(3)J(C2/4-H1') and (3)J(C6/8-H1') scalar spin-spin coupling constants have been calculated for deoxyadenosine, deoxyguanosine, deoxycytidine, and deoxythymidine as functions of the glycosidic torsion angle chi by means of density functional theory. Except for deoxythymidine, (3)J(C2/4-H1') depends little on the base type. On the contrary, (3)J(C6/8-H1') follows the usual trans to cis ratio ((3)J(C-H(cis)) < (3)J(C-H(trans))) for purine nucleosides, but reveals the opposite relation ((3)J(C-H(cis)) > (3)J(C-H(trans))) for pyrimidine nucleosides. Our results compare well with the experiment for deoxyguanosine and predict a novel trend in the case of pyrimidine bases for which no NMR results are available in the syn region. A breakdown of the key Fermi contact part of (3)J(C6/8-H1') into MO contributions rationalizes this trend in terms of an unusual coupling mechanism in the syn orientation that is very effective for pyrimidine nucleosides and considerably weaker for purine nucleosides.

National Centre for Biomolecular Research Faculty of Science Masaryk University Kotlárská 2 CZ 611 37 Brno Czech Republic

References provided by Crossref.org

Revisiting the planarity of nucleic acid bases: Pyramidilization at glycosidic nitrogen in purine bases is modulated by orientation of glycosidic torsion

Experiments for correlating quaternary carbons in RNA bases