were refined at 1.25 A. The [Co(NH3)6]3+ ion forms five hydrogen bonds onto the surface of Z-DNA, bonding to a guanine O6 and N7 as well as to a phosphate group in the ZII conformation. The Mg2+ ion binds through its hydration shell with up to three hydrogen bonds to guanine N7 and O6. Higher charge, specific fitting of more hydrogen bonds, and a more stable complex all contribute to the great effectiveness of [Co(NH3)6]3+ in stabilizing Z-DNA.     

Structural analysis of Cu(II) ligation to the 5′-GMP nucleotide by pulse EPR spectroscopy

Simple copper salts are known to denature poly d(GC). On the other hand, copper complexes of substituted 1,4,7,10,13-pentaazacyclohexadecane-14,16-dione are able to convert the right-handed B form of the same DNA sequence to the corresponding left-handed Z form. A research program was started in order to understand why Cu(II) as an aquated ion melts DNA and induces the conformational change to Z-DNA in the form of an azamacrocyclic complex. In this paper, we present a continuous wave and pulse electron paramagnetic resonance study of the mononucleotide model system Cu(II)–guanosine 5′-monophosphate . Pulse EPR methods like electron–nuclear double resonance and hyperfine sublevel correlation spectroscopy provide unique information about the electronic and geometric structure of this model system through an elaborate mapping of the hyperfine and nuclear quadrupole interactions between the unpaired electron of the Cu(II) ion and the magnetic nuclei of the nucleotide ligand. It was found that the Cu(II) ion is directly bound to N7 of guanosine 5′-monophosphate and indirectly bound via a water of hydration to a phosphate group. This set of experiments opens the way to more detailed structural characterization of specifically bound metal ions in a variety of nucleic acids of biological interest, in particular to understand the role of the metal–(poly)nucleotide interaction. Arthur Schweiger died on 4 January 2006.     

Enhancement of aromatic amino acid-nucleic acid base stacking interaction by metal coordination to base: fluorescence study on a tryptophan-Pt(II)-guanine ternary complex

In order to investigate the effect of the Pt(II) ion on the stacking interaction between tryptophan and a guanine base, the quenching of Trp fluorescence was monitored for some systems in the absence and presence of the metal ion, and the association constants were obtained by the analysis of Eadie-Hofstee plots. All spectral data suggested that the stacking interaction is enhanced by the Pt(II) coordination to the guanine N7 atom. The result indicates the importance of the metal ion as a bookmark in the specific recognition of a nucleic acid base by an aromatic amino acid residue.     

Bis-bidentate bridging ligands containing two N,O-chelating pyrazolyl-phenolate units; double helical complexes with Co(II), Cu(II) and Zn(II)

Two ligands have been prepared in which N,O-bidentate chelating pyrazolyl-phenolate units, based on 3-(2-hydroxyphenyl)pyrazole, are connected via methylene linkages to aromatic (1,4-phenylene or 3,3′-biphenylene) spacers. In each case the two N,O-donor units are too far apart to chelate to a single metal ion. Complexes of both ligands with Co(II), Cu(II) and Zn(II) were prepared and structurally characterised; in all cases the complexes are dinuclear double helicates M₂L₂, with each four-coordinate metal ion bound by a chelating unit from each of the two ligands in the complex. For Co(II) and Zn(II) the two M(NO) planes at each metal are close to perpendicular, indicative of a geometry which may be described as approximately distorted tetrahedral; for the Cu(II) complexes the angle between the two Cu(NO) planes is less, indicative of a distortion towards a more planar coordination geometry.     

A laser Raman spectroscopic study of the interaction of calf-thymus DNA with Cu(II) and Pb(II) ions: metal ion binding and DNA conformational changes.

The interaction of calf-thymus DNA with Cu(II) and Pb(II) ions has been investigated in H2O and D2O solutions at physiological pH, using laser Raman spectroscopy. The results confirm the destabilizing effect of Cu2+ ions, which are shown to bind strongly to the guanine and cytidine bases, perturbing the A-T base pairs and disrupting the double-helical structure of DNA, whose conformation is markedly altered by these interactions. Earlier claims that Pb2+ ions destabilize DNA are not supported by the present study. These ions are found to interact only weakly with the nucleic bases, binding to the N7 position of the guanine bases and also interacting with the A-T pairs. Both types of ions are found to interact with the charged phosphate groups of DNA, although these sites are preferred over the nucleic bases by Pb2+ ions.     

