Journal of Molecular Evolution

, Volume 61, Issue 5, pp 597–607 | Cite as

Error Minimization and Coding Triplet/Binding Site Associations Are Independent Features of the Canonical Genetic Code

Article

Abstract

The canonical genetic code has been reported both to be error minimizing and to show stereochemical associations between coding triplets and binding sites. In order to test whether these two properties are unexpectedly overlapping, we generated 200,000 randomized genetic codes using each of five randomization schemes, with and without randomization of stop codons. Comparison of the code error (difference in polar requirement for single-nucleotide codon interchanges) with the coding triplet concentrations in RNA binding sites for eight amino acids shows that these properties are independent and uncorrelated. Thus, one is not the result of the other, and error minimization and triplet associations probably arose independently during the history of the genetic code. We explicitly show that prior fixation of a stereochemical core is consistent with an effective later minimization of error.

Keywords

Genetic code Stereochemistry Adaptation Error minimization Aptamers SELEX 

Notes

Acknowledgments

This work was supported in part by NIH Grant GM 48080 and NASA Center for Astrobiology Grant NCC2-1052 to M. Yarus. We would like to thank members of the Yarus and Knight labs, Eors Szathmary, and an anonymous reviewer for critical discussion of the manuscript.

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Copyright information

© Springer Science+Business Media, Inc. 2005

Authors and Affiliations

  • J. Gregory Caporaso
    • 1
  • Michael Yarus
    • 2
  • Rob Knight
    • 3
  1. 1.Department of Biochemistry and Molecular GeneticsUniversity of Colorado Health Sciences CenterAuroraUSA
  2. 2.Department of Molecular, Cellular and Developmental BiologyUniversity of Colorado at BoulderBoulderUSA
  3. 3.Department of Chemistry and BiochemistryUniversity of Colorado at BoulderBoulderUSA

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