Heavy metal mutagenicity: insights from bioinorganic model chemistry

Mutagens in raw ewe milk in Orava region, northern Slovakia: metals

The aim of this work was to determine the concentrations of selected mutagenic elements (As, Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb, and Se) in raw ewe milk from undisturbed environment in Orava region, northern Slovakia. There are possible sources of some of the analyzed metals which may be distributed from the metallurgical plants located in the Ostrava region, Czech Republic, and Katowice, Poland. In total, forty milk samples were analyzed in June and August using an inductively coupled plasma optical emission spectrometry. The differences in elements concentrations between the seasonal periods were not significant except of iron (p < 0.0001). The concentrations of most of the metals in ewe milk were low and under the permissible or recommended limits. However, arsenic and selenium concentrations were elevated and could pose a risk of the mutagenic effect, particularly in children. The frequency of element occurrence in June was as follows: Se > Fe > As > Cu > Mn > Ni > Co > Pb > Cr > Cd, and in August: Se > Fe = As > Cu > Mn > Pb > Co > Ni > Cr > Cd. The correlation analysis revealed very strong positive correlation between Cu:Pb (p < 0.05), very strong negative correlation between Fe:Se (p < 0.05). The strong correlations were also found between other elements. The present study showed that milk produced in the relatively undisturbed environment might contain various mutagenic elements. The relationships between the elements might result in the additive or synergistic effects of elements and increase the risk of their mutagenic effects even in low concentrations. Therefore, attention must be paid to the monitoring of metals in the areas where food sources destined especially for child nutrition are produced.

Age-associated alterations in the somatic mutation and DNA methylation levels in plants

Somatic mutations of the nuclear and mitochondrial DNA and alterations in DNA methylation levels in mammals are well known to play important roles in ageing and various diseases, yet their specific contributions await further investigation. For plants, it has also been proposed that unrepaired DNA damage and DNA polymerase errors accumulate in plant cells and lead to increased somatic mutation rate and alterations in transcription, which eventually contribute to plant ageing. A number of studies also show that DNA methylation levels vary depending on the age of plant tissue and chronological age of a whole plant. Recent studies reveal that prolonged cultivation of plant cells in vitro induces single nucleotide substitutions and increases global DNA methylation level in a time-dependent fashion. Changes in DNA methylation are known to influence DNA repair and can lead to altered mutation rates, and, therefore, it is interesting to investigate both the genetic and epigenetic integrity in relationship to ageing in plants. This review will summarise and discuss the current studies investigating somatic DNA mutation and DNA methylation levels in relation to plant ageing and senescence. The analysis has shown that there still remains a lack of clarity concerning plant biological ageing and the role of the genetic and epigenetic instabilities in this process.

Simultaneous co-ordination of three cytosine ligands displaying different binding sites around the copper centres

The reaction of copper with 1,10-phenanthroline and cytosine forms a novel polymeric structure with two different cytosine binding modes coordinated to copper centers. Also the polymeric complex has mixed coordination geometry around the metal centers.

Heavy metals in canned tuna from Italian markets

Fish is a good source of nutrients for humans but can pose a risk to human health because of the possible presence of some xenobiotics such as heavy metals and persistent organic contaminants. Constant monitoring is needed to minimize health risks and ensure product quality and consumer safety. The aim of the present study was to use atomic absorption spectrometry to determine the concentrations of some heavy metals (Hg, Pb, and Cd) in tuna packaged in different kinds of packages (cans or glass) in various countries (Italy and elsewhere). Concentrations of Cd and Hg were within the limits set by European Commission Regulation (EC) No 1881/2006 and in many samples were below the detection limit. Pb concentrations exceeded European limits in 9.8% of the analyzed samples. These results are reassuring in terms of food safety but highlighted the need to constantly monitor the concentrations of heavy metals in fish products that could endanger consumer health.

