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

Abstract

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 R_work/R_free 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 R_work/R_free 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.