DNA thermodynamic pressure: A potential contributor to genome evolution

Mirko J. Zimic, Daniel Guerra, Jorge Arévalo

Research output: Contribution to journalArticlepeer-review

Abstract

Codon usage bias is a feature of living organisms. The origin of this bias might be explained not only by external factors but also by the nature of the structure of deoxyribonucleic acid (DNA) itself. We have developed a point mutation simulation program of coding sequences, in which nucleotide replacement follows thermodynamic criteria. For this purpose we calculated the hydrogen bond-like and electrostatic energies of non-canonical base pairs in a 5 bp neighbourhood. Although the rate of non-canonical base pair formation is extremely low, such pairs occur with a preference towards a guanine (G) or cytosine (C) rather than an adenine (A) or thymine (T) replacement due to thermodynamic considerations. This feature, according to the simulation program, should result in an increase in the GC content of the genome over evolutionary time. In addition, codon bias towards a higher GC usage is also predicted. DNA sequence analysis of genes of the Trypanosomatidae lineage supported the hypothesis that DNA thermodynamic pressure is a driving force that impels increases in GC content and GC codon bias.

Original languageEnglish (US)
Pages (from-to)S15
JournalTransactions of the Royal Society of Tropical Medicine and Hygiene
Volume96
Issue numberSUPPL. 1
DOIs
StatePublished - 2002
Externally publishedYes

Keywords

  • Codon usage bias
  • Crithidia fasciculata
  • DNA thermodynamic pressure
  • Genome evolution
  • Leishamania chagasi
  • Leishmania donovani
  • Leishmaniasis
  • Trypanosoma brucei
  • Trypanosoma cruzi
  • Trypanosomiasis

ASJC Scopus subject areas

  • Parasitology
  • Public Health, Environmental and Occupational Health
  • Infectious Diseases

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