<b>Interaction and Association of Bases and Nucleosides in Aqueous Solutions</b>

Ts’o, Paul O. P.; Melvin, Ingelore S.; Olson, Alfred C.

doi:10.1021/ja00892a016

Cited by 348 publications

(191 citation statements)

References 2 publications

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“…It was shown already more than 40 years ago that purines associate much better than pyrimidines [13]; regarding nucleotides, the situation was less clear for many years [14][15][16]. Today it is generally accepted that self-association of all these species occurs via nucleobase stacking [14,17,18], that it proceeds beyond the dimer stage and that oligomers are formed [14,16,[18][19][20][21][22][23][24].…”

Section: Self-association Of Atpmentioning

confidence: 99%

Adenosine 5'-triphosphate (ATP4-): Aspects of the coordination chemistry of a multitalented biological substrate

Sigel

2004

Pure and Applied Chemistry

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Firstly, the self-stacking properties of ATP 4-and the effects of metal ions and protons on these properties are described. Some examples involving macrochelate formation between phosphate-coordinated metal ions (M 2+ ) and N7 of the adenine residue in M(ATP) 2-are discussed, and this is followed by considerations on mixed ligand complexes consisting of ATP 4-, M 2+ , and amino acid anions with side chains that allow either aromatic-ring stacking or hydrophobic interactions with the adenine moiety; this gives rise to selectivity. Next, the properties of diphosphorylated 9-[2-(phosphonomethoxy)ethyl]adenine (PMEA 2-; Adefovir), i.e., of PMEApp 4-, are compared with those of (2′-deoxy)ATP 4-with regard to their metal ion-binding qualities, and in this way it can be explained why PMEApp 2-is initially an excellent substrate for nucleic acid polymerases. Of course, after incorporation of the PMEA residue into the growing nucleic acid chain, this is terminated and this is how PMEA exerts its antiviral properties [its bis(pivaloyloxymethyl)ester, Adefovir dipivoxil, was recently approved for use in hepatitis B therapy]. Finally, the change in free energy connected with (macro)chelate formation or intramolecular stacking interactions and the effect of a reduced dielectric constant of the solvent on the stability of complexes and their structures in solution is considered.

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Section: Self-association Of Atpmentioning

confidence: 99%

Adenosine 5'-triphosphate (ATP4-): Aspects of the coordination chemistry of a multitalented biological substrate

Sigel

2004

Pure and Applied Chemistry

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“…The fact that the self-association of pyrimidine nucleosides is somewhat less than that of purine nucleosides [49] (Kpurine = 2.1, Kcy,,di,,e = 0.87 [50,51]) cannot explain the very different dephosphorylation tendency of the Cu2+-CTP and CuZ+-ATP systems [ l ) (c:$ also Fig. 2 and Table 3).…”

Section: Metal Ionlphosphate Coordination and Lubilization Of The Y-gmentioning

confidence: 99%

Comparison of the Metal-Ion-Promoted Dephosphorylation of the 5'-Triphosphates of Adenosine, Inosine, Guanosine and Cytidine by Mn2+, Ni2+ and Zn2+ in Binary and Ternary Complexes

