Stability and structure of xanthosine-metal ion complexes in aqueous solution, together with intramolecular adenosine-metal ion equilibria

Kinjo, Yoshiaki; Tribolet, Roger; Corfù, Nicolas A.; Sigel, Helmut

doi:10.1021/ic00307a013

Cited by 47 publications

(63 citation statements)

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“…Monoprotonated H(Xao) + carries a proton at N7, which is released with pK H(Xao) H = 0.74 ± 0.06 [95]. The neutral Xao, as shown in Figure 8, loses a further proton already with pK Xao H = 5.47 ± 0.03 [95] from the (N1)H/(N3)H sites and there is evidence for a tautomeric equilibrium between (N3) -/(N1)H and (N3)H/(N1) - [96,97]. In any case, in the physiological pH range of about 7.5 this nucleoside is present in its anionic form, xanthosinate, and it differs therefore considerably from its relatives inosine and guanosine (Section 4.1; Table 3).…”

Section: Xanthosinementioning

confidence: 99%

“…Stability constants of M(Xao -H) + complexes (including for Cd 2+ ) have been determined [95] and there is evidence that a dichotomy for M 2+ binding between N1 and N7 occurs [95,98];…”

Section: Xanthosinementioning

confidence: 99%

“…There is no doubt that the indicated dichotomy exists, yet the percentages given for the isomers should be considered with some care, even though the agreement between the rather different evaluation methods is surprisingly good. For example, it is concluded that in Cd(Xao -H) + about 75% are N7-coordinated [95,98]; the value for Co(Xao -H) + is about 50% [95,98], whereas for Zn(Xao -H) + N7 binding is given as 58% in ref. [95] and as 38% in ref.…”

Section: Xanthosinementioning

confidence: 99%

“…For example, it is concluded that in Cd(Xao -H) + about 75% are N7-coordinated [95,98]; the value for Co(Xao -H) + is about 50% [95,98], whereas for Zn(Xao -H) + N7 binding is given as 58% in ref. [95] and as 38% in ref. [98].…”

Section: Xanthosinementioning

confidence: 99%

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Complex Formation of Cadmium with Sugar Residues, Nucleobases, Phosphates, Nucleotides, and Nucleic Acids

Sigel

Skilandat

Sigel

et al. 2012

Metal Ions in Life Sciences

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Cadmium(II), commonly classified as a relatively soft metal ion, prefers indeed aromaticnitrogen sites (e.g., N7 of purines) over oxygen sites (like sugar-hydroxyl groups). However, matters are not that simple, though it is true that the affinity of Cd(2+) towards ribose-hydroxyl groups is very small; yet, a correct orientation brought about by a suitable primary binding site and a reduced solvent polarity, as it is expected to occur in a folded nucleic acid, may facilitate metal ion-hydroxyl group binding very effectively. Cd(2+) prefers the guanine(N7) over the adenine(N7), mainly because of the steric hindrance of the (C6)NH(2) group in the adenine residue. This Cd(2+)-(N7) interaction in a guanine moiety leads to a significant acidification of the (N1)H meaning that the deprotonation reaction occurs now in the physiological pH range. N3 of the cytosine residue, together with the neighboring (C2)O, is also a remarkable Cd(2+) binding site, though replacement of (C2)O by (C2)S enhances the affinity towards Cd(2+) dramatically, giving in addition rise to the deprotonation of the (C4)NH(2) group. The phosphodiester bridge is only a weak binding site but the affinity increases further from the mono-to the di-and the triphosphate. The same also holds for the corresponding nucleotides. Complex stability of the pyrimidine-nucleotides is solely determined by the coordination tendency of the phosphate group(s), whereas in the case of purine-nucleotides macrochelate formation takes place by the interaction of the phosphate-coordinated Cd(2+) with N7. The extents of the formation degrees of these chelates are summarized and the effect of a non-bridging sulfur atom in a thiophosphate group (versus a normal phosphate group) is considered. Mixed ligand complexes containing a nucleotide and a further mono-or bidentate ligand are covered and it is concluded that in these species N7 is released from the coordination sphere of Cd(2+). In the case that the other ligand contains an aromatic residue (e.g., 2,2'-bipyridine or the indole ring of tryptophanate) intramolecular stack formation takes place. With buffers like Tris or Bistris mixed ligand complexes are formed. Cd(2+) coordination to dinucleotides and to dinucleoside monophosphates provides some insights regarding the interaction between Cd(2+) and nucleic acids. Cd(2+) binding to oligonucleotides follows the principles of coordination to its units. The available crystal studies reveal that N7 of purines is the prominent binding site followed by phosphate oxygens and other heteroatoms in nucleic acids. Due to its high thiophilicity, Cd(2+) is regularly used in so-called thiorescue experiments, which lead to the identification of a direct involvement of divalent metal ions in ribozyme catalysis.

