Lead(II)-binding properties of the 5'-monophosphates of adenosine (AMP2-), inosine (IMP2-), and guanosine (GMP2-) in aqueous solution. Evidence for nucleobase-lead(II) interactions

Toward the Ultimate Limit of Analyte Detection, in Graphene-Based Field-Effect Transistors

The ultimate sensitivity of field-effect-transistor (FET)-based devices for ionic species detection is of great interest, given that such devices are capable of monitoring single-electron-level modulations. It is shown here, from both theoretical and experimental perspectives, that for such ultimate limits to be approached the thermodynamic as well as kinetic characteristics of the (FET surface)-(linker)-(ion-receptor) ensemble must be considered. The sensitivity was probed in terms of optimal packing of the ensemble, through a minimal charge state/capacitance point of view and atomic force microscopy. Through the fine-tuning of the linker and receptor interaction with the sensing surface, a record limit of detection as well as specificity in the femtomolar range, orders of magnitude better than previously obtained and in excellent accord with prediction, was observed.

Liquid crystal based sensor for antimony ions detection using poly-adenine oligonucleotides

Antimony is highly toxic and a key water pollutant, which needs to be monitored closely. To date, however, most analytical methods for antimony detection are quite limited because they are complicated, expensive, and not suitable for real-time monitoring of antimony. In this study, a label-free and rapid method for antimony ions (Sb3+) detection is developed based on liquid crystals and a 10-mer poly-adenine oligonucleotide as a specific recognition probe for the first time. The working principle is based on the binding of the oligonucleotide to Sb3+, which weakens the interaction between the oligonucleotide and cationic surfactants. As a result, the event induces a planar-to-homeotropic orientational change of liquid crystals and a bright-to-dark optical change under crossed polars. This liquid crystal-based optical sensor exhibits a rapid response to Sb3+ in 10 s, a detection range between 20 nM and 5 μM, and a detection limit at 6.7 nM calculated from 10-mins assay time. It also shows good selectivity against other metal ions including Ag+, Cd2+, Cu2+, Fe3+, K+, Mg2+, Mn2+, Na+, Pb2+, and Zn2+. Moreover, this system can be used to detect Sb3+ in aqueous solutions with different pH or ionic strengths. This simple, fast, and low-cost liquid crystal-based sensing approach with high sensitivity and selectivity has a high potential for detecting Sb3+ in natural environments and industrial wastewater.

Review of recent progress on DNA-based biosensors for Pb2+ detection

Lead (Pb) is a highly toxic heavy metal of great environmental and health concerns, and interestingly Pb²⁺ has played important roles in nucleic acids chemistry. Since 2000, using DNA for selective detection of Pb²⁺ has become a rapidly growing topic in the analytical community. Pb²⁺ can serve as the most active cofactor for RNA-cleaving DNAzymes including the GR5, 17E and 8-17 DNAzymes. Recently, Pb²⁺ was found to promote a porphyrin metalation DNAzyme named T30695. In addition, Pb²⁺ can tightly bind to various G-quadruplex sequences inducing their unique folding and binding to other molecules such as dyes and hemin. The peroxidase-like activity of G-quadruplex/hemin complexes was also used for Pb²⁺ sensing. In this article, these Pb²⁺ recognition mechanisms are reviewed from fundamental chemistry to the design of fluorescent, colorimetric, and electrochemical biosensors. In addition, various signal amplification mechanisms such as rolling circle amplification, hairpin hybridization chain reaction and nuclease-assisted methods are coupled to these sensing methods to drive up sensitivity. We mainly cover recent examples published since 2015. In the end, some practical aspects of these sensors and future research opportunities are discussed.

A review of heavy metal cation binding to deoxyribonucleic acids for the creation of chemical sensors

Various human activities lead to the pollution of ground, drinking, and wastewater with toxic metals. It is well known that metal ions preferentially bind to DNA phosphate backbones or DNA nucleobases, or both. Foreman et al. (Environ Toxicol Chem 30(8):1810-1818, 2011) reported the use of a DNA-dye based assay suitable for use as a toxicity test for potable environmental water. They compared the results of this test with the responses of live-organism bioassays. The DNA-based demonstrated that the loss of SYBR Green I fluorescence dye bound to calf thymus DNA was proportional to the toxicity of the water sample. However, this report raised questions about the mechanism that formed the basis of this quasi-quantitatively test. In this review, we identify the unique and preferred DNA-binding sites of individual metals. We show how highly sensitive and selective DNA-based sensors can be designed that contain multiple binding sites for 21 heavy metal cations that bind to DNA and change its structure, consistent with the release of the DNA-bound dye.

