Structure and Dynamics of the ApA, ApC, CpA and CpC RNA Dinucleoside Monophosphates Resolved with NMR Scalar Spin-Spin Couplings

Zuzana Vokáčová^1,2, Bohdan Schneider¹, Miloš Buděšínský¹, Ivan Rosenberg¹, Jiří Šponer³ and Vladimír Sychrovský¹

¹Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Flemingovo sq. 2, 166 10 Prague, Czech Republic, ²Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 3, 121 16 Praha 2, Czech Republic, ³Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic,

Functional diversity of nucleic acids (NAs) makes their study crucial for deeper understanding of many essential biological processes. Basic structural parameters of NAs are the α, β, γ, δ, ε, ζ backbone torsion angles and the glycosidic torsion angle χ (Figure 1).

In our previous study we correlated the calculated NMR indirect spin-spin coupling constants (J-couplings) with the backbone torsion angles of ribosomal RNA.¹ Each RNA structural pattern was shown to be in principle detectable with specific magnitudes of specific J-couplings assigned to the backbone torsions.¹

In the present study we correlated the J-couplings measured in the ApA, ApC, CpA and CpC RNA dinucleoside monophosphates with the calculated ones. Since the four RNA molecules are higly flexible we used the molecular dynamics (MD) for modeling their dynamical behavior, particularly to sample the motions for the torsion angles (Figure 1). The calculated J-couplings were obtained as the dynamically averaged Karplus equations with distributions of the torsion angles modelled with MD. Other structural features, like the rate of base stacking, evolution and mutual coupling of torsional motions were also analyzed including their dependence on sequence of the four RNA molecules.

Acknowledgement: This work was supported by the IAA400550701Grant Agency of the Czech Academy of Sciences, by the HFSP Grant (VS) and by the Grant Agency of Charles University in Prague (ZV).

[1] Sychrovský, Vokáčová, Šponer, Špačková, Schneider Journal of Physical Chemistry B 110, 45 22894-22902, 2006

[2] Vokáčová, Schneider, Buděšínský, Roesenberg, Šponer, Sychrovský Journal of Physical Chemistry B, 2008 in print