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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:	Refereed Article
Keywords:	genetic systems; ribozymes; systematic evolution of ligands by exponential amplification (SELEX); RNA world
Research Division:	Mathematical Sciences
Research Group:	Applied mathematics
Research Field:	Biological mathematics
Objective Division:	Expanding Knowledge
Objective Group:	Expanding knowledge
Objective Field:	Expanding knowledge in the biological sciences
UTAS Author:	Holland, BR (Professor Barbara Holland)
ID Code:	63085
Year Published:	2003
Web of Science® Times Cited:	12
Deposited By:	Mathematics
Deposited On:	2010-04-14
Last Modified:	2010-05-05
Downloads:	0