Complex Formation of Nickel(II) with Sugar Residues, Nucleobases, Phosphates, Nucleotides, and Nucleic Acids

Sigel, Roland K. O.; Sigel, Helmut

doi:10.1002/9780470028131.ch4

Cited by 9 publications

(15 citation statements)

References 156 publications

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“…Macrochelate formation of guanosine 5'-phosphates involving N7 is wellknown [7][8][9] and therefore also expected for the dinucleotide d(pGpG) 3- (Figure 4) Figure 5). 15 Comparison of the experimentally obtained stability constants for the four systems studied (Table 4, column 2; defined in analogy to eq 1) with the values calculated for the M(R-PO 3 ) complexes Figure 6 exist.…”

Section: Studies Of a Dinucleotide Allowing Macrochelate Formationmentioning

confidence: 84%

“…Since the possibility of intranucleotide macrochelate formation of the phosphate-coordinated M 2+ with guanine-N7 (possibly involving (C6)O in an outersphere manner) 9 is identical in both complexes, the additional stability increase by 0.3 log unit of M[d(pGpG)] -means that a further interaction must occur with the neighboring nucleotide. Self-stacking of guanine residues is wellknown (e.g., To summarize, the stability enhancements of column 4 in Table 6 hold for a single intranucleotide…”

Section: Studies Of a Dinucleotide Allowing Macrochelate Formationmentioning

confidence: 99%

“…This group has no basic but rather acidic properties and may release a proton with p K a ≈ 17 . (iii) Of a more subtle nature, binding of Mg 2+ to N7 does not occur significantly inner-sphere but rather outer-sphere, that is, a coordinated H 2 O forms a hydrogen bond to N7. , A more realistic coordination pattern is shown in Figure B,C. ,, Nevertheless, Szent-Györgyi’s structure had a tremendous influence because it triggered the interest of biochemists and coordination chemists in the metal ion binding properties of nucleotides , and thus indirectly in nucleic acids.…”

Section: Introductionmentioning

confidence: 99%

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A Stability Concept for Metal Ion Coordination to Single-Stranded Nucleic Acids and Affinities of Individual Sites

2010

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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 adds 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 Mg2+, Ca2+, Mn2+, Cu2+, Zn2+, Cd2+, and Pb2+ 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 dear 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 Mg2+, Ca2+, or Mn2+ compared with, for example, that of Cd2+ or Zn2+. In the case of Cd2+ and Zn2+, 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. CONSPECTUSThe three-dimensional architecture and function of nucleic acids strongly depends, among other factors, on the presence of metal ions. Most importantly, metal ions, needed to compensate the negative charge of the phosphate-sugar backbone, allow and induce folding of complicated RNA structures. On the other hand, metal ions bind to spec...

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Section: Studies Of a Dinucleotide Allowing Macrochelate Formationmentioning

confidence: 84%

Section: Studies Of a Dinucleotide Allowing Macrochelate Formationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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A Stability Concept for Metal Ion Coordination to Single-Stranded Nucleic Acids and Affinities of Individual Sites

2010

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“…For multidentate ligands of carbohydrates and glycoproteins in cell walls that carry the Si–wall matrix anions and, as primary binding sites (PBSs), carboxylates or amino residues, the interactions between divalent metal ions (M) and the Si‐modified walls must be reflected in stability enhancement. (Sigel & Sigel, ; Al‐Sogair et al ., ; Knobloch et al ., ). The coordination sites of the metal ion to the walls should increase for the formation of an [Si‐PBS]M complex (the charge of PBSs remaining undefined).…”

Section: Discussionmentioning

confidence: 99%

Inhibition of cadmium ion uptake in rice (Oryza sativa) cells by a wall‐bound form of silicon

Liu

et al. 2013

New Phytologist

174

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SummaryThe stresses acting on plants that are alleviated by silicon (Si) range from biotic to abiotic stresses, such as heavy metal toxicity. However, the mechanism of stress alleviation by Si at the single-cell level is poorly understood.We cultivated suspended rice (Oryza sativa) cells and protoplasts and investigated them using a combination of plant nutritional and physical techniques including inductively coupled plasma mass spectrometry (ICP-MS), the scanning ion-selective electrode technique (SIET) and X-ray photoelectron spectroscopy (XPS).We found that most Si accumulated in the cell walls in a wall-bound organosilicon compound. Total cadmium (Cd) concentrations in protoplasts from Si-accumulating (+Si) cells were significantly reduced at moderate concentrations of Cd in the culture medium compared with those from Si-limiting (ÀSi) cells. In situ measurement of cellular fluxes of the cadmium ion (Cd 2+ ) in suspension cells and root cells of rice exposed to Cd 2+ and/or Si treatments showed that +Si cells significantly inhibited the net Cd 2+ influx, compared with that in ÀSi cells. Furthermore, a net negative charge (charge density) within the +Si cell walls could be neutralized by an increase in the Cd 2+ concentration in the measuring solution. A mechanism of co-deposition of Si and Cd in the cell walls via a [Si-wall matrix]Cd cocomplexation may explain the inhibition of Cd ion uptake, and may offer a plausible explanation for the in vivo detoxification of Cd in rice.

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“…Nickel homeostasis is of primary importance for many organisms and especially for pathogenic and ureolytic bacteria, which use this metal ion as enzymatic cofactor for the catalysis of redox reactions and Lewis acid-like functions, with important medical, agricultural and biotechnological implications1. The human pathogen H. pylori is a paradigmatic example, since its survival in the stomach relies on the catalytic activity of the two nickel-dependent metalloenzymes urease and hydrogenase, respectively involved in acid acclimation and energy metabolism of the bacterium23.…”

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confidence: 99%

Comprehensive mapping of the Helicobacter pylori NikR regulon provides new insights in bacterial nickel responses

Vannini

Pinatel

Costantini

et al. 2017

Sci Rep

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Nickel homeostasis is important for pathogenic and ureolytic bacteria, which use this metal ion as enzymatic cofactor. For example, in the human pathogen Helicobacter pylori an optimal balance between nickel uptake and incorporation in metallo-enzymes is fundamental for colonization of the host. Nickel is also used as cofactor to modulate DNA binding of the NikR regulator, which controls transcription of genes involved in nickel trafficking or infection in many bacteria. Accordingly, there is much interest in a systematic characterization of NikR regulation. Herein we use H. pylori as a model to integrate RNA-seq and ChIP-seq data demonstrating that NikR not only regulates metal-ion transporters but also virulence factors, non-coding RNAs, as well as toxin-antitoxin systems in response to nickel stimulation. Altogether, results provide new insights into the pathobiology of H. pylori and contribute to understand the responses to nickel in other bacteria.

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Complex Formation of Nickel(II) with Sugar Residues, Nucleobases, Phosphates, Nucleotides, and Nucleic Acids

Cited by 9 publications

References 156 publications

A Stability Concept for Metal Ion Coordination to Single-Stranded Nucleic Acids and Affinities of Individual Sites

A Stability Concept for Metal Ion Coordination to Single-Stranded Nucleic Acids and Affinities of Individual Sites

Inhibition of cadmium ion uptake in rice (Oryza sativa) cells by a wall‐bound form of silicon

Comprehensive mapping of the Helicobacter pylori NikR regulon provides new insights in bacterial nickel responses

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