The stem hairpin loop structure of p2Sp1 RNA is required for RNA-cleaving activity

We studied the hairpin-loop structure of an RNA fragment (GUUUCGUACAAAC) (R 13) with the sequence corresponding to the self-cleavage domain in the prec ursor of an RNA molecule from bacteriophage T4-infected Escherichia coli ce lls (p2Sp1 RNA). In order to determine the influence of the hairpin-loop st ructure on these sequence-specific cleavage reactions, we have synthesized oligoribonucleotides containing hairpin-loop, double-helical stem-loop, and single-stranded RNA structures. The cleavage was affected by the hairpin-l oop structure. Furthermore, the helix-stem, which retains the thermodynamic ally extrastable stem hairpin-loop structures, is also important for the cl eavage activity. However, the thermodynamically extrastable helix-stem stru cture reduced the cleavage activity of the adjacent UA and CA sequences at the helix-stem site. For the cleavage reactions of the RNA cleavage product s, the R6 (ACAAAC), R7 (GUUUCGU), and R9 (GUUUCGUAC) mers from the parent R NA, R13 (GUUUCGUACAAAC), a very slight amount of cleavage product (2%) from the RNA 9 was observed, but no reaction occurred for the R6 and R7. We als o describe the influences of the sequences (UA and CA) on the cleavage acti vity. (C) 1999 Elsevier Science B.V. All rights reserved.