Metal ion complexes of nucleoside phosphorothioates reflecting the ambivalent properties of lead(ii)

The lead(ii)-lone pair leads to ambivalency: hemidirected (distorted, non-spherical) coordination spheres result from electronegative O-coordination and holodirected (symmetric, spherical) ones from less electronegative S-coordination.

Biosynthesis of micro- and nanocrystals of Pb (II), Hg (II) and Cd (II) sulfides in four Candida species: a comparative study of in vivo and in vitro approaches

Nature produces biominerals (biogenic minerals) that are synthesized as complex structures, in terms of their physicochemical properties. These biominerals are composed of minerals and biological macromolecules. They are produced by living organisms and are usually formed through a combination of chemical, biochemical and biophysical processes. Microorganisms like Candida in the presence of heavy metals can biomineralize those metals to form microcrystals (MCs) and nanocrystals (NCs). In this work, MCs and NCs of PbS, HgS or HgCl₂ as well as CdS are synthesized both in vitro (gels) and in vivo by four Candida species. Our in vivo results show that, in the presence of Pb²⁺, Candida cells are able to replicate and form extracellular PbS MCs, whereas in the presence of Hg²⁺ and Cd²⁺, they did synthesize intercellular MCs from HgS or HgCl₂ and CdS NCs respectively. The MCs and NCs biologically obtained in Candida were compared with those PbS, HgS and CdS crystals synthetically obtained in vitro through the gel method (grown either in agarose or in sodium metasilicate hydrogels). This is, to our knowledge, the first time that the biosynthesis of the various MCs and NCs (presented in several species of Candida) has been reported. This biosynthesis is differentially regulated in each of these pathogens, which allows them to adapt and survive in different physiological and environmental habitats.

Electrospray ionization-collision-induced dissociation-tandem mass spectrometry study of lead complexes with deprotonated nucleobases

The complexes between the lead cation and deprotonated nucleobases (and deprotonated nucleosides) are studied by using electrospray ionization-collision-induced dissociation-tandem mass spectrometry. It has been found that the deprotonated N9 atom is not the site of lead cation attachment. In ions [A - H + Pb]⁺ and [C - H + Pb]⁺, the lead cation is coordinated by the adenine N1 atom and cytosine  N3 atom and interaction between the lead cation and deprotonated amino groups seems very likely. Deprotonated thymine shows a higher affinity toward lead cation than deprotonated uracil. In the lead-nucleoside complexes lead cation interacts with a sugar moiety.

Investigating the Complexation of the Pb(2+)/Bi(3+) Pair with Dipicolinate Cyclen Ligands

The complexation properties toward Pb(2+) and Bi(3+) of the macrocyclic ligands 6,6'-((1,4,7,10-tetraazacyclododecane-1,7-diyl)bis(methylene))dipicolinic acid (H2do2pa) and 6,6'-((4,10-dimethyl-1,4,7,10-tetraazacyclododecane-1,7-diyl)bis(methylene))dipicolinic acid (H2Me-do2pa) have been investigated. A new three-step synthesis of H2do2pa following the bisaminal methodology has also been developed. The X-ray structures of [Pb(Me-do2pa)]·6H2O and [Bi(Me-do2pa)](NO3)·H2O show that the two metal ions are eight-coordinated by the ligand. The two complexes exist as the racemic Δ(δδδδ)/Λ(λλλλ) mixture both in the solid state and in solution, as indicated by NMR and DFT studies. The stability constants of the lead(II) and bismuth(III) complexes of the two ligands were determined in 0.5 M KCl using potentiometric and spectrophotometric techniques. The stability constants determined for the complexes of Pb(2+) are relatively high (log KML = 16.44 and 18.44 for H2do2pa and H2Me-do2pa, respectively) and exceptionally high for the complexes of Bi(3+) (log KML = 32.0 and 34.2 for H2do2pa and H2Me-do2pa, respectively). The [Pb(Me-do2pa)] complex presents rather fast formation and very good kinetic inertness toward transchelation. Additionally, the [Bi(Me-do2pa)](+) complex was found to present a remarkably fast complexation rate (full complexation in ∼2 min at pH 5.0, acetate buffer) and a very good kinetic inertness with respect to metal ion dissociation (half-life of 23.9 min in 1 M HCl), showing promise for potential applications in α-radioimmunotherapy.

