DNA thermodynamic pressure: A potential contributor to genome evolution

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Zimic M.J.
Guerra D.
Arévalo J.
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Royal Society of Tropical Medicine and Hygiene
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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.
This work was supported by a grant from CONCYTEC. We are very grateful to Holger Valqui and Oscar Moran for their critical comments, and to ClaudiaMachicado and Jose Choufor their comments and help in compiling and analysing part of the DNA sequences that support this work. Thanks also to Arman- do Bernui, Javier Espinoza, Jairzhinho Ramos, Luis Marky and Cristian Orrego, for their contribution to discussions, and especially to Mrs Ellen M. Pragen for her editorial work.
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thymine, adenine, cytosine, guanine, protozoal DNA, protozoal DNA