NMR assignments and solution conformation of the DNA · RNA hybrid duplex d(GTGAACTT) · r(AAGUUCAC)

Nearly complete assignments of the ¹H‐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°, whereas those in the RNA strand are in the range –140° to –160°. 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 10bp/turn on average. This implies a helical structure in the A family of conformations.