Conformational analysis of a hybrid DNA-RNA double helical oligonucleotide in aqueous solution: d(CG)r(CG)d(CG) studied by 1D- and 2D-1H NMR spectroscopy.

The double helical structure of the self-complementary DNA-RNA-DNA hybrid d(CG)r(CG) d(CG) was studied in solution by 500 MHz1H-NMR spectroscopy. The non-exchangeable base protons and the (deoxy)ribose H1', H2' and H2'' protons were unambiguously assigned using 2D-J-correlated (COSY) and 2D-NOE (NOESY) spectroscopy techniques. A general strategy for the sequential assignment of 1H-NMR spectra of (double) helical DNA and RNA fragments by means of 2D-NMR methods is presented. Conformational analysis of the sugar rings of d(CG)r(CG)d(CG) at 300 K shows that the central ribonucleotide part of the helix adopts an A-type double helical conformation. The 5'- and 3'-terminal deoxyribose base pairs, however, take up the normal DNA-type conformation. The A-to-B transition in this molecule involves only one (deoxyribose) base pair. It is shown that this A-to-B conformational transition can only be accommodated by two specific sugar pucker combinations for the junction base pair, i.e. N.S (C3'-endo-C2'-endo, 60%, where the pucker given first is that assigned to the junction nucleotide residue of the strand running 5'----3' from A-RNA to B-DNA) and S.S (C2'-endo-C2'-endo, 40%).