NUCLEAR pre-messenger RNA splicing requires the action of five small nuclear (sn) RNAs, Ul, U2, U4, US and U6, and more than 50 proteins 1,2. The mechanistic similarity of nuclear pre-mRNA splicing and group II self-splicing suggests that many of the central processes of nuclear pre-mRNA splicing are based on RNA-RNA interactions3,4. To understand the mechanism of pre-mRNA splicing, the interactions, and their temporal relationships, that occur between the snRNAs and the pre-mRNA during splicing must be identified. Several snRNA-snRNA5-9 and snRNA-intron 9-12 interactions have been demonstrated but the putative RNA-based interactions that recognize the AG dinucleotide at the 3′ splice site during 3′ cleavage and exon ligation are unknown. We report here the reciprocal suppression between 5′ and 3′ splice site mutations in the yeast actin intron, and propose that the 3′ splice site is positioned for 3′ cleavage and exon ligation, at least in part, through a non-Watson-Crick interaction between the guanosines at the 5′ and 3′ splice sites.