DNA thermodynamic pressure: a potential contributor to genome evolution.

Area of Science:

• Genetics
• Molecular Biology
• Bioinformatics

Background:

• Codon usage bias is a known characteristic of organisms.
• The origins of this bias may stem from internal deoxyribonucleic acid (DNA) structural properties, not solely external factors.

Purpose of the Study:

• To investigate the role of DNA's intrinsic thermodynamic properties in shaping codon usage bias.
• To simulate point mutations based on thermodynamic criteria and predict their impact on genome composition.

Main Methods:

• Developed a point mutation simulation program for coding sequences.
• Calculated hydrogen bond-like and electrostatic energies of non-canonical base pairs within a 5 base pair (bp) neighborhood.
• Analyzed DNA sequences of genes from the Trypanosomatidae lineage.

Main Results:

• Simulations indicated a thermodynamic preference for guanine (G) or cytosine (C) nucleotide replacements, despite the low rate of non-canonical base pair formation.
• The simulation predicted an increase in genomic GC content and GC codon bias over evolutionary time.
• Analysis of Trypanosomatidae genes supported the hypothesis that DNA thermodynamic pressure drives GC content and codon bias increases.

Conclusions:

• DNA's intrinsic thermodynamic properties act as a significant driving force in genome evolution.
• Thermodynamic pressure favors GC-rich sequences, leading to increased GC content and codon usage bias in genomes.
• The findings provide a new perspective on the evolutionary mechanisms shaping genome composition.