Untemplated Nonenzymatic Polymerization of 3′,5′cGMP: A Plausible Route to 3′,5′-Linked Oligonucleotides in Primordia

Abstract

The high-energy 3',5' phosphodiester linkages conserved in 3',5' cyclic GMPs offer a genuine solution for monomer activation required by the transphosphorylation reactions that could lead to the emergence of the first simple oligonucleotide sequences on the early Earth. In this work we provide an in-depth characterization of the effect of the reaction conditions on the yield of the polymerization reaction of 3',5' cyclic GMPs both in aqueous environment as well as under dehydrating conditions. We show that the threshold temperature of the polymerization is about 30 °C lower under dehydrating conditions than in solution. In addition, we present a plausible exergonic reaction pathway for the polymerization reaction, which involves transient formation of anionic centers at the O3' positions of the participating riboses. We suggest that excess Na(+) cations inhibit the polymerization reaction because they block the anionic mechanism via neutralizing the negatively charged O3'. Our experimental findings are compatible with a prebiotic scenario, where gradual desiccation of the environment could induce polymerization of 3',5' cyclic GMPs synthesized in liquid.

Non-Enzymatic Oligomerization of 3’, 5’ Cyclic AMP

“…The two terminal phosphates (one at 5', one at 3') in the reference oligomers cause a slightly slower gel migration relative to the same-sized neo-synthesized oligomers lacking the phosphate group at 3'. [6–7, 9, 16] These phosphates attributions for the reference ladders and for the neo-synthesized oligomers (as shown in Figs 4 and 5) were validated by MALDI (Figs 2–4). RNA hydrolysis in water is less manoeuvrable and regular than that in formamide (see Fig 4).…”

“…[9]. 3’,5’cAMP Na + -free, H + form (that was neither evaporated nor precipitated during the preparation steps) was concentrated from the initial 1mM concentration in MilliQ unbuffered water pH 7.0 by evaporation in Savant under vacuum in Eppendorf plastic tubes and cooling mode till the desired dryness was achieved.…”

“…[5–8], and a plausible reaction mechanism was suggested in ref. [9]. Such a template-free polymerization reaction is preceded by the self-assembling of the cyclic precursors utilizing stacking interactions, which mediate the transphosphorylations among the pillared monomer units, resulting in covalently bound oligonucleotides.…”

Stability of 2′,3′ and 3′,5′ cyclic nucleotides in formamide and in water: a theoretical insight into the factors controlling the accumulation of nucleic acid building blocks in a prebiotic pool

“…Table 1 compares the relative stability of 2',3' and 3',5' cyclic nucleotides derived from BOMD simulations performed in water at room temperature as well as at the temperature where most oligomerization experiments reported in the literature have been conducted. 1,[9][10][11][12] Albeit the energy data derived from BOMD are approximate (our estimation for the error bar referred to the energetically converged part of the simulations is about 2-3 kcal/mol, see the Supplementary Material), the computations show that in aqueous environment the 2',3' cyclic nucleotides are more stable than their 3',5' cyclic counterpart. Thus, in this environment the relative stability of cyclic nucleotides follows the trend one can derive from hydrolysis heats 3 rather than from the extent of the ring strain of the cyclic phosphodiester linkages.…”

“…5 This observation fostered the efforts aimed at the oligomerization of 3',5' cyclic nucleotides, which has been demonstrated on the example of 3',5' cyclic guanosine monophosphate (GMP) under a variety of conditions. [9][10][11][12] Since the anionic ring opening polymerization of 3',5' cyclic GMPs is so far the only known chemistry that leads to selectively 3',5'-linked oligomers (all other known methods lead to a mixture of 2',5'-and 3',5'-linkages), 12 it provides a plausible answer to the question about the evolutionary selection pressure which led to the 3',5'-linkage selectivity in modern RNA-molecules.…”