The metal site of stellacyanin: EXAFS studies of the Cu(II), Cu(I), Ni(II) and Co(II) derivatives

Extended X-ray absorption fine structure (EXAFS) studies of Cu(II) (oxidized), Cu(I) (reduced), Ni(II) and Co(II) stellacyanin from Rhus vernicifera are reported. For Cu(II) stellacyanin, the coordination by three close ligands, viz. 2 N and 1 S, with the presence of smaller shells pointing to imidazole coordination, indicates similarities with the coordination in other so-called type 1 or 'blue'-copper proteins. Upon reduction, slightly longer ligand distances and an additional sulphur ligand are found. Ni(II) and Co(II) stellacyanin resemble Cu(I) and Cu(II) stellacyanin, respectively, in ligand distances, but have a tendency for three rather than two N (or O) ligands in the first shell. The results are compared with the three-dimensional model derived from 1H-NMR relaxation measurements for Co(II) stellacyanin, and are consistent with the proposal that apart from the three close ligands found in all blue-copper proteins, a sulphur from a disulphide bridge and the amide oxygen from an asparagine residue come to within coordinating distance of the metal in stellacyanin.     

Tetrahedral 1:1 adducts of guanine with cobalt(II), copper(II) and zinc(II) chlorides

Adducts of the M(guH)Cl₂ type were prepared by refluxing 2:1 molar mixtures of guanine (guH) and MCl₂ (M = Co, Cu, Zn) in ethanol-triethyl orthoformate for 2–3 days. Characterization studies suggest that all three new complexes involve distorted tetrahedral configurations. A linear chainlike polymeric structural type with a single-bridged (-MguH-)_n backbone and two terminal chloro ligands per metal ion (MN₂Cl₂ chromophore) is proposed for these compounds, in view of their poor solubility in organic media, their stoichiometry in conjunction with their tetrahedral symmetry, and the reported crystal structures of 9-methyladenine analogs (M = Co, Zn), which are polymeric with single bridges of the adenine derivative between adjacent metal ions. Bidentate bridging guH coordinates exclusively through ring nitrogens, and is most probably N(7), N(9)-bonded. The possibility of use of exocyclic potential ligand sites of guH (CO oxygen or NH₂ nitrogen) in coordination is ruled out by the infrared evidence [1].     

Metal--glutathione interaction in aqueous solution. Nickel(II), cobalt(II) and copper(II) complexes with oxidized glutathione.

The interaction of copper(II), nickel(II) and cobalt(II) ions with oxidized glutathione in aqueous solutions have been examined by spectroscopic methods. Cu(II) is the only ion which interacts with disulphide bridge and forms dimeric species containing the Cu(II)-S-S-Cu(II) unit. Ni(II) and Co(II) bind mainly with the terminal NH2 and COO- groups of glutamic acid, and the complexes formed are of nearly octahedral symmetry. At high pH, in the Co(II)-GSSG solution Co(II) is oxidized to Co(III) with the concomitant reduction of GSSG to GSH. Considerable differences were observed between the oxidized and reduced form of glutathione in the coordination ability towards metal ions.     

Transitions of poly(dI-dC), poly(dI-methyl5dC) and poly(dI-bromo5dC) among and within the B-, Z-, A- and X-DNA families of conformations.

It is shown, using circular dichroism spectroscopy, that poly(dI-dC) is capable to isomerize into both Z-DNA and A-DNA in concentrated NaCl + NiCl2 and trifluoroethanol solutions, respectively. This polynucleotide also undergoes a cooperative, two-state transition in ethanol into a structure which most probably is a canonical B-DNA. This implies that the conformation of poly(dI-dC) is unusual in low-salt aqueous solution. The canonical B-DNA is also adopted by poly(dI-methyl5dC) in trifluoroethanol while this polynucleotide adopts Z-DNA not only in NaCl + NiCl2 but also in the presence of MgCl2. Poly(dI-methyl5dC) partially adopts X-DNA in concentrated CsF and mainly ethanolic solutions. Poly(dI-bromo5dC) isomerizes into Z-DNA not only in concentrated NaCl even in the absence of NiCl2 but also in concentrated MgCl2. This polynucleotide transforms between two distinct variants of Z-DNA in ethanol or trifluoroethanol solutions.     

Copper (II) interaction with proline-containing tetrapeptides

The Cu(II) interactions with four tetrapeptides: Ala-Ala-Ala-Ala, Ala-Ala-Ala-Pro, Ala-Ala-Pro-Ala, and Pro-Ala-Ala-Ala were studied by the absorption, circular dichroism, and electron paramagnetic resonance spectra. The results clearly show that proline residue is a specific structural factor in the formed complexes and, on the other hand, it is a break point in the metal ion coordination to the consecutive peptide bond nitrogens. The only position of proline residue ina peptide sequence that makes proline nitrogen available for the metal ion coordination is the N-terminal position. But even in this case (i.e., in the Cu(II) Pro-Ala-Ala-Ala system) proline plays a critical role in the creation of the specific structures in the complex formed in solution.     

