Purine-rich exonic splicing enhancers (ESEs) have
been identified in many alternatively spliced exons. Alternative
splicing of several ESE-containing exons has been shown
to depend on subsets of the SR protein family of pre-mRNA
splicing factors. In this report, we show that purified
SR protein family member SRp55 by itself binds a 30-nt
ESE-containing exon, the alternatively spliced exon 5 of
avian cardiac troponin T. We show that purified SRp55 binds
specifically to this RNA sequence with an apparent
Kd of 60 nM as assayed
by gel mobility retardation experiments. Mutations in
the exon 5 sequence that increase or decrease exon 5
inclusion in vivo and in vitro have correspondingly
different affinities for SRp55 in our assays. The exon
5 sequence contains two purine-rich motifs, common to many
ESEs, and both are required for SRp55 binding. Hill plot
analysis of binding titration reactions indicates that
there is a cooperative binding of at least two SRp55 proteins
to the exon sequence. Chemical modification interference
studies using kethoxal show that SRp55 binding to exon
5 requires the N1 and/or the N2 of almost every G residue
in the exon. Dimethylsulfate modification interference
studies indicate that none of the N1 positions of A residues
in the exon are important for binding. We postulate that
SRp55 may recognize both primary sequence and RNA secondary
structural elements within pre-mRNA.