Nucleoside triples from the group I intron.

Oligonucleotides modeled on a proposed base-triple domain in the P4/P6 region of the self-splicing group I intron have been characterized by NMR. The NMR data indicate that single-stranded nucleotides in this domain are in the minor groove of an adjacent helix within hydrogen bonding distance of 2'-hydroxyl groups in an interaction we term a nucleoside triple. Oligonucleotides containing the two most frequently occurring sequences among group I introns in the P4/P6 region formed nucleoside triples in the minor groove, whereas oligonucleotides containing sequences which are not conserved did not form triples. Surprisingly, the structures of the nucleoside triples in the oligonucleotides containing the two most frequently occurring sequences are different. If this difference were maintained in the context of the whole intron, it would suggest that the triples are not directly involved in catalysis, but rather that the nucleoside triples function by aligning the helical domains within the catalytic core of the intron.