Structure of the Pb²⁺-deprotonated dGMP complex in the gas phase: a combined MS-MS/IRMPD spectroscopy/ion mobility study

The structure of the Pb(2+)-deprotonated 2'-deoxyguanosine-5'-monophosphate (dGMP) complex, generated in the gas phase by electrospray ionization, was examined by combining tandem mass spectrometry, mid-infrared multiple-photon dissociation (IRMPD) spectroscopy and ion mobility. In the gas phase, the main binding site of Pb(2+) onto deprotonated dGMP is the deprotonated phosphate group, but the question is whether an additional stabilization of the metallic complex can occur via participation of the carbonyl group of guanine. Such macrochelates indeed correspond to the most stable structures according to theoretical calculations. A multiplexed experimental approach was used to characterize the gas-phase conformation of the metallic complex and hence determine the binding mode of Pb(2+) with [dGMP](-). MS/MS analysis, observation of characteristic bands by IRMPD spectroscopy, and measurement of the ion mobility collision cross section suggest that gaseous [Pb(dGMP)-H](+) complexes adopt a macrochelate folded structure, which consequently differs strongly from the zwitterionic forms postulated in solution from potentiometric studies.

Intrinsic acid-base properties of a hexa-2'-deoxynucleoside pentaphosphate, d(ApGpGpCpCpT): neighboring effects and isomeric equilibria

The intrinsic acid-base properties of the hexa-2'-deoxynucleoside pentaphosphate, d(ApGpGpCpCpT) [=(A1∙G2∙G3∙C4∙C5∙T6)=(HNPP)⁵⁻] have been determined by ¹H NMR shift experiments. The pKa values of the individual sites of the adenosine (A), guanosine (G), cytidine (C), and thymidine (T) residues were measured in water under single-strand conditions (i.e., 10% D₂O, 47 °C, I=0.1 M, NaClO₄). These results quantify the release of H⁺ from the two (N7)H⁺ (G∙G), the two (N3)H⁺ (C∙C), and the (N1)H⁺ (A) units, as well as from the two (N1)H (G∙G) and the (N3)H (T) sites. Based on measurements with 2'-deoxynucleosides at 25 °C and 47 °C, they were transferred to pKa values valid in water at 25 °C and I=0.1 M. Intramolecular stacks between the nucleobases A1 and G2 as well as most likely also between G2 and G3 are formed. For HNPP three pKa clusters occur, that is those encompassing the pKa values of 2.44, 2.97, and 3.71 of G2(N7)H⁺, G3(N7)H⁺, and A1(N1)H⁺, respectively, with overlapping buffer regions. The tautomer populations were estimated, giving for the release of a single proton from five-fold protonated H₅(HNPP)(±) , the tautomers (G2)N7, (G3)N7, and (A1)N1 with formation degrees of about 74, 22, and 4%, respectively. Tautomer distributions reveal pathways for proton-donating as well as for proton-accepting reactions both being expected to be fast and to occur practically at no "cost". The eight pKa values for H₅(HNPP)(±) are compared with data for nucleosides and nucleotides, revealing that the nucleoside residues are in part affected very differently by their neighbors. In addition, the intrinsic acidity constants for the RNA derivative r(A1∙G2∙G3∙C4∙C5∙U6), where U=uridine, were calculated. Finally, the effect of metal ions on the pKa values of nucleobase sites is briefly discussed because in this way deprotonation reactions can easily be shifted to the physiological pH range.

Extent of intramolecular π-stacks in aqueous solution in mixed-ligand copper(II) complexes formed by heteroaromatic amines and several 2-aminopurine derivatives of the antivirally active nucleotide analog 9-[2-(phosphonomethoxy)ethyl]adenine (PMEA)