Amsler

Sigel

1976

Eur J Biochem

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The dependence of the rate of dephosphorylation of ATP, ITP, GTP and CTP (= NTP), expressed as first-order rate constants (50 "C; I = 0.1 M, NaCIO,), on pH (2 to lo), in the absence and presence of Mn2+, Ni2+ and Zn2+, was investigated. The reaction is accelerated by Zd2+ and passes through a pH optimum at about 8 for the system Zn2f.-ATP or 9 for Zn2+-ITP and Zn2+-GTP; this is analogous to observations made earlier with the corresponding Cu2+ systems. By computing the pH dependence of the distribution of the several species present in these systems it is shown that the highest rates are observed in the pH regions where the concentration of Zn(ATP)2-, Zn(lTP-H)3-, or Zn(GTP-H)3 -dominates. By evaluating the pH dependence evidence is given that the attacking nucleophije is OH-or H 2 0 for Zn(ATP)'-and H20 for Zn(ITP-H)3-or Zn(GTP-H)3 -. For all these complexes metal-ion/nucleic-base interactions are known, leading to the formation of macrochelates. These metal-ion/nucleic-base interactions are crucial for the observation of a metal-ion-promoted dephosphorylation ; in agreement with this, and the small tendency of the cytosine moiety to coordinate, the CTP systems are rather stable towards dephosphorylation. It should be noted that these experimental results do not necessarily mean that the macrochelates usually described are the reactive complexes, but only that the active complex must be closely related to them (e.g. isomers, etc.). Although for the Ni2+ systems with ATP, ITP and GTP, and for the Mn2+-ATP system a metal-ion/nucleic-base interaction is also known, these systems are not very sensitive to hydrolytic cleavage of the terminal P-0-P bond. The only known significant structural difference between the Ni2 +-NTP or the Mn2 +-ATP complexes and those of Cu2+ or Zn2+ is that Ni2+ and Mn2+ coordinate to all three phosphate groups, whereas Cu2 + and Zn2 + involve only the fl and y ones. This structure-reactivity relationship is rationalized by the suggestion that in the active species the metal ion should be coordinated to the a,/?-phosphate groups leaving the 1'-group open to nucleophilic attack. Obviously, an initial PJ-COordination is suitable for a shift of the metal ion along the phosphate back-bone into the reactive a,P-position, while for an a,/?,?-coordination only the less favorable removal of the coordinated pgroup remains. The metal-ion/nucleic-base interaction is considered as being important for achieving this reactive structure. The connection between trans-phosphorylations in vitro and in vivo is discussed. It is also shown that the formation of mixed-ligand or ternary complexes inhibits the dephosphorylation process. This is on the one hand of interest with regard to the transport of hydrolysis-sensitive phosphates in nature, while on the other it casts doubts on conclusions based on experiments carried out in the presence of buffers, because these contain weak bases and hence potential ligands.Considering the importance of phosphoryl and nucleotidyl transfers in nature and because the enzymes ...

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“…If more than one organic compound is present in solution, the absorption behavior cannot be deduced from the absorptions of the compounds separately because of their possible interactions with each other, either in solution or after absorption in/on the clay. Extensive studies by Ts'o et al have shown that important interactions may take place in aqueous solutions between purines, pyrimidines and their nucleosides (Ts'o et al 1963Chan et al 1964;Schweizer et al 1965) and they have deduced that the interaction is a vertical stacking of the molecules with a partial ring overlap, in preference to horizontal hydrogen bonding. If a similar vertical stacking should occur in the absorbed state, it would be easily measurable by X-ray diffractometry of the samples under equilibrium conditions.…”

Section: Introductionmentioning

confidence: 99%

Specific Co-Absorption of Purines and Pyrimidines by Montmorillonite (Clay-Organic Studies XV)

Lailach

1969

Clays and Clay Minerals

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Abstract-The co-absorptions of various purines and pyrimidines from aqueous solutions by Na-and Ca-montmorillonite are studied in the range of pH 1-6. The pyrimidines, thymine and uracil, which are not absorbed from solutions of these compounds alone, are appreciably absorbed from solutions containing also adenine or 2,6-diaminopurine, are weakly absorbed from solutions containing hypoxanthine, and are not absorbed from solutions containing purine, cytosine, and caffeine. The specific co-absorption is tentatively attributed to hydrogen-bond formation between the molecules in solution rather than to an overlapping of the molecular configurations (vertical stacking). The montmorilloniteorganic associations have a basal spacing of about 12.5 -~ which permits only a single molecular layer between successive silicate layers.

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Interaction and Association of Bases and Nucleosides in Aqueous Solutions

Cited by 348 publications

References 2 publications

Adenosine 5'-triphosphate (ATP4-): Aspects of the coordination chemistry of a multitalented biological substrate

Adenosine 5'-triphosphate (ATP4-): Aspects of the coordination chemistry of a multitalented biological substrate

Comparison of the Metal-Ion-Promoted Dephosphorylation of the 5'-Triphosphates of Adenosine, Inosine, Guanosine and Cytidine by Mn2+, Ni2+ and Zn2+ in Binary and Ternary Complexes

Specific Co-Absorption of Purines and Pyrimidines by Montmorillonite (Clay-Organic Studies XV)

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