Evidence of reciprocal tertiary interactions between conserved motifs involved in organizing RNA structure essential for internal initiation of translation

RNase T2 probing of domain 3. RNA harboring the wild-type GUAA or UACG and GUAG substitution in the GNRA motif was incubated with RNase T2 in native (N) or denaturing (D) buffer conditions. A 5′-labeled primer was then used in a reverse transcriptase reaction, and cDNA products were subsequently analyzed on 6% acrylamide 7 M urea gels. A wild-type DNA sequence, prepared with the same oligonucleotide, was run in parallel to identify the RT stops. Residues are marked as the complementary sense sequence. Asterisks denote new attacks observed in the mutant RNAs relative to the GUAA sequence.