The acidity constants of twofold protonated, antivirally active, acyclic nucleoside phosphonates (ANPs), H(2)(PE)(±), where PE(2-)=9-[2-(phosphonomethoxy)ethyl]adenine (PMEA(2-)), 2-amino-9-[2-(phosphonomethoxy)ethyl]purine (PME2AP(2-)), 2,6-diamino-9-[2-(phosphonomethoxy)ethyl]purine (PMEDAP(2-)), or 2-amino-6-(dimethylamino)-9-[2-(phosphonomethoxy)ethyl]purine (PME(2A6DMAP)(2-)), as well as the stability constants of the corresponding ternary Cu(Arm)(H;PE)(+) and Cu(Arm)(PE) complexes, where Arm=2,2'-bipyridine (bpy) or 1,10-phenanthroline (phen), are compared. The constants for the systems containing PE(2-)=PMEDAP(2-) and PME(2A6DMAP)(2-) have been determined now by potentiometric pH titrations in aqueous solution at I=0.1M (NaNO(3)) and 25°; the corresponding results for the other ANPs were taken from our earlier work. The basicity of the terminal phosphonate group is very similar for all the ANP(2-) species, whereas the addition of a second amino substituent at the pyrimidine ring of the purine moiety significantly increases the basicity of the N(1) site. Detailed stability-constant comparisons reveal that, in the monoprotonated ternary Cu(Arm)(H;PE)(+) complexes, the proton is at the phosphonate group, that the ether O-atom of the -CH(2)-O-CH(2)-P(O)(2)(-)(OH) residue participates, next to the P(O)(2)(-)(OH) group, to some extent in Cu(Arm)(2+) coordination, and that π-π stacking between the aromatic rings of Cu(Arm)(2+) and the purine moiety is rather important, especially for the H·PMEDAP(-) and H·PME(2A6DMAP)(-) ligands. There are indications that ternary Cu(Arm)(2+)-bridged stacks as well as unbridged (binary) stacks are formed. The ternary Cu(Arm)(PE) complexes are considerably more stable than the corresponding Cu(Arm)(R-PO(3)) species, where R-PO(3)(2-) represents a phosph(on)ate ligand with a group R that is unable to participate in any kind of intramolecular interaction within the complexes. The observed stability enhancements are mainly attributed to intramolecular-stack formation in the Cu(Arm)(PE) complexes and also, to a smaller extent, to the formation of five-membered chelates involving the ether O-atom present in the -CH(2)-O-CH(2)-PO(3)(2-) residue of the PE(2-) species. The quantitative analysis of the intramolecular equilibria involving three structurally different Cu(Arm)(PE) isomers shows that, e.g., ca. 1.5% of the Cu(phen)(PMEDAP) system exist with Cu(phen)(2+) solely coordinated to the phosphonate group, 4.5% as a five-membered chelate involving the ether O-atom of the -CH(2)-O-CH(2)-PO(3)(2-) residue, and 94% with an intramolecular π-π stack between the purine moiety of PMEDAP(2-) and the aromatic rings of phen. Comparison of the various formation degrees of the species formed reveals that, in the Cu(phen)(PE) complexes, intramolecular-stack formation is more pronounced than in the Cu(bpy)(PE) species. Within a given Cu(Arm)(2+) series the stacking intensity increases in the order PME2AP(2-) <PMEA(2-) <PMEDAP(2-) <PME(2A6DMAP)(2-). One could speculate that the reduced stacking intensity of PME2AP(2-), together with a different H-bonding pattern, could well lead to a different orientation of the 2-aminopurine moiety (compared to the adenine residue) in the active site of nucleic acid polymerases and thus be responsible for the reduced antiviral activity of PME2AP compared with that of PMEA and the other ANPs containing a 6-amino substituent.

Characterization of metal ion-nucleic acid interactions in solution

Metal ions are inextricably involved with nucleic acids due to their polyanionic nature. In order to understand the structure and function of RNAs and DNAs, one needs to have detailed pictures on the structural, thermodynamic, and kinetic properties of metal ion interactions with these biomacromolecules. In this review we first compile the physicochemical properties of metal ions found and used in combination with nucleic acids in solution. The main part then describes the various methods developed over the past decades to investigate metal ion binding by nucleic acids in solution. This includes for example hydrolytic and radical cleavage experiments, mutational approaches, as well as kinetic isotope effects. In addition, spectroscopic techniques like EPR, lanthanide(III) luminescence, IR and Raman as well as various NMR methods are summarized. Aside from gaining knowledge about the thermodynamic properties on the metal ion-nucleic acid interactions, especially NMR can be used to extract information on the kinetics of ligand exchange rates of the metal ions applied. The final section deals with the influence of anions, buffers, and the solvent permittivity on the binding equilibria between metal ions and nucleic acids. Little is known on some of these aspects, but it is clear that these three factors have a large influence on the interaction between metal ions and nucleic acids.

Direct evidence for tautomerization of the uracil moiety within the Pb2+/uridine-5'-monophosphate complex: a combined tandem mass spectrometry and IRMPD study

The structure of the [Pb(UMP)-H](+) (UMP = uridine-5'-monophosphate) complex was studied in the gas phase by combining electrospray ionization (ESI), tandem mass spectrometry, and mid-infrared multiple photon dissociation (IRMPD) spectroscopy. The results obtained show that Pb(2+) ions interact not only with the deprotonated phosphate group but also with a carbonyl group of the nucleobase moiety by folding of the mononucleotide, resulting in macrochelates that are not likely to be present in solution. Comparison between the IRMPD and DFT-computed spectra suggests that the ESI-generated complex likely corresponds to a mixture of several structures, and establishes the enolic tautomers as the most abundant species for the [Pb(UMP)-H](+) ion, while the very weak IRMPD signal observed at ∼1763 cm(-1) points to a minor population of oxo forms. Our data also suggest that losing the nucleobase residue under CID conditions does not necessarily mean a lack of interaction between the metal and the nucleobase moiety, as commonly reported in the literature for large oligonucleotides.

