Cation valence dependence of hydrogen bond and stacking potentials in DNA mesoscopic models

Maria Izabel Muniz, Adrian H. Bustos, Sofie Slott, Kira Astakhova, Gerald Weber*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review


Monovalent and divalent cations play a crucial role in living cells and for molecular techniques such as PCR. Here we evaluate DNA melting temperatures in magnesium (Mg2+) and magnesium‑potassium (Mg2++ K+) buffers with a mesoscopic model that allows us to estimate hydrogen bonds and stacking interaction potentials. The Mg2+ and Mg2++ K+ results are compared to previous calculations for sodium ions (Na+), in terms of equivalent sodium concentration and ionic strength. Morse potentials, related to hydrogen bonding, were found to be essentially constant and unaffected by cation conditions. However, for stacking interactions we find a clear dependence with ionic strength and cation valence. The highest ionic strength variations, for both hydrogen bonds and stacking interactions, was found at the sequence terminals. This suggests that end-to-end interactions in DNA will be strongly dependent on cation valence and ionic strength.
Original languageEnglish
Article number106949
JournalBiophysical Chemistry
Number of pages10
Publication statusPublished - 2023


  • DNA Mg2 +
  • DNA ion competition
  • Mesoscopic model
  • Peyrard-Bishop model


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