Structure of an RNA hairpin from HRV-14

The 5 ' noncoding region of the picornaviral genome begins with a cloverlea f which is required for viral replication, due at least in part to an inter action with the viral RNA polymerase as part of a fusion with the predomina nt viral protease, The necessary region of the cloverleaf has previously be en narrowed to a highly conserved stem-loop. The solution structure of a 14 -nucleotide RNA hairpin, which is part of the conserved stem-loop from huma n rhinovirus isotype 14, is presented here. The secondary structure of the hairpin is identical to predictions: a five base pair stem is bounded by a triloop with sequence UAU. However, the fold of the triloop is novel, with stacking of the second loop base onto the closing base pair of the stem, an d deviations from A form geometry are introduced into the stem regions bord ering the triloop, particularly on the 3 ' side. These deviations and the a ssociated triloop structure could help to explain the distinct sequence con servation and mutational analysis data observed for the stem region of the hairpin, as compared to a second sequentially similar stem in the intact st em-loop.