A stability concept for metal ion coordination to single-stranded nucleic acids and affinities of individual sites

The three-dimensional architecture and function of nucleic acids strongly depend on the presence of metal ions, among other factors. Given the negative charge of the phosphate-sugar backbone, positively charged species, mostly metal ions, are necessary for compensation. However, these ions also allow and induce folding of complicated RNA structures. Furthermore, metal ions bind to specific sites, stabilizing local motifs and positioning themselves correctly to aid (or even enable) a catalytic mechanism, as, for example, in ribozymes. Many nucleic acids thereby exhibit large differences in folding and activity depending not only on the concentration but also on the kind of metal ion involved. As a consequence, understanding the role of metal ions in nucleic acids requires knowing not only the exact positioning and coordination sphere of each specifically bound metal ion but also its intrinsic site affinity. However, the quantification of metal ion affinities toward certain sites in a single-stranded (though folded) nucleic acid is a demanding task, and few experimental data exist. In this Account, we present a new tool for estimating the binding affinity of a given metal ion, based on its ligating sites within the nucleic acid. To this end, we have summarized the available affinity constants of Mg(2+), Ca(2+), Mn(2+), Cu(2+), Zn(2+), Cd(2+), and Pb(2+) for binding to nucleobase residues, as well as to mono- and dinucleotides. We have also estimated for these ions the stability constants for coordinating the phosphodiester bridge. In this way, stability increments for each ligand site are obtained, and a clear selectivity of the ligating atoms, as well as their discrimination by different metal ions, can thus be recognized. On the basis of these data, we propose a concept that allows one to estimate the intrinsic stabilities of nucleic acid-binding pockets for these metal ions. For example, the presence of a phosphate group has a much larger influence on the overall affinity of Mg(2+), Ca(2+), or Mn(2+) compared with, for example, that of Cd(2+) or Zn(2+). In the case of Cd(2+) and Zn(2+), the guanine N7 position is the strongest intrinsic binding site. By adding up the individual increments like building blocks, one derives an estimate not only for the overall stability of a given coordination sphere but also for the most stable complex if an excess of ligating atoms is available in a binding pocket saturating the coordination sphere of the metal ion. Hence, this empirical concept of adding up known intrinsic stabilities, like building blocks, to an estimated overall stability will help in understanding the accelerating or inhibiting effects of different metal ions in ribozymes and DNAzymes.

Selective chelation of Cd(II) and Pb(II) versus Ca(II) and Zn(II) by using octadentate ligands containing pyridinecarboxylate and pyridyl pendants

Herein we report the coordination properties toward Cd(II), Pb(II), Ca(II), and Zn(II) of a new octadentate ligand (py-H(2)bcpe) based on a ethane-1,2-diamine unit containing two picolinate and two pyridyl pendants, which is structurally derived from the previous reported ligand bcpe. Potentiometric studies have been carried out to determine the protonation constants of the ligand and the stability constants of the complexes with these cations. The introduction of the pyridyl pendants in bcpe provokes a very important increase of the logK(ML) values obtained for the Pb(II) and Cd(II) complexes, while this effect is less important in the case of the Zn(II) analogue. As a result, py-bcpe shows a certain selectivity for Cd(II) and Pb(II) over Zn(II) while keeping good Pb(II)/Ca(II) and Cd(II)/Ca(II) selectivities, and the new receptor py-bcpe can be considered as a new structural framework for the design of novel Cd(II) and Pb(II) extracting agents. Likewise, the stabilities of the Cd(II) and Pb(II) complexes are higher than those of the corresponding EDTA analogues. The X-ray crystal structure of [Zn(py-bcpe)] shows hexadentate binding of the ligand to the metal ion, the coordination polyhedron being best described as a severely distorted octahedron. However, the X-ray crystal structure of the Pb(II) analogue shows octadentate binding of the ligand to the metal ion. A detailed investigation of the structure in aqueous solution of the complexes by using nuclear magnetic resonance (NMR) techniques and density functional theory (DFT) calculations (B3LYP) shows that while in the Zn(II) complex the metal ion is six-coordinated, in the Pb(II) and Ca(II) analogues the metal ions are eight-coordinated. For the Cd(II) complex, our results suggest that in solution the complex exists as a mixture of seven- and eight-coordinated species. DFT calculations performed both in the gas phase and in aqueous solution have been also used to investigate the role of the Pb(II) lone pair in the structure of the [Pb(py-bcpe)] complex.

