Crystal structure of an adenine bulge in the RNA chain of a DNA center dotRNA hybrid, d(CTCCTCTTC)center dot r(gaagag(a)under-bargag)

Crystal structure of a DNA RNA hybrid, d(CTCCTCTTC) . r(gaagagagag), with a n adenine bulge in the polypurine RNA strand was determined at 2.3 Angstrom resolution. The structure was solved by the molecular replacement method a nd refined to a final X-factor of 19.9 % (R-free 22.2 %). The hybrid duplex crystallized in the space group I222 with unit cell dimensions, a = 46.66 Angstrom, b = 47.61 Angstrom and c = 54.05 Angstrom; 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' torsio n angles in gf except two tuans angles, in conformity with the C3'-endo rig id 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 backb one conformation at the bulged adenine site is very similar to that found i n the crystal structure of a protein-RNA complex. (C) 2000 Academic Press.