Structure and bonding of Ag(I)-DNA base complexes and Ag(I)-adenine-cytosine mispairs: An ab Initio study

High level ab initio calculations have been carried out to characterize the structure, bonding and energetics of Ag(I)-DNA base complexes, including adenine or cytosine, as well as Ag(I)-adenine-cytosine mispairs. The interactions of the Ag cation in all binding sites of all adenine and cytosine tautomers have been considered. The calculations show that in gas phase the canonical form of cytosine is stabilized upon metalation, whereas the lowest energy structure of Ag-adenine correspond to a rare tautomer. Interestingly, the theoretical inspection of metalated adenine-cytosine mispair reveals that the most stable structures are formed from the canonical cytosine and adenine tautomers. The lowest energy structure is planar with adenine and cytosine hydrogen-bonded. Within few kcal/mol nonplanar, conformationally very flexible structures are found, in which the Ag(I) crosslinks an endocyclic nitrogen of adenine and the oxygen of cytosine. Metalated reverse-Wobble type of structures, on the contrary, are predicted much higher in energy.

Ca, Cd, Zn, and Their Ions Interacting with Cytosine: A Theoretical Study

Metal atoms play a major role in the chemical behavior of biological systems. In this work, known issues of the metal-base interactions, such as the stabilization of different tautomers of cytosine that could be incompatible with the DNA double helix, are researched using DFT methods. Ca-, Zn-, and Cd-cytosine in neutral and ionic forms were studied at the B3LYP/LANL2DZ level. Several neutral and ionic isomers were found within an interval of 10 kcal/mol of relative stability, with the most stable isomer in each group being a compound derived from the canonical isomer of cytosine, except for the dications where two iso-energetic isomers were found. Interatomic lengths from each metal atom to the nearest atoms in cytosine's ring were larger than 2 A, discouraging the possibility of a covalent interaction, as supported by additional evidence from molecular orbitals. The interaction between metal and cytosine, electrostatic in nature, is reinforced with the increase of the metal's nuclear charge. Additionally, the ionization energies of the metal-cytosine compounds exhibit a significant reduction (below 6 eV) compared with that of plain cytosine (8.7 eV), posing an interesting possibility with respect to the experimental determination of the photoelectron spectra of these compounds. Analyses of the energetics of the global reactions to form cationic species show that metal cations bind more strongly to neutral cytosine than to neutral metals. Metal dications form the most stable compounds with neutral cytosine, and the stabilities of these systems decrease as (Zn-cyt)2+ > (Cd-cyt)2+ > (Ca-cyt)2+. Aromaticities computed via the HOMA indexes also support the observation regarding the greater affinity of cytosine for metal cations.

Adenine tautomers: relative stabilities, ionization energies, and mismatch with cytosine

In this study, we have investigated 12 tautomers of the DNA base adenine at the BP86/TZ2P and BP86/QZ4P levels of density functional theory. The vertical and adiabatic ionization energies of all tautomers were determined as the difference in energy between the radical cation and the corresponding neutral system. Furthermore, an evaluation is made for the eigenvalue spectra calculated with the SAOP functional, which is shown to lead to substantial improvements for orbital energies compared to BP86. We have also explored the correlations between the Kohn-Sham orbitals of the different tautomers at the BP86/QZ4P and SAOP/QZ4P levels. Finally, we discuss implications of the existence of the tautomeric forms of adenine for the DNA replication.

Theoretical study of guanine–Cu and uracil–Cu (neutral, anionic, and cationic). Is it possible to carry out a photoelectron spectroscopy experiment?

