Crystal structures of two forms of a 14-mer RNA/DNA chimer duplex with double UU bulges: A novel intramolecular U*(A center dot U) base triple

The RNA/DNA 14-mer, (gguauuucgguaCc)(2) with consecutive uridine bulges (un derlined) on each strand has been determined in two crystal forms, spermine bound (Sp-form) and spermine free (Sp-free). The former was solved by the MAD method with three-wavelength data collected at Brookhaven National Labo ratory (BNL); the later isomorphous structure was solved by the molecular r eplacement method using data collected on our Raxis IIc imaging plate syste m. The two crystal forms belong to the space group C2 with one molecule of double-stranded 14 mer in the asymmetric unit. The Sp-form has cell constan ts, a = 60.06, b = 29.10, C = 52.57 Angstrom, beta = 120.79 degrees and was refined to 1.7 Angstrom resolution with a final R-work/R-free of 19.8%/22. 7% using 8,549 independent reflections. The Sp-free structure has cell cons tants, a = 60.06, b = 29.58, c = 52.50 Angstrom, beta = 120.85 degrees and was refined to 1.8 Angstrom with a final R-work/R-free of 20.8%/23.2% using 6,285 unique reflections. The two structures are identical, except that th e Sp-form has a spermine bound in the major groove, parallel to the RNA hel ical axis. One of the uridine bulges forms a novel intramolecular U*(A(.)U) base triple. The helices are in the C3'-endo conformation (A-form), but th e bulges adopt the C2'-endo sugar pucker. Furthermore, the bulges induce a kink (30 degrees) in the helix axis and a very large twist (55 degrees) bet ween the base pairs flanking the bulges. The Sp-form has one Mg2+ ion where as the Sp-free form has two Mg2+ ions.