Calculation of structural behavior of indirect NMR spin-spin couplings in the backbone of nucleic acids
Language English Country United States Media print
Document type Journal Article, Research Support, Non-U.S. Gov't
PubMed
17092041
DOI
10.1021/jp065000l
Knihovny.cz E-resources
- MeSH
- Algorithms * MeSH
- Dinucleoside Phosphates chemistry MeSH
- DNA chemistry MeSH
- Nucleic Acid Conformation MeSH
- Magnetic Resonance Spectroscopy methods MeSH
- RNA chemistry MeSH
- Carbon chemistry MeSH
- Hydrogen chemistry MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Names of Substances
- Dinucleoside Phosphates MeSH
- DNA MeSH
- RNA MeSH
- Carbon MeSH
- Hydrogen MeSH
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.
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