The structure and bonding of guanine-Cu and uracil-Cu (neutral, anionic, and cationic) are discussed on the basis of the calculated structures and energies. The interaction of the metal atom with guanine and uracil has been analyzed using the B3LYP density-functional approach. The removal of one electron from the neutral complexes produces the stabilization of one of the isomers, while the addition of one electron leads to a system where the metal atom is weakly bounded to guanine or uracil, according to the metal-bases bond distance that is long (2.29-2.90). For guanine-Cu and uracil-Cu, the vertical ionization energy of the anion is close to the dissociation energy of one hydrogen atom from guanine-Cu or uracil-Cu. In these cases, it could be possible to produce the detachment of one electron from the anion and also the removal of one hydrogen atom. This is important since the photoelectron spectroscopy of atomic or mixed-atomic cluster anions has proven to be a very effective tool in the study of small systems. For the analysis of copper atoms with DNA bases such as guanine and uracil, it is expected that the photoelectron spectra of the anion-bases complexes strongly resemble the spectrum of Cu(-1), just shifted to higher electron binding energies due to the product stabilization. Hopefully, this information will be useful for the experimental groups.

Structural models for the interaction of Cd(II) with DNA: trans-[Cd(9-RGH-N7)2(H2O)4]2+

Reactions of Cd(NO(3))(2) with the model nucleobases 9-alkylguanine in water at neutral pH, give the compounds trans-[Cd(9-RGH-N7)(2)(H(2)O)(4)](NO(3))(2)(R=Me, Et), with the 9-alkylguanine ligands bound to the metal cation at the N(7) position. The X-ray structures of both compounds are reported. The six-coordinate Cd(II) complexes consist of a highly regular octahedral geometry in which the two 9-alkylguanine ligands are in a trans position to each other and approximately collinear with the metal cation. In addition, the networks of both compounds show interesting features. Thus, intramolecular H-bonds between O(6) and a coordinated water molecule are present, and self-association of guanines via H-bonding of N(3)-H...N(2) take place, leading to a 1D supramolecular polymeric ribbon. Density functional theory calculations have been applied to both compounds in order to study the stability of N(7) metalated guanine-guanine associations by comparing experimental and theoretical results. The potential relevance with regard to possible Cd(II)-DNA cross-links is briefly discussed.

Regulation of resistance to copper in Xanthomonas axonopodis pv. vesicatoria

Copper-resistant strains of Xanthomonas axonopodis pv. vesicatoria were previously shown to carry plasmid-borne copper resistance genes related to the cop and pco operons of Pseudomonas syringae and Escherichia coli, respectively. However, instead of the two-component (copRS and pcoRS) systems determining copper-inducible expression of the operons in P. syringae and E. coli, a novel open reading frame, copL, was found to be required for copper-inducible expression of the downstream multicopper oxidase copA in X. axonopodis. copL encodes a predicted protein product of 122 amino acids that is rich in histidine and cysteine residues, suggesting a possible direct interaction with copper. Deletions or frameshift mutations within copL, as well as an amino acid substitution generated at the putative start codon of copL, caused a loss of copper-inducible transcriptional activation of copA. A nonpolar insertion of a kanamycin resistance gene in copL resulted in copper sensitivity in the wild-type strain. However, repeated attempts to complement copL mutations in trans failed. Analysis of the genomic sequence databases shows that there are copL homologs upstream of copAB genes in X. axonopodis pv. citri, X. campestris pv. campestris, and Xylella fastidiosa. The cloned promoter area upstream of copA in X. axonopodis pv. vesicatoria did not function in Pseudomonas syringae or in E. coli, nor did the P. syringae cop promoter function in Xanthomonas. However, a transcriptional fusion of the Xanthomonas cop promoter with the Pseudomonas copABCDRS was able to confer resistance to copper in Xanthomonas, showing divergence in the mechanisms of regulation of the resistance to copper in phytopathogenic bacteria.

