Interactions of divalent metal ions with inorganic and nucleoside phosphates. 8. Thermodynamics and kinetics of the nickel(II)-2'-AMP,-3'-AMP, and -5'-AMP systems

Thomas, John C.; Frey, Cheryl Miller; Stuehr, J. E.

doi:10.1021/ic50204a045

Cited by 17 publications

(9 citation statements)

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“…These results agree in general well with the listed equilibrium constants, especially if the differences in the experimental conditions are taken into account. The most remarkable observation in these studies is that under certain conditions Ni(AMP) 2 2Ϫ complexes are also observed [14,[120][121][122] and their formation may be attributed to stacking between the purine residues in these 1:2 species [122]. This interpretation is in accord with the fact that no Ni(CMP) 2 2Ϫ complexes were observed [13,120].…”

Section: Properties Of Purine-nucleoside 5ј-monophosphate Complexessupporting

confidence: 57%

“…Finally, it needs to be mentioned that in the context of kinetic and calorimetric studies, the complex stabilities have also been investigated of the Ni 2ϩ systems with CMP [13,120], AMP [14,20,[120][121][122], IMP [19,122], and GMP [122]. These results agree in general well with the listed equilibrium constants, especially if the differences in the experimental conditions are taken into account.…”

Section: Properties Of Purine-nucleoside 5ј-monophosphate Complexessupporting

confidence: 55%

“…Of course, the rate constants for other ligands differ numerically, but the relative ordering remains the same. This relatively slow ligand exchange rate, appropriate for the temperature-jump technique, is the reason why kinetic studies of nucleotide-complex formation have mainly been made with Ni 2ϩ [13][14][15][16][17][18][19][20]. These Met.…”

Section: Introductionmentioning

confidence: 99%

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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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Section: Properties Of Purine-nucleoside 5ј-monophosphate Complexessupporting

confidence: 57%

Section: Properties Of Purine-nucleoside 5ј-monophosphate Complexessupporting

confidence: 55%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

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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“…Those for the guanine derivatives [34,35] are roughly about 0.1 to 0.2 pK units higher than the values listed in Table 1, the differences most likely originating from different calibration procedures of the electrodes used. The values measured by Stuehr et al [36] for H 2 Table 1 is evident from the interrelations between the various acidity constants shown in Figure 2, where the pK a=PO 2 ðOHÞ and pK a/N1H values of the guanine derivatives are plotted in dependence on the pK a/N7H constants. The various acid-base sites are expected to affect each other in a systematic way, and this is nicely observed.…”

Section: Potentiometric Ph Titrationsmentioning

confidence: 80%

Comparison of the Acid–Base Properties of Ribose and 2′‐Deoxyribose Nucleotides

Mucha¹,

Knobloch²,

Jeżowska‐Bojczuk³

et al. 2008

Chemistry A European J

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The extent to which the replacement of a ribose unit by a 2'-deoxyribose unit influences the acid-base properties of nucleotides has not hitherto been determined in detail. In this study, by potentiometric pH titrations in aqueous solution, we have measured the acidity constants of the 5'-di- and 5'-triphosphates of 2'-deoxyguanosine [i.e., of H(2)(dGDP)(-) and H(2)(dGTP)(2-)] as well as of the 5'-mono-, 5'-di-, and 5'-triphosphates of 2'-deoxyadenosine [i.e., of H(2)(dAMP)(+/-), H(2)(dADP)(-), and H(2)(dATP)(2-)]. These 12 acidity constants (of the 56 that are listed) are compared with those of the corresponding ribose derivatives (published data) measured under the same experimental conditions. The results show that all protonation sites in the 2'-deoxynucleotides are more basic than those in their ribose counterparts. The influence of the 2'-OH group is dependent on the number of 5'-phosphate groups as well as on the nature of the purine nucleobase. The basicity of N7 in guanine nucleotides is most significantly enhanced (by about 0.2 pK units), while the effect on the phosphate groups and the N1H or N1H(+) sites is less pronounced but clearly present. In addition, (1)H NMR chemical shift change studies in dependence on pD in D(2)O have been carried out for the dAMP, dADP, and dATP systems, which confirmed the results from the potentiometric pH titrations and showed the nucleotides to be in their anti conformations. Overall, our results are not only of relevance for metal ion binding to nucleotides or nucleic acids, but also constitute an exact basis for the calculation, determination, and understanding of perturbed pK(a) values in DNAzymes and ribozymes, as needed for the delineation of acid-base mechanisms in catalysis.

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“…One of the coordinate bonds is outer sphere: either N-7 inner-and a-phosphate outer sphere or N-7 outer sphere and a-phosphate inner sphere" (79), but the entirely inner sphere structure (iii) does not. However, there are indications from kinetic studies that both phosphate and base may bind inner sphere to the metal ion (80)(81)(82)(83)(84), and space-filling molecular models allow the construction of such a macrochelate without strain (68). In addition, kinetic and product studies (85,86) for the reaction between cisPt(NH3)2 2+ and 5'-(2'-deoxy)GMP 2 -indicate a direct coordination of the metal ion to N-7 and the phosphate group.…”

Section: Structural Considerations For Macrochelates Formed With Purimentioning

confidence: 99%

Metal—Nucleotide Interactions

Sigel

1989

ACS Symposium Series

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Nucleotides and their metal ion complexes undergo self-association via base-stacking in aqueous solution. The extent of this association is quantified for several systems, and conditions are given which should be used in studies directed toward determination of the properties of the monomeric species. Stability constants determined by potentiometric pH titrations for the complexes between Mg 2+ , Ca 2+ , Mn 2+ , Co 2+ , Ni 2+ , Cu 2+ , Zn 2+ or Cd 2+ and adenosine 5'-triphosphate (ATP 4-) and the three pyrimidine nucleoside 5'-triphosphates are listed; evaluation of stability differences allows calculation of the degree of formation of the macrochelated N-7 back-bound species in M(ATP) 2-complexes. There is evidence (including NMR and ultraviolet perturbation studies) that coordination to N-7 may occur either directly or outer sphere, i.e. via a coordinated water molecule. For monophosphate esters (R-MP 2-) the relationship between complex stability and phosphate group basicity is established. The extent of the nucleic base-metal ion interaction is quantified for the M(NMP) species of several nucleoside monophosphates (NMP 2-) including pyrimidine and purine derivatives (e.g., 2'-AMP 2-, 3'-AMP 2-, 5'-AMP 2-, and 5'-GMP 2-). The properties of several mixed ligand complexes, as well as some conclusions relating to interactions between metal ions and nucleic acids, are indicated.NUCLEOTIDES AND METAL IONS are involved in the basic metabolic processes of life (1-3). Since Szent-Gyorgyi (4) proposed in 1956 a macrochelate for the complex formed between adenosine 5'-triphosphate (ATP) and Mg 2+ , this idea has fascinated many chemists and molecular biologists. Today we know that the binding sites of ATP are only in part those originally suggested (4). Many of the early advances were made by

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Interactions of divalent metal ions with inorganic and nucleoside phosphates. 8. Thermodynamics and kinetics of the nickel(II)-2'-AMP,-3'-AMP, and -5'-AMP systems

Cited by 17 publications

References 0 publications

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

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

Comparison of the Acid–Base Properties of Ribose and 2′‐Deoxyribose Nucleotides

Metal—Nucleotide Interactions

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