Crystal structure of an adenine bulge in the RNA chain of a DNA·RNA hybrid, d(CTCCTCTTC)·r(gaagagagag)

Abstract Crystal structure of a DNA·RNA hybrid, d(CTCCTCTTC)·r(gaagag a gag), with an adenine bulge in the polypurine RNA strand was determined at 2.3 A resolution. The structure was solved by the molecular replacement method and refined to a final R -factor of 19.9 % ( R free 22.2 %). The hybrid duplex crystallized in the space group I 222 with unit cell dimens ions, a = 46.66 A, b = 47.61 A and c = 54.05 A, and adopts the A -form conformation. All RNA and DNA sugars are in the C3′- endo conformation, the glycosyl angles in anti conformation and the majority of the C4′-C5′ torsion angles in g+ except two trans angles, in conformity with the C3′- endo rigid nucleotide hypothesis. The adenine bulge is looped out and it is also in the anti C3′- endo conformation. The bulge is involved in a base-triple (C·g) ∗ a interaction with the end base-pair (C9·g10) in the minor groove of a symmetry-related molecule. The 2′ hydroxyl group of g15 is hydrogen bonded to O2P and O5′ of g17, skipping the bulged adenine a16 and stabilizing the sugar-phosphate backbone of the hybrid. The hydrogen bonding and the backbone conformation at the bulged adenine site is very similar to that found in the crystal structure of a protein-RNA complex.