Complex Formation of Isocytosine Tautomers with PdII and PtII

Isocytosine (ICH) exists in solution as two major tautomers, the keto form with N1 carrying a proton (1a) and the keto form with N3 being protonated (1b). In water, 1a and 1b exist in equilibrium with almost equal amounts of both forms present. Reactions with a series of Pd(II) and Pt(II) am(m)ine species such as (dien)Pd(II), (dien)Pt(II), and trans-(NH(3))(2)Pt(II) reveal, however, a distinct preference of these metals for the N3 site, as determined by (1)H NMR spectroscopy. Individual species have been identified by the pD dependence of the ICH resonances. pK(a) values (calculated for H(2)O) for deprotonation of the individual tautomers complexes are 6.5 and 6.4 for the N3 linkage isomers of dienPd(II) and dienPt(II), respectively, as well as 6.2 and 6.0 for the N1 linkage isomers. The dimetalated species [(dienM)(2)(IC-N1,N3)](3+) (M = Pd(II) or Pt(II)) are insensitive over a wide range of pD. The crystal structure analysis of [(dien)Pd(ICH-N3)](NO(3))(2) is reported. Ab initio calculations have been performed for tautomer compounds of composition [(NH(3))(3)Pt(ICH)](2+), cis- and trans-[(NH(3))(2)PtCl(ICH)](+), as well as trans-[(NH(3))(2)Pt(ICH)(2)](2+). Without exception, N3 linkage isomers are more stable, in agreement with experimental findings. As to the reasons for this binding preference, an NBO (natural bond orbital) analysis for [(NH(3))(3)Pt(ICH-N3)](2+)strongly suggests that intramolecular hydrogen bonding between trans-positioned NH(3) ligands and the two exocyclic groups of the ICH is of prime importance. The calculations furthermore show a marked pyramidalization of the NH(2) group of ICH in the complex once the heterocyclic ligand forms a dihedral angle <90 degrees with the Pt coordination plane.

Integrated capillary fluorescence DNA biosensor

Covalent attachment of dsDNA molecules inside a glass capillary without the need for hybridization is described. It is shown that the glass capillary has a surface density of 2.5 x 10(13) molecules/cm(2) with specific binding capacity of 62.5%. The resulting substrate was used to develop a biosensor for determining fluorescent organic analytes and metal binding with DNA. The biosensor combines highly specific immobilization chemistry with a capillary-geometry flow cell arrangement. The results show that fluorescent dyes are retained in the dsDNA-modified surface and that exposure to concentrations of nickel and lead ions resulted in a recoverable, highly reproducible diminishment of the fluorescence intensity.

Minor groove site coordination of adenine by platinum group metal ions: effects on basicity, base pairing, and electronic structure

Dithioether- or diamine-tethered adenine derivatives react with Pt(II), Pd(II), and Rh(III) ions to give N3-coordinated complexes of the types [MCl(SSN)](+) (M = Pt or Pd), [RhCl(3)(SSN)], or [RhCl(3)(NNN)] (where SSN = 1-(N9-adenine)-3,6-dithia-heptane or 1-(N9-adenine)-4,7-dithia-octane; NNN = ethylenediamine-N,9-ethyladenine). Single-crystal X-ray analysis confirms the nature of the metal-nucleobase interaction and highlights a conserved intermolecular hydrogen-bonding motif for all the complexes, irrespective of the metal-ion geometry. Coordination significantly reduces the basicity of the adeninyl group, as indicated by a pK(a) value of -0.16 for [PtCl(N3-1-(N9-adenine)-3,6-dithia-heptane)]BF(4), compared to a pK(a) value of 4.2 for 9-ethyladenine. The site of proton binding, N1 or N7, could not be unambiguously assigned from the (1)H NMR data, because of the similar effect on the chemical shifts of the H2 and H8 protons. Density functional calculations at the BP-LACVP level suggest N1 as the site of protonation for this type of complex. This is in contrast to the N7-protonation reported for [Pt(dien)(N3-6,6',9-trimethyladenine)](2+), as reported elsewhere (Meiser et al., Chem.-Eur. J. 1997, 3, 388). However, further electronic structure calculations in the gas phase reveal that the preferred site for protonation for N3-bound complexes is conformationally dependent. N3 coordination was also found to reduce the extent of base pairing between adenine and thymine in dimethylsulfoxide for the self-complementary complex [PtCl(L3)](+) (L3 = 1-(N9-adenine)-3,6-dithia-9-(N1-thymine)nonane), compared to that for the uncomplexed ligand.

