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

The crystal structure of the RNA octamer duplex r(CCCIUGGG)(2) has been elu cidated at 2.5 Angstrom resolution, The crystals belong to the space group P2(1) and have unit cell constants a = 33.44 Angstrom, b = 43.41 Angstrom, c = 49.39 Angstrom and beta = 104.7 degrees with three independent duplexes (duplexes 1-3) in the asymmetric unit, The structure was solved by the mol ecular replacement method and refined to an R-work/R-free of 0.185/0.243 us ing 3765 reflections between 8.0 and 2.5 Angstrom. 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 degrees between the mismatch sites, while duplexes 2 and 3 have two kinks each of 19 degrees an d 27 degrees, and 24 degrees and 29 degrees, respectively, on either side o f the tandem mismatches. At the I.U/U.I mismatch steps, duplex 1 has a twis t angle of 33.9 degrees, close to the average for all base pair steps, but duplexes 2 and 3 are underwound, with twist angles of 24.4 degrees and 26.5 degrees, respectively, The tandem I.U wobbles show intrastrand purine-pyri midine stacking but exhibit interstrand purine-purine stacking with the fla nking C.G pairs. The three independent duplexes are stacked non-coaxially i n a head-to-tail fashion to form infinite pseudocontinuous helical columns which form intercolumn hydrogen bonding interactions through the 2'-hydroxy l groups where the minor grooves come together.