CONFORMATION OF AN RNA MOLECULE THAT MODELS THE P4 P6 JUNCTION FROM GROUP-I INTRONS/

We present a three-dimensional structure of a 34-nucleotide RNA molecu le determined by NMR spectroscopy, The molecule was designed to form a junction between two double-helical stems whose sequence was based on the P4/P6 domain from group I introns. There are 5' and 3' single-str and overhangs at the junction of the stems. Contrary to our expectatio ns, we found that the 3' end of the molecule is placed in the minor an d not the major groove of the P4 helix. As a result of tertiary contac ts and stacking interactions from nucleotides in the 3' end, the junct ion helices are rotated in a left-handed fashion and do not stack coax ially. This conformation is highly dependent on the presence of single -stranded nucleotides at the 3' overhang. When the 3' end is removed, the molecule assumes a radically different structure with the 5' end i n the minor groove of the P6 helix and an overall right-handed rotatio n between the stems. Only one nucleotide at the 3' end is sufficient t o change the energy of the junction.