The RNA/DNA 14-mer, (gguauuucgguaCc)2 with
consecutive uridine bulges (underlined) 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
Laboratory (BNL); the later isomorphous structure was solved
by the molecular replacement method using data collected on
our Raxis IIc imaging plate system. 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 constants, a = 60.06, b = 29.10, c = 52.57 Å, β
= 120.79° and was refined to 1.7 Å resolution with
a final Rwork/Rfree of 19.8%/22.7% using
8,549 independent reflections. The Sp-free structure has cell
constants, a = 60.06, b = 29.58, c = 52.50 Å, β =
120.85° and was refined to 1.8 Å with a final
Rwork/Rfree of 20.8%/23.2% using 6,285
unique reflections. The two structures are identical, except
that the Sp-form has a spermine bound in the major groove, parallel
to the RNA helical axis. One of the uridine bulges forms a novel
intramolecular U*(A[bull ]U) base triple. The helices are in the
C3′-endo conformation (A-form), but the bulges adopt the
C2′-endo sugar pucker. Furthermore, the bulges induce
a kink (30°) in the helix axis and a very large twist (55°)
between the base pairs flanking the bulges. The Sp-form has one
Mg2+ ion whereas the Sp-free form has two Mg2+
ions.