STRUCTURE OF A U-CENTER-DOT-U PAIR WITHIN A CONSERVED RIBOSOMAL-RNA HAIRPIN

A conserved hairpin corresponding to nt 1057-1081 of large subunit rRN A (Escherichia coli numbering) is part of a domain targeted by antibio tics and ribosomal protein L11. The stem of the hairpin contains a U . U juxtaposition, found as either U . U or U . C in virtually all rRNA sequences, This hairpin has been synthesized and most of the aromatic and sugar protons were assigned by two-dimensional proton NMR. Distan ces and sugar puckers deduced from the NMR data were combined with res trained molecular dynamics calculations to deduce structural features of the hairpin, The two U residues are stacked in the helix, form one NH3-O4 hydrogen bond and require an extended backbone conformation (tr ans alpha and gamma) at one of the U nucleotides. The hairpin loop, UA GAAGC closed by a U-A pair, is the same size as tRNA anticodon loops, but nea as well ordered.