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Journal of Molecular Evolution

, Volume 40, Issue 3, pp 318–325 | Cite as

Intrastrand parity rules of DNA base composition and usage biases of synonymous codons

  • Noboru Sueoka
Article

Abstract

When there are no biases in mutation and selection between the two strands of DNA, the 12 possible substitution rates of the four nucleotides reduces to six (type 1 parity rule or PR1), and the intrastrand average base composition is expected to be A = T and G = C at equilibrium without regard to the G + C content of DNA (type 2 parity rule or PR2). Significant deviations from the parity rules in the third codon letters of the four-codon amino acids result mostly from selective biases rather than mutational biases between the two strands of DNA during evolution. The parity rules lay the foundation for evaluating the biases in synonymous codon usage in terms of (1) directional mutation pressure for variation of the DNA G + C content due to mutational biases between α-bases (A or T) and γ-bases (G or C), (2) strand-bias mutation, for example, by DNA repair during transcription, and (3) functional selection in evolution, for example, due to tRNA abundance. The present analysis shows that, although the PR2 violation is common in the third codon letters of four-codon amino acids, the contribution of PR2 violation to the DNA G + C content of the third codon position is small and, in majority of cases, mildly counteracts the effect of the directional mutation pressure on the G + C content.

Key words

Parity rules, PR1 and PR2 Strand biases of mutation and selection Codon-usage biases Directional mutation pressure DNA G + C content 

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Copyright information

© Springer-Verlag New York Inc. 1995

Authors and Affiliations

  • Noboru Sueoka
    • 1
  1. 1.Department of Molecular, Cellular, and Developmental BiologyUniversity of ColoradoBoulderUSA

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