Crystal structure of an RNA octamer duplex r(CCCIUGGG)2 incorporating tandem I·U wobbles

Abstract

The crystal structure of the RNA octamer duplex r(CCCIUGGG)2 has been elucidated at 2.5 Å resolution. The crystals belong to the space group P21 and have unit cell constants a = 33.44 Å, b = 43.41 Å, c = 49.39 Å and β = 104.7°with three independent duplexes (duplexes 1-3) in the asymmetric unit. The structure was solved by the molecular replacement method and refined to an R(work)/R(free) of 0.185/0.243 using 3765 reflections between 8.0 and 2.5 Å. This is the first report of an RNA crystal structure incorporating I·U wobbles and three molecules in the asymmetric unit. Duplex 1 displays a kink of 24°between the mismatch sites, while duplexes 2 and 3 have two kinks each of 19°and 27°, and 24°and 29°, respectively, on either side of the tandem mismatches. At the I·U/U·I mismatch steps, duplex 1 has a twist angle of 33.9°, close to the average for all base pair steps, but duplexes 2 and 3 are underwound, with twist angles of 24.4°and 26.5°, respectively. The tandem I·U wobbles show intrastrand purine-pyrimidine stacking but exhibit interstrand purine-purine stacking with the flanking C·G pairs. The three independent duplexes are stacked non-coaxially in a head-to-tail fashion to form infinite pseudo-continuous helical columns which form intercolumn hydrogen bonding interactions through the 2'-hydroxyl groups where the minor grooves come together.