Calculation of structural behavior of indirect NMR spin-spin couplings in the backbone of nucleic acids.
Calculated indirect NMR spin-spin coupling constants (J-couplings) between (31)P, (13)C, and (1)H nuclei were related to the backbone torsion angles of nucleic acids (NAs), and it was shown that J-couplings can facilitate accurate and reliable structural interpretation of NMR measurements and help to discriminate between their distinct conformational classes. A proposed stepwise procedure suggests assignment of the J-couplings to torsion angles from the sugar part to the phosphodiester link. Some J-couplings show multidimensional dependence on torsion angles, the most prominent of which is the effect of the sugar pucker. J-couplings were calculated in 16 distinct nucleic acid conformations, two principal double-helical DNAs, B- and A-, the main RNA form, A-RNA, as well as in 13 other RNA conformations. High-level quantum mechanics calculations used a baseless dinucleoside phosphate as a molecular model, and the effect of solvent was included. The predicted J-couplings correlate reliably with available experimental data from the literature.
Sychrovský
Vladimír
V
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic. bohdan@uochb.cas.cz
Vokácová
Zuzana
Z
Sponer
Jirí
J
Spacková
Nad'a
N
Schneider
Bohdan
B
D000465:Algorithms; D002244:Carbon / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D015226:Dinucleoside Phosphates / Q000737:chemistry; D006859:Hydrogen / Q000737:chemistry; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*
D015226:Dinucleoside Phosphates; D012313:RNA; D002244:Carbon; D006859:Hydrogen; D004247:DNA