Comparison of the Extent of Macrochelate Formation in Complexes of Divalent Metal Ions with Guanosine (GMP2-), Inosine (IMP2-), and Adenosine 5'-Monophosphate (AMP2-). The Crucial Role of N-7 Basicity in Metal Ion-Nucleic Base Recognition

Sigel, Helmut; Massoud, Salah S.; Corfù, Nicolas A.

doi:10.1021/ja00086a028

Cited by 286 publications

(358 citation statements)

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“…In contrast, it rather promotes complex stability by forming outersphere bonds to a water molecule of the N7-bound metal ion. 25,38 The conclusion of this observation is that one expects for all complexes of guanine nucleotides higher formation degrees of the macrochelates than for the corresponding adenine nucleotide complexes.…”

Section: Table 3 Close To Herementioning

confidence: 84%

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Effect of the ribose versus 2′-deoxyribose residue on the metal ion-binding properties of purine nucleotides

et al. 2008

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The interaction between metal ions and nucleotides is well characterized, as is their importance for metabolic processes, e.g. in the synthesis of nucleic acids. Hence, it is surprising to find that no detailed comparison is available of the metal ion-binding properties between nucleoside 5'-phosphates and 2'-deoxynucleoside 5'-phosphates. Therefore, we have measured here by potentiometric pH titrations the stabilities of several metal ion complexes formed with 2'-deoxyadenosine 5'-monophosphate (dAMP2-), 2'-deoxyadenosine 5'-diphosphate (dADP3-) and 2'-deoxyadenosine 5'-triphosphate (dATP4-). These results are compared with previous data measured under the same conditions and available in the literature for the adenosine 5'-phosphates, AMP(2-), ADP(3-) and ATP(4-), as well as guanosine 5'-monophosphate (GMP(2-)) and 2'-deoxyguanosine 5'-monophosphate (dGMP(2-)). Hence, in total four nucleotide pairs, GMP(2-)/dGMP(2-), AMP(2-)/dAMP(2-), ADP(3-)/dADP(3-) and ATP(4-)/dATP(4-) (= NP/dNP), could be compared for the four metal ions Mg2+, Ni2+, Cu2+ and Zn2+ (= M2+). The comparisons show that complex stability and extent of macrochelate formation between the phosphate-coordinated metal ion and N7 of the purine residue is very similar (or even identical) for the AMP(2-)/dAMP(2-) and ADP(3-)/dADP(3-) pairs. In the case of the complexes formed with ATP(4-)/dATP(4-) the 2'-deoxy complexes are somewhat more stable and show also a slightly enhanced tendency for macrochelate formation. This is different for guanine nucleotides: the stabilities of the M(dGMP) complexes are clearly higher, as are the formation degrees of their macrochelates, than is the case with the M(GMP) complexes. This enhanced complex stability and greater tendency to form macrochelates can be attributed to the enhanced basicity (DeltapKaca. 0.2) of N7 in the 2'-deoxy compound. These results allow general conclusions regarding nucleic acids to be made. Among the 2'-deoxyribose nucleotides (dNMP 2-, dNDP 3-, dNTP 4-) the complexes of dGMP 2-and to a smaller extent also of dATP 4-are somewhat more stable than the corresponding ribose nucleotides (NMP 2-, NDP 3-, NTP 4-) and macrochelate formation involving N7 is also more pronounced. 3 SummaryThe interaction between metal ions and nucleotides is well characterized, as is their importance for metabolic processes, e.g., in the synthesis of nucleic acids. Hence, it is surprising to find that no detailed comparison is available of the metal ion-binding properties between nucleoside 5'-phosphates and 2'-deoxynucleoside 5'-phosphates. Therefore, we have measured here by potentiometric pH titrations the stabilities of several metal ion complexes formed with 2'-deoxyadenosine 5'-monophosphate (dAMP 2-), 2'-deoxyadenosine 5'-diphosphate (dADP 3-) and 2'-deoxyadenosine 5'-triphosphate (dATP 4-). These results are compared with previous data measured under the same conditions and available in the literature for the adenosine 5'-phosphates, AMP 2-, ADP 3-and ATP 4-as well as guanosine 5'-monophosphate (GMP 2-...

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Section: Table 3 Close To Herementioning

confidence: 84%

“…The same is true for the formation degree of the macrochelates, which is in accord with the increased basicity of N7 in dGMP 2- (Table 3). 17,19,25,41 It is thus evident that in this respect considerably more work needs to be done.…”

Section: Discussionmentioning

confidence: 99%

Effect of the ribose versus 2′-deoxyribose residue on the metal ion-binding properties of purine nucleotides

et al. 2008

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“…The acidity constants of these ligands and the stability constants of their corresponding Cd 2+ complexes are defined by equations (3) and (2), respectively. The corresponding results are listed in entries 1 to 6 of Table 3 [70][71][72][73][74][75].…”

Section: Cadmium(ii) Complexes Of Purine Derivativesmentioning

confidence: 99%

“…Two such examples are shown in Figure 10 [11 -14,50]. It is the phosphate residue in nucleotides which determines to a very large part the stability of the complexes formed with labile metal ions including Cd 2+ [74,117,119,130] independent of the kind of nucleobase involved or whether a nucleoside mono-, di-, or triphosphate is considered.…”

mentioning

confidence: 99%

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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“…The N7 of purine bases is thereby of special interest as this atom constitutes a prominent coordination site for metal ions in nucleic acids. 5,6,[13][14][15] The ring nitrogens of the purine bases in the hammerhead ribozyme have been probed for M n+ binding by observing the change of 15 N chemical shift using direct 15 N detection. 16 Recently, the coordination of Hg 2+ to N3 of thymine has been proven by the same method by incorporating specifically labelled nucleotides into a DNA duplex.…”

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confidence: 99%

Metal ion-N7 coordination in a ribozyme branch domain by NMR

Erat¹,

Kovacs²,

Sigel³

2010

Journal of Inorganic Biochemistry

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The N7 of purine nucleotides presents one of the most dominant metal ion binding sites in nucleic acids. However, the interactions between kinetically labile metal ions like Mg2+ and these nitrogen atoms are inherently difficult to observe in large RNAs. Rather than using the insensitive direct N-15 detection, here we have used (2)J-H-1,N-15]-HSQC (Heteronuclear Single Quantum Coherence) NMR experiments as a fast and efficient method to specifically observe and characterize such interactions within larger RNA constructs. Using the 27 nucleotides long branch domain of the yeast-mitochondrial group II intron ribozyme Sc.ai5 gamma as an example, we show that direct N7 coordination of a Mg2+ ion takes place in a tetraloop nucleotide. A second Mg2+ ion, located in the major groove at the catalytic branch site, coordinates mainly in an outer-sphere fashion to the highly conserved flanking GU wobble pairs but not to N7 of the sandwiched branch adenosine. (C)

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Comparison of the Extent of Macrochelate Formation in Complexes of Divalent Metal Ions with Guanosine (GMP2-), Inosine (IMP2-), and Adenosine 5'-Monophosphate (AMP2-). The Crucial Role of N-7 Basicity in Metal Ion-Nucleic Base Recognition

Cited by 286 publications

References 1 publication

Effect of the ribose versus 2′-deoxyribose residue on the metal ion-binding properties of purine nucleotides

Effect of the ribose versus 2′-deoxyribose residue on the metal ion-binding properties of purine nucleotides

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

Metal ion-N7 coordination in a ribozyme branch domain by NMR

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