  Ion-mediated interaction is critical to the structure and stability of
nucleic acids. Recent experiments suggest that the multivalent ion-induced
aggregation of double-stranded (ds) RNAs and DNAs may strongly depend on the
topological nature of helices, while there is still lack of an understanding on
the relevant ion-mediated interactions at atomistic level. In this work, we
have directly calculated the potentials of mean force (PMF) between two dsRNAs
and between two dsDNAs in Cobalt Hexammine ion (Co-Hex) solutions by the
atomistic molecular dynamics simulations. Our calculations show that at low
[Co-Hex], the PMFs between B-DNAs and between A-RNAs are both (strongly)
repulsive.However, at high [Co-Hex], the PMF between B-DNAs is strongly
attractive, while those between A-RNAs and between A-DNAs are still (weakly)
repulsive. The microscopic analyses show that for A-form helices, Co-Hex would
become internal binding into the deep major groove and consequently cannot form
the evident ion-bridge between adjacent helices, while for B-form helices
without deep grooves, Co-Hex would exhibit external binding to strongly bridge
adjacent helices. In addition, our further calculations show that, the PMF
between A-RNAs could become strongly attractive either at very high [Co-Hex] or
when the bottom of deep major groove is fixed with a layer of water.
