Article ID | Journal | Published Year | Pages | File Type |
---|---|---|---|---|
2819587 | Gene | 2007 | 9 Pages |
Abstract
We used Archaea sequences of both precursor and derivative tRNAs in order to examine the plastic repertoires or sets of suboptimal structures at a defined free energy interval. We grouped secondary structures according to their helix nesting and adjacency using abstract shapes analysis. This clustering enabled us to infer a consensus sequence for all shapes that fit the clover leaf secondary structure [Giegerich, R., et al., Nucleic Acids Res 2004; 32 (16): 4843-51.]. This consensus sequence was then folded in order to retrieve a set of suboptimal structures. For each pair of precursor and derivative tRNAs, we compared these plastic repertoires based on the number of secondary structures, the thermostability of the minimum free energy structure and two structural parameters (base pair propensity (P) and mean length of helical stem structures (S)), which were measured for every representative secondary structure [Schultes, E.A., et al., J Mol Evol 1999; 49 (1): 76-83.]. We found that derivative tRNAs have fewer numbers of shapes, higher thermostability and more stable parameters than precursor tRNAs, a fact in full agreement with Wong's coevolution theory of the genetic code.
Keywords
Related Topics
Life Sciences
Biochemistry, Genetics and Molecular Biology
Genetics
Authors
Hernán A. Burbano, Eugenio Andrade,