RNA Captures More Cations than DNA: Insights from Molecular Dynamics Simulations

• DOI: 10.1021/acs.jpcb.2c04488
• Publication Date: 2022-10-19T19:42:19Z
• Authors: Sergio Cruz-León; Nadine Schwierz
• Keywords: Biomolecule; Divalent; Valency; Nucleic acid structure; DNA condensation

The distribution of cations around nucleic acids is essential for a broad variety processes ranging from DNA condensation and RNA folding to the detection biomolecules in biosensors. Predicting exact ions remains challenging since and, hence, acid properties depend on salt concentration, valency ions, ion type. Despite importance, general theory quantify ion-specific effects highly charged still lacking. Moreover, recent experiments reveal that despite their similar building blocks, duplexes can react differently same ionic conditions. aim our current work provide comprehensive set molecular dynamics simulations using more than 180 μs simulation time. For mono- divalent Li+, Na+, K+, Cs+, Ca2+, Sr2+, Ba2+, allow us distributions binding patterns duplexes. microscopic insights display origin ion-specificity shed light question why show opposing behavior Finally, detailed capture DNA.