부산대학교 도서관

We have used a variety of theoretical and experimental techniques to study the role of four basic amino acids–Arginine, Lysine, Ornithine and L-2,4-Diaminobutyric acid–on the structure, flexibility and sequence-dependent stability of DNA. We found that the presence of organic ions stabilizes the duplexes and significantly reduces the difference in stability between AT- and GC-rich duplexes with respect to the control conditions. This suggests that these amino acids, ingredients of the primordial soup during abiogenesis, could have helped to equalize the stability of AT- and GC-rich DNA oligomers, facilitating a general non-catalysed self-replication of DNA. Experiments and simulations demonstrate that organic ions have an effect that goes beyond the general electrostatic screening, involving specific interactions along the grooves of the double helix. We conclude that organic ions, largely ignored in the DNA world, should be reconsidered as crucial structural elements far from mimics of small inorganic cations. Author summary: Over time, scientists have proposed many different theories for the "biomolecular" origin of life. The best-known theory is the "Prebiotic or primordial soup" theory hypothesized in 1924. In this theory, nucleic acids and protein-like molecules (among others) were created from their building blocks in an aqueous environment that was supposed to be dense and enriched in organic cations and without the help of enzymatic machinery. In particular, the primordial soup was supposed to be enriched in basic, proteinogenic (Arg and Lys) and non-proteinogenic (Orn and DABA), amino acids. In such conditions, self-replication of DNA molecules was thought to occur through heat/cold cycles of duplex melting/renaturing, a process that only could have been efficient if the relative stability of AT- and GC-rich duplexes were to be similar (in contrast to what happens in normal dilute physiological conditions). Through the combination of experiments and computational simulations, we found conditions compatible with prebiotic times, where the difference in stability between AT- and GC-rich duplexes is reduced by 20 degrees in amino acids-rich solutions compared to dilute control conditions, a requirement for the self-replication of nucleic acids, the only mechanism for copying DNA information available in that early times. [ABSTRACT FROM AUTHOR]