NMR ASSIGNMENTS AND SOLUTION CONFORMATION OF THE DNA . RNA HYBRID DUPLEX D(GTGAACTT) . R(AAGUUCAC)

Nearly complete assignments of the H-1-NMR spectrum of the DNA . RNA hybrid d(GTGAACTT) . r(AAGUUCAC) have been obtained by two-dimensional methods. Three-bond coupling constants measured from cross-sections of two-dimensional NOE spectra and double quantum-filtered correlation spectra showed that the sugars in the DNA strand are predominantly in the S domain of puckers, whereas the ribofuranoses are mainly C3'-endo. Analysis of time-dependent NOE intensities from one- and two-dimensional experiments showed that the glycosidic torsion angles in the DNA strand are near -120-degrees, whereas those in the RNA strand are in the range -140-degrees to -160-degrees. These nucleotide conformations correspond to those typically found in B-DNA and A-RNA, respectively. The circular dichroism of the duplex is similar to that of A-form RNA, consistent with a global A-like conformation. A large number of duplex structures was generated in which the nucleotides were fixed in the experimentally determined conformations. A subset of these structures was found that satisfied the internucleotide NOE intensities, backbone constraints and had acceptable Lennard-Jones energies. The base pairs in the duplex were found to have positive inclinations, a translation (Dx) of about 0.4 nm from the helix axis, and more than 10 bp/tum on average. This implies a helical structure in the A family of conformations.