Molecular basis of Arginine and Lysine DNA sequence-dependent thermo-stability modulation

• Published in: PLoS computational biology Vol. 18; no. 1; p. e1009749
• Main Authors: Martin, Benjamin, Dans, Pablo D., Wieczór, Milosz, Villegas, Nuria, Brun-Heath, Isabelle, Battistini, Federica, Terrazas, Montserrat, Orozco, Modesto
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.01.2022; Public Library of Science (PLoS)
• Subjects: Abiogenesis; Amino acids; Amino Acids, Basic - analysis; Amino Acids, Basic - chemistry; Aminobutyrates - chemistry; Base Composition; Base Sequence; Biology and Life Sciences; Cations; Deoxyribonucleic acid; DNA; DNA - analysis; DNA - chemistry; DNA biosynthesis; DNA sequencing; Eigenvalues; Electrostatic properties; Experiments; Gene expression; Grooves; Hydrogen bonds; Hypotheses; Ions; Lysine; Methods; Molecular Dynamics Simulation; Nucleotide sequence; Nucleotide sequencing; Origin of Life; Ornithine; Physical Sciences; Physiological aspects; Prebiotics; Proteins; Simulation; Structural members; Thermodynamics; United States
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.1009749

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.