The new loop-loop interactions between the peripheral domains and three-dimensional model of Tetrahymena group I intron.

Abstract

The long-range interactions between the peripheral domains of Tetrahymena group I intron were studied by NMR. The 20mer RNA contained the 9.1a loop region (AUGCAA) and the 17mer RNA contained the 2.1 loop region (AGAUUGC) were synthesized and studied by NMR. They form both hairpin structures at low NaCl concentration. The 20mer RNA forms dimer by loop-loop interaction, while the 17mer RNA is monomer. On the addition of the 17mer to the 20mer, the new imino proton signals induced by the interaction between the 9.1a and 2.1 loops were not observed. It is found that the 9.1a loop-loop interaction (GCAA-GCAA) with two base pairs prefers to that between the 9.1a and 2.1 loops (GCAA-UUGC) with four base pairs. By my model of intact folding structure containing A-minor tertiary interaction and the compared with sequence, it is presumed that the 9.1a loop does not bind to the 2.1 loop, but to the 5c loop (UGCAA), while the 2.1 loop binds to 3' exon (UAA).