Kinetic Analysis of Oligo(C) Formation from the 5′-Monophosphorimidazolide of Cytidine with Pb(II) Ion Catalyst at 10–75°C

Abstract

The temperature dependence of the rate constants for the formation of oligocytidylate (oligo(C)) from the 5'-monophosphorimidazolide of cytidine (ImpC) in the presence of Pb(II) ion catalyst has been investigated at 10-75 degrees C. The rate constants for the formation of oligo(C) increased in the order of the formation of 2-mer < 3-mer < or = 4-mer; this trend resembles the trend in the cases of the template-directed and the clay-catalyzed formations of oligonucleotides. While the rate constants of the formation of oligo(C) increased with increasing temperature, the yield of oligo(C) decreased with increasing temperature. This is due to the fact that the relative magnitude of the rate constants of the formation of 2-mer, 3-mer, and 4-mer to that of the hydrolysis of ImpC decreased with increasing temperature. This is probably due to the fact that association between ImpC with the elongating oligo(C) decreases with increasing temperature. The apparent activation energy was 61.9 +/- 8.5 kJ mol(-1) for the formation of 2-mer, 49.3 +/- 2.9 kJ mol(-1) for 3-mer, 51.8 kJ mol(-1) for 4-mer, and 66.8 +/- 4.5 kJ mol(-1) for the hydrolysis of ImpC. The significance of the temperature dependence of the formation rate constants of the model prebiotic formation of RNA is discussed.

Cascade of Reduced Speed and Accuracy after Errors in Enzyme-Free Copying of Nucleic Acid Sequences

“…Whether the template and primer were RNA or DNA and whether the leaving group was ImH or OAt – did not have a major effect on stalling after a mismatch. Nucleoside 5′-phosphorimidazolides have been used by several different laboratories as a model system for nonenzymatic extension. ,,,− The substituents of the imidazole ring have been found to influence the rate and regiospecificity of the polymerization reaction of RNA monomers, with 2-methylimidazole giving the greatest yield, although 2-methylimidazole was shown in other studies to be a poorer catalyst for the extension of 2′-aminoterminal DNA primers than other imidazoles. , Imidazoles and 4-aminopyridines were also found to be favorable leaving groups for montmorillonite-promoted RNA polymerization as compared to other possibilities . However, the influence of the leaving group on mutation rates and stalling was previously unknown.…”

Creating Prebiotic Sanctuary: Self-Assembling Supramolecular Peptide Structures Bind and Stabilize RNA

“…Assessment of the Kinetic Impact of RNA Stabilization The calculations were performed using the kinetic data acquired by Kawamura and Maeda (Kawamura and Maeda 2007) for the oligomerization of diribonucleotide.…”

“…4 Graphs depicting the equilibrium concentration of diribonucleotide based on Eq. 9, using the kinetic data acquired by Kawamura and Maeda (Kawamura and Maeda 2007) for the oligomerization and degradation of RNA in the presence of Pb +2 ions. a The equilibrium concentration of diribonucleotide in: an open system (X-marked line); a semi-closed system (triangle-marked line); a semi-closed system which induce stabilization of the diribonucleotide (square-marked line); and the initial concentration of ribonucleotide monomers in the environment (dashed line).…”

Kinetics and Activation Parameter Analysis for the Prebiotic Oligocytidylate Formation on Na+-Montmorillonite at 0−100 °C

“…All the other reagents used were of analytical grade. High-performance liquid chromatography (HPLC) was carried out on an LC10A HPLC system (Shimadzu, Japan) with a DNA-NPR anion-exchange column from Tosoh Co., Japan using a gradient of 0.3−1.5 M NaCl at pH 9 with 0.02 M 2-amino-2-hydroxymethyl-1,3-propanediol (Tris) buffer and an ODS-2 column from GL Science Co., Japan using a gradient of 0.005 M NaH 2 PO 4 in water at pH 3.5 mixed with 0.01 M NaH 2 PO 4 in 40% CH 3 OH at pH 4.0 …”

“…A few investigations concerning the degradation of RNA and its precursors have been conducted from the standpoint of the hydrothermal origin of life. ,,,,– According to the empirical data regarding the stability of RNA molecules, it is considered that the RNA molecules are too labile under redox-constrained hydrothermal conditions, , although some minerals appear to protect nucleotides and their precursors from degradations. , On the other hand, while the prebiotic formation of RNA was rarely investigated at high temperatures, we have recently accumulated kinetic data on the temperature dependence of prebiotic RNA polymerase model reactions, that is, the TD reaction, cyclization reaction of hexanucleotides, and Pb 2+ -ion-catalyzed oligonucleotide formation (PB reaction). – These investigations not only showed that the phosphodiester bond becomes labile at high temperatures but also suggested that its prebiotic formation could be faster than its degradation at high temperatures. – Naturally, this estimation does not give a direct proof of the accumulation of the RNA molecules could under the primitive hydrothermal conditions. Nevertheless, it would be theoretically true that the accumulation of the RNA molecules may be kinetically controlled in an open system by both the formation and decomposition rates of RNA, even at high temperatures. , In particular, it has been elucidated that mineral catalysts could have played important roles in the spontaneous formation of long oligonucleotides from monomeric nucleotides. ,, Thus, for the RNA world hypothesis and hydrothermal origin of life hypothesis to be compatible, it is important to accumulate kinetic data regarding the temperature dependence of the prebiotic simulation reactions of the RNA molecules to validate the rate of the prebiotic formation of RNA at high temperatures.…”