Optimal alphabets for an RNA world

Gardner, P., Holland, B., Moulton, V., Hendy, M. and Penny, D. (2003) Optimal alphabets for an RNA world. Proceedings of the Royal Society B: Biological Sciences, 270 (1520). pp. 1177-1182. ISSN 0962-8452

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Abstract

Experiments have shown that the canonical AUCG genetic alphabet is not the only possible nucleotide alphabet. In this work we address the question 'is the canonical alphabet optimal?' We make the assumption that the genetic alphabet was determined in the RNA world. Computational tools are used to infer the RNA secondary structure (shape) from a given RNA sequence, and statistics from RNA shapes are gathered with respect to alphabet size. Then, simulations based upon the replication and selection of fixed–sized RNA populations are used to investigate the effect of alternative alphabets upon RNA's ability to step through a fitness landscape. These results show that for a low copy fidelity the canonical alphabet is fitter than two–, six– and eight–letter alphabets. In higher copy–fidelity experiments, six–letter alphabets outperform the four–letter alphabets, suggesting that the canonical alphabet is indeed a relic of the RNA world.

Item Type: Article
Faculty \ School: Faculty of Science > School of Computing Sciences
Depositing User: Vishal Gautam
Date Deposited: 13 Jun 2011 11:43
Last Modified: 17 Mar 2020 17:24
URI: https://ueaeprints.uea.ac.uk/id/eprint/23653
DOI: 10.1098/rspb.2003.2355

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