NMR parameters in RNA molecules and their correlation with molecular structure
Zuzana Vokáčová, Bohdan Schneider and Vladimír Sychrovský
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 166 10 Praha
Structure of nucleic acids (NAs) is described by several structural parameters: six torsion angles (a, b, g, d, e, z) in the backbone, sugar conformation (C2’-endo or C3’-endo), and glycosidic torsion angle (c) which designate orientation of nitrogenous base relative to sugar moiety.
We studied correlation between NMR parameters and the local architecture of distinct patterns of RNA dinucleotides.
Model compounds of RNA were studied by quantum chemistry calculation methods with the aim to obtain NMR shifts and spin-spin coupling constants. We used different atomic bases Iglo II or Iglo III and water solvent was modeled by the PCM method. Calculated NMR parameters, in particular the J-couplings, were correlated with the structure of RNA dinucleotides. In addition we monitored influence of nitrogenous bases on J-coupling in the backbone.
The three bond J-coupling constants can be used for the determination of torsion angles. Our calculations were compared with available data from the literature as well as with empirical Karplus curves [1, 2].
The torsion angles can be naturally grouped according to their similar correlation with relevant NMR parameters: a with z, b with e, and g with d. Torsions b and e can be determined by the coupling constants of the type 3J(C,P) and 3J(H,P) which are frequently measured. Torsion angles g and d can be correlated with the 3J(H,H), 3J(H,C) coupling constants. Torsions a and z can’t be associated with any three-bond coupling constants that would unequivocally describe their values but we were able to identity their weak correlation with the two bond coupling constants 2J(C,P).
1. Karplus, M., Contact electron-spin coupling of nuclear magnetic moments. J. Chem. Phys., 1959. 30: p. 11-15.
2. Marino, J.P., H. Schwalbe, and C. Griesinger, J-coupling restraints in RNA structure determination. Accounts of Chemical Research, 1999. 32(7): p. 614-623.