Reaction of cis-diamminedichloroplatinum (II) and DNA in B or Z conformation

The nature of the adducts and the conformational changes produced in poly(dG-m5dC).poly(dG-m5dC) by cis-diamminedichloroplatinum(II) (cisPt) have been studied. In the reaction of cisPt and B-DNA, the main adduct is bidentate and arises from an intrastrand cross-link between two guanine residues separated by a cytosine. This was deduced from the study of the compounds by t.l.c. after acid hydrolysis of the polymer. The platinated polymer is not digested by S1 nuclease. The antibodies to Z-DNA bind to the platinated polymer with a smaller affinity than to poly (dG-br5dC).poly(dG-br5dC). The c.d. spectrum differs from that of poly(dG-br5dC).poly(dG-br5dC) or poly(dG-m5dC).poly-(dG-m5dC) in Z conformation. It is concluded that the bidentate adduct induces a conformational change from the B form towards a distorted Z form. In the reaction of cisPt and Z-DNA, a monodentate adduct is formed. This adduct stabilizes the Z conformation as shown by c.d. and binding to the anti-Z-DNA antibodies. At room temperature, the second function of the drug can still react with small ligands such as NH4HCO3. By heating, the second function reacts with a guanine residue. A bidentate adduct is formed as in the reaction of cisPt and B-DNA and it induces a transition from the Z form to the distorted Z form.     

Supramolecular structures of metronidazole and its copper(II), cobalt(II) and zinc(II) coordination compounds

In this work we present the synthesis and structural and spectroscopic characterization of Cu(II), Co(II) and Zn(II) coordination compounds with the antibiotic metronidazole ([double bond]emni). Coordination to metal ions is through its imidazolic nitrogen, while the hydroxyethyl and nitro groups act as supramolecular synthons. [Co(emni)(2)Br(2)], and [Zn(emni)(2)X(2)] (X(-)=Cl, Br) stabilize zig-zag chains, and a 2D supramolecular structure is formed by inter-chain contacts through inter-molecular hydrogen-bonding. Pleated sheet or layers are formed by [Co(emni)(2)Cl(2)] and [Cu(emni)(2)Cl(H(2)O)](2)Cl(2), respectively. The dinuclear Cu(II) compound [Cu(emni)mu(O(2)CMe)(2)](2) gives a one-dimensional zig-zag arrangement. The contribution of metal ions in metronidazole coordination compounds is shown in the stabilization of the different aggregate structures.     

Interaction of the antitumor antibiotic mitomycin C with Z-DNA

Mitomycin C (MC), an antitumor antibiotic, alkylated Z-DNAs such as poly(dG-dC)/Co(NH3)3+(6), poly(dG-m5dC)/Mg2+ and brominated poly(dG-dC) upon reductive activation. Computer-generated energy-minimized molecular models indicated that monofunctional alkylation of Z-DNA at the N2-position of guanine by MC did not distort Z-DNA geometry, but bifunctional alkylation, leading to interstrand crosslinks between two N2-positions of guanine was sterically unfavorable. The above three Z-DNA's were exposed both to monofunctionally and bifunctionally activated MC in separate experiments and the resulting covalent MC-polynucleotide complexes were examined for conformation and for covalent MC-adducts, by circular dichroism (CD) spectroscopy and HPLC analysis of nuclease digests, respectively. Monofunctionally activated MC alkylated all three polynucleotides in their Z-forms, resulting in the same monofunctional N2-guanine adduct as that known to be formed with B-DNA. Upon bifunctional activation of MC, poly(dG-dC/Co(NH3)3+(6) reverted to the B-form and bifunctional (cross-link) adducts were detected, identical again with those formed with B-DNA. Poly(dG-m5dC), however, remained in the Z-form after the alkylation and only a monofunctional adduct could be detected. It was concluded that Z-DNA is subject to monofunctional alkylation by MC but cannot be cross-linked. The latter process occurs only when the Z-DNA is labile enough [as is in the case of poly(dG-dC)] to have some B-form in equilibrium at the site of the first formed monolinked adduct; the cross-linking then occurs at such local B-sites, pulling the overall B in equilibrium Z equilibrium irreversibly to the left. These results are in accord with the predictions from the above modeling. The irreversible "lock" by the MC cross-link on B-DNA may be exploited for probing Z-DNA intermediacy in various DNA functions.     

