Abstract
Base pairing between the 5′ end of U1 snRNA and
the conserved 5′ splice site of pre-mRNA is important
for commitment complex formation in vitro. However, the
biochemical mechanisms by which pre-mRNA is initially recognized
by the splicing machinery is not well understood. To evaluate
the role of this base pairing interaction, we truncated
U1 snRNA to eliminate the RNA–RNA interaction and
surprisingly found that U1 snRNP can still form a nearly
normal RNA–protein complex and maintain sequence
specificity. We propose that some feature of U1 snRNP,
perhaps one or more protein factors, is more important
than the base pairing for initial 5′ splice site
recognition. In addition, at least five sets of interactions
contribute to complex formation or stability. Only one
of these is base pairing between the 5′ splice site
and the 5′ end of U1 snRNA, without which the U1
snRNP–pre-mRNA complex is less stable and has a somewhat
altered conformation.