An. Lane et al., NMR ASSIGNMENTS AND SOLUTION CONFORMATION OF THE DNA . RNA HYBRID DUPLEX D(GTGAACTT) . R(AAGUUCAC), European journal of biochemistry, 215(2), 1993, pp. 297-306
Nearly complete assignments of the H-1-NMR spectrum of the DNA . RNA h
ybrid 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 s
pectra showed that the sugars in the DNA strand are predominantly in t
he S domain of puckers, whereas the ribofuranoses are mainly C3'-endo.
Analysis of time-dependent NOE intensities from one- and two-dimensio
nal experiments showed that the glycosidic torsion angles in the DNA s
trand are near -120-degrees, whereas those in the RNA strand are in th
e range -140-degrees to -160-degrees. These nucleotide conformations c
orrespond to those typically found in B-DNA and A-RNA, respectively. T
he 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 e
xperimentally determined conformations. A subset of these structures w
as 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 a
verage. This implies a helical structure in the A family of conformati
ons.