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Section: Xanthosinementioning

confidence: 99%

“…Stability constants of M(Xao -H) + complexes (including for Cd 2+ ) have been determined [95] and there is evidence that a dichotomy for M 2+ binding between N1 and N7 occurs [95,98];…”

Section: Xanthosinementioning

confidence: 99%

Section: Xanthosinementioning

confidence: 99%

Section: Xanthosinementioning

confidence: 99%

See 2 more Smart Citations

Complex Formation of Cadmium with Sugar Residues, Nucleobases, Phosphates, Nucleotides, and Nucleic Acids

Sigel

Skilandat

Sigel

et al. 2012

Metal Ions in Life Sciences

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“…[7] Because metal ions like to bind in aqueous solution to N7 of neutral xanthosine [37] as well as in related hypoxanthine and guanine derivatives, [21,[38][39][40] one expects that this binding mode due to the positive charge close to N7 favors (N1)H deprotonation [41] also in xanthine derivatives. Of course, the negative charge at (N1) À will partially be delocalized to the neighboring carbonyl groups ( Figure 4).…”

Section: àmentioning

confidence: 99%

Acid–Base and Metal‐Ion‐Binding Properties of Xanthosine 5′‐Monophosphate (XMP) in Aqueous Solution: Complex Stabilities, Isomeric Equilibria, and Extent of Macrochelation

Sigel¹,

Massoud²,

Song³

et al. 2006

Chemistry A European J

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The four acidity constants of threefold protonated xanthosine 5'-monophosphate, H3(XMP)+, reveal that at the physiological pH of 7.5 (XMP-H)(3-) strongly dominates (and not XMP(2-) as given in textbooks); this is in contrast to the related inosine (IMP(2-)) and guanosine 5'-monophosphate (GMP(2-)) and it means that XMP should better be named as xanthosinate 5'-monophosphate. In addition, evidence is provided for a tautomeric (XMP-HN1)(3-)/(XMP-HN3)(3-) equilibrium. The stability constants of the M(H;XMP)+ species were estimated and those of the M(XMP) and M(XMP-H)- complexes (M2+=Mg2+, Ca2+, Sr2+, Ba2+, Mn2+, Co2+, Ni2+, Cu2+, Zn2+, Cd2+) measured potentiometrically in aqueous solution. The primary M2+ binding site in M(XMP) is (mostly) N7 of the monodeprotonated xanthine residue, the proton being at the phosphate group. The corresponding macrochelates involving P(O)2(OH)- (most likely outer-sphere) are formed to approximately 65% for nearly all M2+. In M(XMP-H)- the primary M2+ binding site is (mostly) the phosphate group; here the formation degree of the N7 macrochelates varies widely from close to zero for the alkaline earth ions, to approximately 50% for Mn2+, and approximately 90% or more for Co2+, Ni2+, Cu2+, Zn2+, and Cd2+. Because for (XMP-H)(3-) the micro stability constants quantifying the M2+ affinity of the xanthosinate and PO3(2-) residues are known, one may apply a recently developed quantification method for the chelate effect to the corresponding macrochelates; this chelate effect is close to zero for the alkaline earth ions and it amounts to about one log unit for Co2+, Ni2+, Cu2+. This method also allows calculation of the formation degrees of the monodentatally coordinated isomers; this information is of relevance for biological systems because it demonstrates how metal ions can switch from one site to another through macrochelate formation. These insights are meaningful for metal-ion-dependent reactions of XMP in metabolic pathways; previous mechanistic proposals based on XMP(2-) need revision.

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

Sigel¹,

Sigel²

2007

Nickel and Its Surprising Impact in Nature

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Stability and structure of xanthosine-metal ion complexes in aqueous solution, together with intramolecular adenosine-metal ion equilibria

Cited by 47 publications

References 0 publications

Complex Formation of Cadmium with Sugar Residues, Nucleobases, Phosphates, Nucleotides, and Nucleic Acids

Complex Formation of Cadmium with Sugar Residues, Nucleobases, Phosphates, Nucleotides, and Nucleic Acids

Acid–Base and Metal‐Ion‐Binding Properties of Xanthosine 5′‐Monophosphate (XMP) in Aqueous Solution: Complex Stabilities, Isomeric Equilibria, and Extent of Macrochelation

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

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