Interactions of 1,12-diamino-4,9-dioxadodecane (OSpm) and Cu(II) ions with pyrimidine and purine nucleotides: adenosine-5'-monophosphate (AMP) and cytidine-5'-monophosphate (CMP)

The interactions of Cu(II) ions with adenosine-5'-monophosphate (AMP), cytidine-5'-monophosphate (CMP) and 1,12-diamino-4,9-dioxadodecane (OSpm) were studied. A potentiometric method was applied to determine the composition and stability constants of complexes formed, while the mode of interactions was analysed by spectral methods (ultraviolet and visible spectroscopy (UV-Vis), electron paramagnetic resonance (EPR), (13)C NMR, (31)P NMR). In metal-free systems, molecular complexes nucleotide-polyamine (NMP)H(x)(OSpm) were formed. The endocyclic nitrogen atoms of the purine ring N(1), N(7), the nitrogen atom of the pyrimidine ring N(3), the oxygen atoms of the phosphate group of the nucleotide and the protonated nitrogen atoms of the polyamine were the reaction centres. The mode of interaction of the metal ion with OSpm and the nucleotides (AMP or CMP) in the coordination compounds was established. In the system Cu(II)/OSpm the dinuclear complex Cu(2)(OSpm) forms, while in the ternary systems Cu(II)/nucleotide/OSpm the species type MH(x)LL' and MLL' appear. In the MH(x)LL' type species, the main centres of copper (II) ion binding in the nucleotide are the phosphate groups. The protonated amino groups of OSpm are involved in non-covalent interaction with the nitrogen atoms N(1), N(7) or N(3) of the purine or pyrimidine ring, whereas at higher pH, deprotonated nitrogen atoms of polyamine are engaged in metallation in MLL' species.     

Bromination stabilizes poly(dG-dC) in the Z-DNA form under low-salt conditions

Using circular dichroism studies, Pohl & Jovin (1972) [Pohl, F.M., & Jovin, T.M. (1972) J. Mol. Biol. 67, 375-396] demonstrated that poly(dG-dC) undergoes a salt-dependent conformational change characterized by a spectral inversion. The low-salt form corresponds to the right-handed B form of DNA and the high-salt form to the left-handed Z-DNA helix. Modification of poly(dG-dC) by adding bromine atoms to the C8 position of guanine and the C5 position of cytosine residues stabilized this polymer in the Z-DNA form under low-salt conditions. The guanine residues were found to be twice as reactive as the cytosine residues. With a modification of 38% Br8G and 18% Br5C, the polymers formed a stable Z-DNA helix under physiological conditions. The bromination produced spectroscopic features very similar to poly(dG-dC) in 4 M NaCl. However, bromination did not freeze the Z structure as was shown by ethidium bromide intercalation studies. Addition of the dye favored an intercalated B-DNA form. The conversion of B- to Z-DNA leads to profound conformational changes which were also seen by a reduced insensitivity to various exo- and endonucleases. Comparative studies showed that the brominated polymers have a high affinity to nitrocellulose filters. In 1 M NaCl, there was virtually no binding of B-DNA, but a substantial binding of Z-DNA was found even at rather low levels of bromination.(ABSTRACT TRUNCATED AT 250 WORDS)     

An FTIR Spectroscopic Study of Calf-thymus DNA Complexation with Al(III) and Ga(III) Cations

Abstract

The interaction of calf-thymus DNA with trivalent Al and Ga cations, in aqueous solution at pH =6–7 with cation/DNA(P) (P=phosphate) molar ratios (r) 1/80, 1/40, 1/20, 1/10, 1/4 and 1/2 was characterized by Fourier Transform infrared (FTIR) difference spectroscopy.

Spectroscopic results show the formation of several types of cation-DNA complexes. At low metal ion concentration (r=l/80, 1/40), both cations bind mainly to the backbone PO₂ group and the guanine N-7 site of the G-C base pairs (chelation). Evidence for cation chelate formation comes from major shifting and intensity increase of the phosphate antisymmetric stretch at 1222 cm-¹ and the mainly guanine band at 1717 cm¹. The perturbations of A-T base pairs occur at high cation concentration with major helix destabilization. Evidence for cation binding to A-T bases comes from major spectral changes of the bands at 1663 and 1609 cm-¹ related mainly to the thymine and adenine in-plane vibrations. A major reduction of the B-DNA structure occurs in favor of A-DNA upon trivalent cation coordination.     

