Ribozyme Activity of RNA Nonenzymatically Polymerized from 3′,5′-Cyclic GMP

Abstract

3′,5′-Cyclic GMP spontaneously nonenzymatically polymerizes in a base-catalyzed reaction affording G oligonucleotides. When reacted with fully or partially sequence-complementary RNA (oligo C), the abiotically generated oligo G RNA displays a typical ribozyme activity consisting of terminal ligation accompanied by cleavage of an internal phosphate site of the donor oligonucleotide stem upon attack of the acceptor 3′ terminal OH. This reaction is dubbed Ligation following Intermolecular Cleavage (LIC). In a prebiotic perspective, the ability of oligo G polynucleotides to react with other sequences outlines a simple and possible evolutionary scenario based on the autocatalytic properties of RNA.

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).…”

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

“…In the present analysis the polymerization products were routinely characterized by denaturing PAGE; validation by MALDI 19,23 is also shown. Denaturing PAGE analyses of 5′ 32 Plabeled oligomers are at least 1 order of magnitude more sensitive than other detection techniques (MALDI ToF MS included), and the gel denaturating conditions used ensure that stacked structures do not interfere with the evaluation of the polymerized molecules.…”

Tetraloop‐like Geometries Could Form the Basis of the Catalytic Activity of the Most Ancient Ribooligonucleotides

“…At the dawn of the RNA world,2 the repertoire of chemical interactions available for short oligonucleotides to develop their catalytic function was much more restricted. So far not much attention has been devoted to this ancient era,3 and reports on catalysis that utilizes exclusively short (<20 nucleotide) sequences are scarce in the literature 4–6…”

“…In reference 6 we proposed a mechanism for the ligation reaction that utilized the overhangs formed owing to imperfect pairing to promote the transphosphorylation reaction between the 3′‐end of the acceptor and the 5′‐phosphorylated end of the donor (see Scheme ). In addition, we showed that an analogous model could be used to explain the experimentally observed simple ribozyme activity.…”

“…The resulting 5′‐phosphorylated nucleotide then underwent a terminal recombination step with the 3′‐end of the acceptor oligonucleotide strand. The proposed two‐step catalytic mechanism is called “ligation following intermolecular cleavage” (abbreviated as LIC) and is schematically summarized in Scheme 6…”