How is a-rna treated by different force fields and salt conditions?


Ivana Beššeová,1,2 Michal Otyepka,1,3 Kamila Réblová1 and Jiří Šponer1


1Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135

612 65, Brno, Czech Republic.

2Gilead Sciences & IOCB Research Center, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí. 2, 166 10, Prague 6, Czech Republic

3Department of Physical Chemistry and Centre for Biomolecular and Complex Molecular Systems, Palacký University, tr. Svobody 26, 771 46 Olomouc, Czech Republic


An extensive molecular dynamics study (totaling 0.6 ms) of three different A-RNA duplexes is presented. We investigated the dependence of the A-RNA geometry on AMBER force fields (Parm99 [1] and Parmbsc0 [2]) and salt strength conditions (0.18 M net-neutralizing Na+ and 0.3 M KCl).

The A-RNA duplexes were more compact when using the Parmbsc0 force field compared to the Parm99. In addition, the Parmbsc0 temporarily reduced α/γ t/t flips. Nevertheless, since the α/γ t/t sub-state occurs to a certain extent in experimental A-RNA structures, we consider both force fields as viable. The effects of the Parmbsc0 force field included visible reduction of the major groove width, increase of the base pair roll, larger helical inclination and small increases of twist. The Parmbsc0 shifted the simulated duplexes more deeply into the A-form. [3]

A narrowing of the deep major groove was observed in excess salt simulations, again accompanied by larger roll, inclination and twist. [3]

The differences between Parm99/lower-salt and Parmbsc0/higher-salt Parmbsc0 conditions were small; nevertheless their cumulation induced visible stabilization of the A-RNA helices. In addition, the effects of the force field and salt conditions were sequence-dependent. Thus, the compactness of A-RNA is sensitive to the sequence and the salt strength which may, for example, modulate the end-to-end distance of the A-RNA helix.

1. J. M. Wang, P. Cieplak and P. A. Kollman, J. Comput. Chem., 21 (2000) 1049–1074.

2. A. Perez, I. Marchan, D. Svozil, J. Sponer, T. E. Cheatham, C. A. Laughton and M. Orozco, Biophys. J., 92 (2007) 3817–3829.

3. I. Besseova, M. Otyepka, K. Reblova and J. Sponer, Phys. Chem. Chem. Phys., 11 (2009) 10701-10711.


Figure 1. A-RNA simulations: ionic conditions influence the major groove width and compactness of the helix.