Eight-coordinate Zn(II), Cd(II), and Pb(II) complexes based on a 1,7-diaza-12-crown-4 platform endowed with a remarkable selectivity over Ca(II)

The thermodynamic stability of the Pb(II), Cd(II), Zn(II), and Ca(II) complexes with the dianionic macrocyclic ligand N,N'-bis[(6-carboxy-2-pyridyl)methyl]-1,7-diaza-12-crown-4 (H(2)bp12c4) has been investigated by pH-potentiometric titrations at 25 degrees C in 0.1 M KNO(3). The stability constants vary in the following order: Cd(II) > Zn(II) approximately Pb(II) > Ca(II). As a consequence, H(2)bp12c4 present an important Cd(II)/Ca(II) selectivity, as well as a certain selectivity for Cd(II) over Zn(II). To rationalize these results, a detailed investigation of the structure of these complexes has been carried out both in solid state and in aqueous solution. Furthermore, the [M(bp12c4)] complexes (M = Ca, Zn, Cd, or Pb) were characterized by means of density functional theory (DFT) calculations (B3LYP model) to obtain information on their solution structures and to investigate the possible stereochemical activity of the Pb(II) lone pair. Our results show that in all cases the metal ion is octacoordinated by the ligand, a situation that is particularly rare for Zn(II) complexes. The coordination polyhedra observed in the solid state for the [M(bp12c4)] complexes (M = Zn, Cd, or Ca) is closely related to the conformation adopted by the ligand in the corresponding complex: The Zn(II) complex adopts a Delta(lambdalambdalambdalambda) conformation in the solid state, which results in a square antiprismatic coordination, while the Delta(deltadeltadeltadelta) conformation observed for the Cd(II) and Ca(II) analogues yields inverted-square antiprismatic geometries. The X-ray crystal structure of the Pb(II) analogue shows that the metal ion is directly bound to the eight donor atoms of the ligand, but the bond distances of the metal coordination environment indicate an asymmetrical coordination of the cation by the ligand, which is attributed to the stereochemical activity of the Pb(II) lone pair. In aqueous solution the Ca(II), Zn(II), and Cd(II) complexes show rigid C(2) symmetries, while the Pb(II) analogue presents a more flexible structure.

Metal-ion-coordinating properties of the dinucleotide 2'-deoxyguanylyl(5'-->3')-2'-deoxy-5'-guanylate (d(pGpG)3-): isomeric equilibria including macrochelated complexes relevant for nucleic acids

The interaction between divalent metal ions and nucleic acids is well known, yet knowledge about the strength of binding of labile metal ions at the various sites is very scarce. We have therefore studied the stabilities of complexes formed between the nucleic acid model d(pGpG) and the essential metal ions Mg2+ and Zn2+ as well as with the generally toxic ions Cd2+ and Pb2+ by potentiometric pH titrations; all four ions are of relevance in ribozyme chemistry. A comparison of the present results with earlier data obtained for M(pUpU)- complexes allows the conclusion that phosphate-bound Mg2+ and Cd2+ form macrochelates by interaction with N7, whereas the also phosphate-coordinated Pb2+ forms a 10-membered chelate with the neighboring phosphate diester bridge. Zn2+ forms both types of chelates with formation degrees of about 91% and 2.4% for Zn[d(pGpG)]cl/N7 and Zn[d(pGpG)]-cl/PO, respectively; the open form with Zn2+ bound only to the terminal phosphate group, Zn[d(pGpG)]-op, amounts to about 6.8 %. The various intramolecular equilibria have also been quantified for the other metal ions. Zn2+, Cu2+, and Cd2+ also form macrochelates in the monoprotonated M[H;d(pGpG)] species (the proton being at the terminal phosphate group), that is, the metal ion at N7 interacts to some extent with the P(O)2(OH)- group. Thus, this study demonstrates that the coordinating properties of the various metal ions toward a pGpG unit in a nucleic acid differ: Mg2+, Zn2+, and Cd2+ have a significant tendency to bridge the distance between N7 and the phosphate group of a (d)GMP unit, although to various extents, whereas Pb2+ (and possibly Ca2+) prefer a pure phosphate coordination.

Acid-base and metal-ion binding properties of the RNA dinucleotide uridylyl-(5'-->3')-[5']uridylate (pUpU3-)

It is well known that Mg2+ and other divalent metal ions bind to the phosphate groups of nucleic acids. Subtle differences in the coordination properties of these metal ions to RNA, especially to ribozymes, determine whether they either promote or inhibit catalytic activity. The ability of metal ions to coordinate simultaneously with two neighboring phosphate groups is important for ribozyme structure and activity. However, such an interaction has not yet been quantified. Here, we have performed potentiometric pH titrations to determine the acidity constants of the protonated dinucleotide H2(pUpU)-, as well as the binding properties of pUpU3- towards Mg2+, Mn2+, Cd2+, Zn2+, and Pb2+. Whereas Mg2+, Mn2+, and Cd2+ only bind to the more basic 5'-terminal phosphate group, Pb2+, and to a certain extent also Zn2+, show a remarkably enhanced stability of the [M(pUpU)]- complex. This can be attributed to the formation of a macrochelate by bridging the two phosphate groups within this dinucleotide by these metal ions. Such a macrochelate is also possible in an oligonucleotide, because the basic structural units are the same, despite the difference in charge. The formation degrees of the macrochelated species of [Zn(pUpU)]- and [Pb(pUpU)]- amount to around 25 and 90 %, respectively. These findings are important in the context of ribozyme and DNAzyme catalysis, and explain, for example, why the leadzyme could be selected in the first place, and why this artificial ribozyme is inhibited by other divalent metal ions, such as Mg2+.