A switch‐off fluorescence probe towards Pb(II) and cu(II) ions based on a calix[4]pyrrole bearing amino‐quinoline group

A new fluorescence receptor calix[4]pyrrole‐N‐(quinoline‐8‐yl) acetamide (CAMQ) containing a pyrrolic ring connected via the meso‐position was synthesized, purified and characterized by elemental analysis, NMR and mass spectroscopy. This compound was examined for its fluorescence properties towards different metal ions e.g. Ag(I), Hg(II), Co(II), Ca(II), Ni(II), Zn(II), Cr(II), Ba(II), Fe(II), Cu(II), Pb(II)and Mg(II) ions by spectrophotometry and spectrofluorometry. It was concluded that the compound (CAMQ) possessed significantly enhanced selectivity for Pb(II) and Cu(II) ions in dimethyl sulfoxide (DMSO) even at very low concentrations (1 μM). It exhibit ‘turn‐on’ fluorescence when exposed to Pb(II) and Cu(II) and did so in preference to other metal ions. The binding constants, stoichiometry and quantum yields have been determined. The quenching mechanism was assessed using the Stern–Volmer equation and was also discussed.     

Crystal structures of A-DNA duplexes

All crystal structures of A-DNA duplexes exhibit a typical crystal packing, with the termini of one molecule abutting the shallow grooves of symmetry related neighbors, while all other forms (B, Z, and RNA) tend to form infinitely stacked helices. The A-DNA arrangement leads to the formation of shallow groove base multiples that have implications for the structure of DNA in compacted states. The characteristic packing leaves big solvent channels, which can be sometimes occupied by B-DNA duplexes. Comparisons of the structures of the same oligomer crystallizing in two different space groups and of different sequences crystallizing in the same space group show that the lattice forces dominate the A-DNA conformation in the crystals, complicating the effort to elucidate the influence of the base sequence on the structures. Nevertheless, in both alternating and nonalternating fragments some sequence effects can still be uncovered. Furthermore, several studies have started to define the minimal sequence changes or chemical modifications that can interconvert the oligomers between different double-helical conformers (A-, B-, and Z-form). Overall, it is seen that the rigid nucleotide principle applies to the oligomeric fragments. Besides the structures of the naked DNAs, their interactions with water, polyamines, and metal ions have attracted considerable attention. There are conserved patterns in the hydration, involving both the grooves and the backbone, which are different from those of B-DNA or Z-DNA. Overall, A-DNA seems to be more economically hydrated than B-DNA, particularly around the sugar-phosphate backbone. Spermine was found to be able to bind exclusively to either of the grooves or to the phosphate groups of the backbone, or exhibit a mixed binding mode. The located metal cations prefer binding to guanine bases and phosphate groups. The only mispairs investigated in A-DNA are the wobble pairs, yielding structural insight into their effects on helix stabilities and hydration. G · T wobble pairs have been determined in various sequence contexts, where they differentially affect the conformations and stableness of the duplexes. The structure of a G · ^m5C base pair, which surprisingly also adopted the wobble conformation, suggests that a similar geometry may transiently exist for G · C pairs. These results from the crystalline state will be compared to the solution state and discussed in relation to their relevance in biology. © 1997 John Wiley & Sons, Inc. Biopoly 44: 45–63, 1997     

Covalent modification of guanine bases in double-stranded DNA. The 1.2-A Z-DNA structure of d(CGCGCG) in the presence of CuCl2

We have solved the single crystal structure to 1.2-A resolution of the Z-DNA sequence d(CGCGCG) soaked with copper(II) chloride. This structure allows us to elucidate the structural properties of copper in a model that mimics a physiologically relevant environment. A copper(II) cation was observed to form a covalent coordinate bond to N-7 of each guanine base along the hexamer duplex. The occurrence of copper bound at each site was dependent on the exposure of the bases and the packing of the hexamers in the crystal. The copper at the highest occupied site was observed to form a regular octahedral complex, with four water ligands in the equatorial plane and a fifth water along with N-7 of the purine base at the axial positions. All other copper complexes appear to be variations of this structure. By using the octahedral complex as the prototype for copper(II) binding to guanine bases in the Z-DNA crystal, model structures were built showing that duplex B-DNA can accommodate octahedral copper(II) complexes at the guanine bases as well as copper complexes bridged at adjacent guanine residues by a reactive dioxygen species. The increased susceptibility to oxidative DNA cleavage induced by copper(II) ions in solution of the bases located 5' to one or more adjacent guanine residues can thus be explained in terms of the cation and DNA structures described by these models.