Open AccessMolecular basis of Arginine and Lysine DNA sequence-dependent thermo-stability modulation
Author(s) -
Bernice M. Martin,
Pablo D. Dans,
Miłosz Wieczór,
Núria Villegas,
Isabelle Brun-Heath,
Federica Battistini,
Montserrat Terrazas,
Modesto Orozco
Publication year - 2022
Publication title -
plos computational biology/plos computational biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.628
H-Index - 182
eISSN - 1553-7358
pISSN - 1553-734X
DOI - 10.1371/journal.pcbi.1009749
Subject(s) - lysine , dna , arginine , amino acid , chemistry , molecular dynamics , ion , helix (gastropod) , biophysics , biochemistry , stereochemistry , crystallography , biology , computational chemistry , organic chemistry , ecology , snail
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.