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  • Title: Kinetics and activation parameter analysis for the prebiotic oligocytidylate formation on Na(+)-montmorillonite at 0-100 degrees C.
    Author: Kawamura K, Maeda J.
    Journal: J Phys Chem A; 2008 Sep 04; 112(35):8015-23. PubMed ID: 18693705.
    Abstract:
    The kinetic analysis of the temperature dependence of the formation of oligocytidylate (oligo(C)) from the 5'-monophosphorimidazolide moiety of cytidine (ImpC) in the presence of Na (+)-montmorillonite (Na (+)-Mont) catalyst has been carried out at 0-100 degrees C. The rate constants for the formation of oligo(C), hydrolysis of ImpC with and without Na (+)-Mont and degradation of oligo(C) were determined. The apparent activation parameters were 30.8 +/- 3.9 kJ mol (-1) ( Ea), 28.3 +/- 4.0 kJ mol (-1) (Delta H++), and -231 +/- 13 J mol (-1) K (-1) (Delta S++) for the formation of the 2-mer; 45.6 +/- 2.9 kJ mol (-1) ( Ea), 43.0 +/- 3.0 kJ mol (-1) (Delta H++), -164 +/- 10 J mol (-1) K (-1) (Delta S++) for the 3-mer; and 45.2 +/- 0.6 kJ mol (-1) ( Ea), 42.7 +/- 0.7 kJ mol (-1) (Delta H++), -159 +/- 2 J mol (-1) K (-1) (Delta S++) for the 4-mer in the presence of Na (+)-Mont. An increasing trend for the rate constants for the formation of oligo(C) in the order 2-mer << 3-mer <4-mer was observed at high temperatures, which is consistent with that observed at low temperatures. These analyses implied for the first time that the associate formation between an activated nucleotide monomer and an elongating oligonucleotide prior to the phosphodiester bond formation during the elongation of an oligonucleotide on a clay surface would be based on the interaction between the two reactants at the phosphoester and/or ribose moieties rather than at the nucleotide bases. The hydrolysis rate of ImpC at 25-100 degrees C was 5.3-10.6 times greater in the presence of Na (+)-Mont than in its absence. Although the degradation of oligo(C) in the presence of Na (+)-Mont was slower than the formation of the 3-mer and longer oligo(C) on Na (+)-Mont, its yield decreased with temperature. This is mainly because the ratios of the rate constant of the 2-mer formation to those of ImpC hydrolysis and the 3-mer and 4-mer formation decrease with an increase in temperature, which is attributed to the enthalpy and entropy changes for the formation of the 2-mer. This trend resembles the case of the template-directed formation of oligo(G) on a poly(C) template but is different from the Pb (2+)-ion-catalyzed oligo(C) formation. According to the kinetics and activation parameter analyses regarding the clay reaction and other prebiotic polymerase models, the possible pathways for the oligonucleotide formation are discussed and compared.
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