Replication elongates short DNA, reduces sequence bias and develops trimer structure

The origin of molecular evolution required the replication of short oligonucleotides to form longer polymers. Prebiotically plausible oligonucleotide pools tend to contain more of some nucleobases than others. It has been unclear whether this initial bias persists and how it affects replication. To investigate this, we examined the evolution of 12-mer biased short DNA pools using an enzymatic model system. This allowed us to study the long timescales involved in evolution, since it is not yet possible with currently investigated prebiotic replication chemistries. Our analysis using next-generation sequencing from different time points revealed that the initial nucleotide bias of the pool disappeared in the elongated pool after isothermal replication. In contrast, the nucleotide composition at each position in the elongated sequences remained biased and varied with both position and initial bias. Furthermore, we observed the emergence of highly periodic dimer and trimer motifs in the rapidly elongated sequences. This shift in nucleotide composition and the emergence of structure through templated replication could help explain how biased prebiotic pools could undergo molecular evolution and lead to complex functional nucleic acids. Graphical Abstract

Automated summary

The initial nucleotide bias in short DNA pools disappears after isothermal replication, but the nucleotide composition at each position in the elongated sequences remains biased, with variations depending on the position and initial bias. Highly periodic dimer and trimer motifs emerge in the rapidly elongated sequences. These findings are important for understanding how biased prebiotic pools undergo molecular evolution and give rise to complex functional nucleic acids.