Structure and dynamics of the ApA, ApC, CpA, and CpC RNA dinucleoside monophosphates resolved with NMR scalar spin-spin couplings

The Journal of Physical Chemistry. B
Zuzana VokácováVladimír Sychrovský

Abstract

The measured NMR scalar coupling constants (J-couplings) in the XpY, (X,Y = adenine (A) or cytosine (C)) RNA dinucleoside monophosphates (DMPs) were assigned to the backbone (alpha, beta, gamma, delta, epsilon, zeta) and glycosidic (chi) torsion angles in order to resolve the global structure of the DMP molecules. The experimental J-couplings were correlated with the theoretical J-couplings obtained as the dynamical averages of the Karplus equations relevant to the torsion angles. The dynamical information was captured using the molecular dynamics (MD) calculation method. The individual conformational flexibility of the four DMP molecules was thus consistently probed with the NMR J-couplings. The calculated structure and flexibility of the DMP molecules depend on the sequence considered with respect to the 5' and 3' end of the DMP molecules (5'-XpY-3'). The dynamical characteristics of the two nucleosides are not equivalent even for the ApA and CpC homologues. An enhancement of the sampling in the MD calculations was achieved using five different starting structural motives classified previously for the RNA backbone in the solid phase (Richardson et al. RNA 2008, 14, 465-481). The initial structures were selected on the basis o...Continue Reading

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