Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Multivalent ion-mediated nucleic acid helix-helix interactions: RNA
  versus DNA   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.

10
The categories of this paper are: q-bio
14
The categories of this paper are: math-ph
23
The categories of this paper are: solv-int
32
The categories of this paper are: atom-ph
15
The categories of this paper are: nucl-ex
0
The categories of this paper are: hep-ph
16
The categories of this paper are: stat
37
The categories of this paper are: supr-con
34
The categories of this paper are: chem-ph
30
The categories of this paper are: q-alg
31
The categories of this paper are: ao-sci
20
The categories of this paper are: acc-phys
6
The categories of this paper are: astro-ph
36
The categories of this paper are: cmp-lg
28
The categories of this paper are: alg-geom
12
The categories of this paper are: nucl-th