BASE-PAIRING INTERACTIONS INVOLVING THE 5' AND 3'-TERMINAL NUCLEOTIDES OF GROUP-II SELF-SPLICING INTRONS

By combining comparative sequence analyses and nucleotide replacements, we show that formation of the active center of group II introns rests in part on two novel long-range base-pairing interactions. (1) The last nucleotide of group II introns forms a solitary Watson-Crick base-pair with one of the nucleotides in the short sequence stretch connecting domains II and III. Formation of this base-pair is rate-limiting for the 3′ cleavage and ligation step. (2) Nucleotides 3 and 4 form base-pairs with two consecutive nucleotides in a well-conserved internal loop of domain I. This interaction is involved in both the 5′ and 3′ cleavage steps. Possible relationships between group II and nuclear pre-mRNA introns are reassessed by taking into account these new pieces of information. © 1990 Academic Press Limited.