Loss of Hoogsteen pairing ability upon N1 adenine platinum binding

Chloroform- and Freon-soluble mixed thymine, adenine complexes trans-[Pt(MeNH(2))(2)(ChmT-N3)(ChmA-N1)]NO(3) (2) and trans-[Pt(MeNH(2))(2)(ChmT-N3)(TBDMS-ado-N1)]BF(4) (3) (ChmT = anion of 1-cyclohexylmethylthymine ChmTH, ChmA = 9-cyclohexylmethyladenine, TBDMS-ado = 2',3',5'-tri-tert-butyldimethylsilyladenosine) have been prepared and characterized to study their propensity to undergo Hoogsteen and/or reversed Hoogsteen pairing in solution with free ChmTH and free 3',5'-diacetyl-2'-deoxyuridine, respectively. No Hoogsteen or reversed Hoogsteen pairing between 2 and ChmT takes place in CDCl(3). In Freon, partial H bonding between N1 platinated TBDMS-ado and 3',5'-diacetyl-2'-deoxyuridine as well as its [3-(15)N] labeled analogue is unambiguously observed only below 150 K. Comparison of (1)J ((15)N-(1)H) coupling constants of 3',5'-diacetyl-2'-deoxyuridine involved in Hoogsteen pairing with free and N1 platinated adenine suggests that the interaction is inherently weaker in the case of platinated adenine. To better understand the complete absence of hydrogen bonding between the ChmA ligand in 2 and free ChmTH, ab initio calculations (gas phase, 0 K) have been carried out for Hoogsteen pairs involving adenine (A) and thymine (T), as well as simplified analogues of 2 and T, both in the presence and absence of counteranions. The data strongly suggest that reduction of the effective positive charge of the heavy metal ion Pt(2+) by counterions diminishes interaction energies. With regard to mixtures of 2 and ChmTH in chloroform, this implies that ion pair formation between the cation of 2 and NO(3)(-) may be responsible for the lack of any measurable Hoogsteen pairing in this solvent.

Silver(I) complexes with DNA and RNA studied by Fourier transform infrared spectroscopy and capillary electrophoresis

Ag(I) is a strong nucleic acids binder and forms several complexes with DNA such as types I, II, and III. However, the details of the binding mode of silver(I) in the Ag-polynucleotides remains unknown. Therefore, it was of interest to examine the binding of Ag(I) with calf-thymus DNA and bakers yeast RNA in aqueous solutions at pH 7.1-6.6 with constant concentration of DNA or RNA and various concentrations of Ag(I). Fourier transform infrared spectroscopy and capillary electrophoresis were used to analyze the Ag(I) binding mode, the binding constant, and the polynucleotides' structural changes in the Ag-DNA and Ag-RNA complexes. The spectroscopic results showed that in the type I complex formed with DNA, Ag(I) binds to guanine N7 at low cation concentration (r = 1/80) and adenine N7 site at higher concentrations (r = 1/20 to 1/10), but not to the backbone phosphate group. At r = 1/2, type II complexes formed with DNA in which Ag(I) binds to the G-C and A-T base pairs. On the other hand, Ag(I) binds to the guanine N7 atom but not to the adenine and the backbone phosphate group in the Ag-RNA complexes. Although a minor alteration of the sugar-phosphate geometry was observed, DNA remained in the B-family structure, whereas RNA retained its A conformation. Scatchard analysis following capillary electrophoresis showed two binding sites for the Ag-DNA complexes with K(1) = 8.3 x 10(4) M(-1) for the guanine and K(2) = 1.5 x 10(4) M(-1) for the adenine bases. On the other hand, Ag-RNA adducts showed one binding site with K = 1.5 x 10(5) M(-1) for the guanine bases.