Domain 5 binds near a highly conserved dinucleotide in the joiner linking domains 2 and 3 of a group II intron

Photocrosslinking has identified the joiner between domains 2 and 3 [J(23)] as folding near domain 5 (D5), a highly conserved helical substructure of group II introns required for both splicing reactions. D5 RNAs labeled with the photocrosslinker 4-thiouridine (4sU) reacted with highly conserved nucleotides G₅₈₈ and A₅₈₉ in J(23) of various intron acceptor transcripts. These conjugates retained some ribozyme function with the lower helix of D5 crosslinked to J(23), so they represent active complexes. One partner of the γ · γ' tertiary interaction (A₅₈₇·U₈₈₇) is also in J(23); even though γ·γ' is involved in step 2 of the splicing reaction, D5 has not previously been found to approach γ · γ'. Similar crosslinking patterns between D5 and J(23) were detected both before and after step 1 of the reaction, indicating that the lower helix of D5 is positioned similarly in both conformations of the active center. Our results suggest that the purine-rich J(23) strand is antiparallel to the D5 strand containing U₃₂ and U₃₃. Possibly, the interaction with J(23) helps position D5 correctly in the ribozyme active site; alternatively, J(23) itself might participate in the catalytic center.