Analysis of platinum adducts with DNA nucleotides and nucleosides by capillary electrophoresis coupled to ESI-MS: indications of guanosine 5'-monophosphate O6-N7 chelation

DNA is the ultimate target of platinum-based anticancer therapy. Since the N7 of guanine is known to be the major binding site of cisplatin and its analogues, adduct formation with model nucleotides, especially 2'-deoxyguanosine 5'-monophosphate (dGMP), has been studied in detail. During the last few years a coupled capillary eletrophoresis/electrospray-ionization mass spectrometry (CE/ESI-MS) method has been advantageously used in order to separate and identify platinum adducts with nucleotides in submillimolar concentrations in aqueous solutions. Beside the bisadduct, [Pt(NH(3))(2)(dNMP)(2)](2-) (NMP=2'-deoxynucleoside 5'-monophosphate), and the well-known monochloro and monohydroxo adducts, [Pt(NH(3))(2)Cl(dNMP)](-) and [Pt(NH(3))(2)(dNMP)OH](-), respectively, a third kind of monoadduct species with a composition of [Pt(NH(3))(2)(dNMP)](-) can be separated by CE and detected through the m/z values measured with ESI-MS. Different experimental setups indicate the existence of an O(6)-N7 chelate, whereas the formation of N7-alphaPO(4) macrochelates or dinuclear species is unlikely. Additionally, offline MS experiments with 2'-deoxyguanosine (dG) and stabilization of the controversially discussed O(6)-N7 chelate by oxidation with hydrogen peroxide support the assumption of the existence of O(6)-N7 chelation.

A quantitative appraisal of the ambivalent metal ion binding properties of cytidine in aqueous solution and an estimation of the anti–syn energy barrier of cytidine derivatives

The recently defined log K (M)(M)(L) versus pK(H)(H)(L) straight-line plots for L = pyridine-type (PyN) and ortho-aminopyridine-type (oPyN) ligands now allow the evaluation in a quantitative manner of the stability of the 1:1 complexes formed between cytidine (Cyd) and Ca(2+), Mg(2+), Mn(2+), Co(2+), Ni(2+), Cu(2+), Zn(2+) or Cd(2+) (M(2+)); the corresponding stability constants, K(M)(M)(Cyd) including the acidity constant, K(H)(H)(Cyd) for the deprotonation of the (N3)H(+) site had been determined previously under exactly the same conditions as the mentioned plots. Since the stabilities of the M(PyN)(2+) and M(oPyN)(2+) complexes of Ca(2+) and Mg(2+) are practically identical, it is concluded that complex formation occurs in an outer-sphere manner, and this is in accord with the fact that in the p K(a) range 3-7 metal ion binding is independent of K(H)(H)(Pyn) or K(H)(H)(oPyN). Ca(Cyd)(2+) and Mg(Cyd)(2+) are more stable than the corresponding (outer-sphere) M(PyN)(2+) complexes and this means that the C2 carbonyl group of Cyd must participate, next to N3 which is most likely outer-sphere, in metal ion binding, leading thus to chelates; these have formation degrees of about 50% and 35%, respectively. Co(Cyd)(2+) and Ni(Cyd)(2+) show no increased stability based on the log K(M)(M)(oPyN) versus pK(H)(H)(oPyN) hence, the (C2)O group does not participate in metal ion binding, but the inner-sphere coordination to N3 is strongly inhibited by the (C4)NH(2) group. In the M(Cyd)(2+) complexes of Mn(2+), Cu(2+), Zn(2+) and Cd(2+), this inhibiting effect on M(2+) binding at N3 is partially compensated by participation of the (C2)O group in complex formation and the corresponding chelates have formation degrees between about 30% (Zn(2+)) and 83% (Cu(2+)). The different structures of the mentioned chelates are discussed in relation to available crystal structure analyses. (1). There is evidence (crystal structure studies: Cu(2+), Zn(2+), Cd(2+)) that four-membered rings form, i.e. there is a strong M(2+) bond to N3 and a weak one to (C2)O. (2). By hydrogen bond formation to (C2)O of a metal ion-bound water molecule, six-membered rings, so-called semichelates, may form. (3). For Ca(2+) and Mg(2+), and possibly Mn(2+), and their Cyd complexes, six-membered chelates are also likely with (C2)O being inner-sphere (crystal structure) and N3 outer-sphere. (4). Finally, for these metal ions also complexes with a sole outer-sphere interaction may occur. All these types of chelates are expected to be in equilibrium with each other in solution, but, depending on the metal ion, either the one or the other form will dominate. Clearly, the cytidine residue is an ambivalent binding site which adjusts well to the requirements of the metal ion to be bound and this observation is of relevance for single-stranded nucleic acids and their interactions with metal ions. In addition, the anti- syn energy barrier has been estimated as being in the order of 6-7.5 kJ/mol for cytidine derivatives in aqueous solution at 25 degrees C.

