The effects of disrupting 5S RNA helical structures on the binding of Xenopus transcription factor IIIA

Block mutations were constructed in helical stems II, III, IV and V of Xenopus laevis oocyte 5S RNA. The affinities of these mutants for binding to transcription factor IIIA (TFIIIA) were determined using a nitrocellulose filter binding assay. Mutations in stems III and IV had little or no effect on the binding affinity of TFIIIA for 5S RNA. However, single mutants in stems II and V (positions 16-21, 57-62, 71-72, and 103-104) which disrupt the double helix, reduce the binding of TFIIIA by a factor of two to three fold. In contrast, double mutants (16-21/57-62, 71-72/103-104) which restore the helical structure of these stems, but with altered sequences, fully restore the TFIIIA binding affinity. The experiments reported here indicate that the double helical structures of stems II and V, but not the sequences, are required for optimal TFIIIA binding.