Template-directed RNA polymerization: the taming of the milieu

The strength of the template effect attracting nucleotides to naked DNA

The transmission of genetic information relies on Watson–Crick base pairing between nucleoside phosphates and template bases in template–primer complexes. Enzyme-free primer extension is the purest form of the transmission process, without any chaperon-like effect of polymerases. This simple form of copying of sequences is intimately linked to the origin of life and provides new opportunities for reading genetic information. Here, we report the dissociation constants for complexes between (deoxy)nucleotides and template–primer complexes, as determined by nuclear magnetic resonance and the inhibitory effect of unactivated nucleotides on enzyme-free primer extension. Depending on the sequence context, K_d′s range from 280 mM for thymidine monophosphate binding to a terminal adenine of a hairpin to 2 mM for a deoxyguanosine monophosphate binding in the interior of a sequence with a neighboring strand. Combined with rate constants for the chemical step of extension and hydrolytic inactivation, our quantitative theory explains why some enzyme-free copying reactions are incomplete while others are not. For example, for GMP binding to ribonucleic acid, inhibition is a significant factor in low-yielding reactions, whereas for amino-terminal DNA hydrolysis of monomers is critical. Our results thus provide a quantitative basis for enzyme-free copying.

Fixation and accumulation of thermotolerant catalytic competence of a pair of ligase ribozymes through complex formation and cross ligation

In the early stages of the hypothetical RNA world, some primitive RNA catalysts (ribozymes) may have emerged through self-assembly of short RNA oligomers. Although they may be unstable against temperature fluctuations and other environmental changes, ligase ribozymes (ribozymes with RNA strand-joining activity) may resolve structural instability of self-assembling RNAs by converting them to the corresponding unimolecular formats. To investigate this possibility, we constructed a model system using a cross-ligation system composed of a pair of self-assembling ligase ribozymes. Their abilities to act as catalysts, substrates, and a cross-ligation system were analyzed with or without thermal pretreatment before the reactions. A pair of self-assembling ligase ribozymes, each of which can form multiple conformations, demonstrated that thermotolerance was acquired and accumulated through complex-formation that stabilized the active forms of the bimolecular ribozymes and also cross-ligation that produced the unimolecular ribozymes.