Acid-base and metal ion binding properties of guanylyl(3'-->5')guanosine (GpG-) and 2'-deoxyguanylyl(3'-->5')-2'-deoxyguanosine [d(GpG)-] in aqueous solution

The acidity constants of guanylyl(3'-->5')guanosine (GpG(-)) and 2'-deoxyguanylyl(3'-->5')-2'-deoxyguanosine [d(GpG)(-)] for the deprotonation of their (N1)H sites were measured by potentiometric pH titrations in aqueous solution (25 degrees C; I = 0.1 M, NaNO(3)). The same method was used for the determination of the stability constants of the 1:1 complexes formed between Mg(2+), Ni(2+), or Cd(2+) (= M(2+)) and (GG-H)(2-), and in the case of Mg(2+) also of (GG-2H)(3-), where GG(-) = GpG(-) or d(GpG)(-). The stability constants of the M(GG)(+) complexes were estimated. The acidity constants of the H(dGuo)(+) and dGuo species (dGuo = 2'-deoxyguanosine) and the stability constants of the corresponding M(dGuo)(2+) and M(dGuo-H)(+) complexes were also measured. Comparison of these and related data allows the conclusion that N7 of the 5'G unit in GG(-) is somewhat more basic than the one in the 3'G moiety; the same holds for the (N1)(-) sites. On the basis of comparisons with the stability constants measured for the dGuo complexes, it is concluded that M(2+) binding of the GG dinucleoside monophosphates occurs predominantly in a mono-site fashion, meaning that macrochelate formation is not very pronounced. Indeed, it was a surprise to find that the stabilities of the complexes of dGuo or (dGuo-H)(-) and the corresponding ones derived from GG(-) are so similar. Consequently, it is suggested that in the M(GG)(+) and M(GG-H) complexes the metal ion is mainly located at N7 of the 5'G unit since this is the more basic site allowing also an outer-sphere interaction with the C6 carbonyl oxygen and because this coordination mode is also favorable for an electrostatic interaction with the negatively charged phosphodiester bridge. It is further suggested that Mg(2+) binding (which is rather weak compared to that of Ni(2+) and Cd(2+)) occurs mainly in an outer-sphere mode, and on the basis of the so-called Stability Ruler it is concluded that the binding properties of Zn(2+) to the GG species are similar to those of Ni(2+) and Cd(2+).

Holo- and hemidirected lead(II) in the polymeric [Pb(4)(mu-3,4-TDTA)2(H2O)2]*4H2O complex. N,N,N',N'-tetraacetate ligands derived from o-phenylenediamines as sequestering agents for lead(II)

The coordinating ability of the ligands 3,4-toluenediamine-N,N,N',N'-tetraacetate (3,4-TDTA), o-phenylenediamine-N,N,N',N'-tetraacetate (o-PhDTA), and 4-chloro-1,2-phenylenediamine-N,N,N',N'-tetraacetate (4-Cl-o-PhDTA) (H4L acids) toward lead(II) is studied by potentiometry (25 degrees C, I = 0.5 mol x dm(-3) in NaClO4), UV-vis spectrophotometry, and 207Pb NMR spectrometry. The stability constants of the complex species formed were determined. X-ray diffraction structural analysis of the complex [Pb4(mu-3,4-TDTA)4(H2O)2]*4H2O (1) revealed that 1 has a 2-D structure. The layers are built up by the polymerization of centrosymmetric [Pb4L2(H2O)2] tetranuclear units. The neutral layers have the aromatic rings of the ligands pointing to the periphery, whereas the metallic ions are located in the central part of the layers. In compound 1, two types of six-coordinate lead(II) environments are produced. The Pb(1) is coordinated to two nitrogen atoms and four carboxylate oxygens from the ligand, whereas Pb(2) has an O6 trigonally distorted octahedral surrounding. The lead(II) ion is surrounded by five carboxylate oxygens and a water molecule. The carboxylate oxygens belong to four different ligands that are also joined to four other Pb(1) ions. The selective uptake of lead(II) was analyzed by means of chemical speciation diagrams as well as the so-called conditional or effective formation constants K(Pb)eff. The results indicate that, in competition with other ligands that are strong complexing agents for lead(II), our ligands are better sequestering agents in acidic media.