Abstract
The RNA world hypothesis states that the early evolution of life went through a stage in which RNA served both as genome and as catalyst. The central catalyst in an RNA world organism would have been a ribozyme that catalyzed RNA polymerization to facilitate self-replication. An RNA polymerase ribozyme was developed previously in the lab but it is not efficient enough for self-replication. The factor that limits its polymerization efficiency is its weak sequence-independent binding of the primer/template substrate. Here we tested whether RNA polymerization could be improved by a cationic arginine cofactor, to improve the interaction with the substrate. In an RNA world, amino acid-nucleic acid conjugates could have facilitated the emergence of the translation apparatus and the transition to an RNP world. We chose the amino acid arginine for our study because this is the amino acid most adept to interact with RNA. An arginine cofactor was positioned at ten different sites on the ribozyme, using conjugates of arginine with short DNA or RNA oligonucleotides. However, polymerization efficiency was not increased in any of the ten positions. In five of the ten positions the arginine reduced or modulated polymerization efficiency, which gives insight into the substrate-binding site on the ribozyme. These results suggest that the existing polymerase ribozyme is not well suited to using an arginine cofactor.
Highlights
According to the RNA world hypothesis, an early stage of life used RNA both as genome and as catalyst [1,2,3,4] for recent reviews see [5,6]
The amino acid portion of the conjugate is accessible for interactions with the substrate
The dependence followed a pattern that coincided with the periodicity of an A-form helix (11 base pairs), with the exception of the 7 base pair duplex. These results showed that the distal terminus of the 59-duplex entered the catalytic site of the ribozyme, confirming the hypothesis that the 39-terminal 29-hydroxyl group of 59-terminal RNA/RNA duplexes could inhibit polymerization by insertion into the catalytic site
Summary
According to the RNA world hypothesis, an early stage of life used RNA both as genome and as catalyst [1,2,3,4] for recent reviews see [5,6]. To recapitulate an RNA world in the lab, RNA polymerase ribozymes were developed and improved in several laboratories [7,8,9,10] These polymerase ribozymes have a length in the range of 200 nucleotides. By concatenating multiple copies of this sequence it was possible to extend a primer by 95 nucleotides [10] Such a template could not encode a ribozyme. Polymerization reaches usually less than 10 nucleotides, and recent improvements made it possible to polymerize 20–30 nucleotides [9,10,11,12] This is still far below the level required for self-replication. The ribozyme would have to employ a positively charged cofactor
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