Figure 8.

Computer-assisted folding of the 5' UTR of Tat RNA. Folding of the 5' UTR of Tat1 RNA was carried out as indicated in methods. Small-case letters indicate that the folding of the given nucleotides was constrained in Mfold (see methods). Sequences and SL structures of importance are indicated, namely from 5' to 3' TAR, polyA (pA), PBS, the SD-SA border, and the Tat AUG (circled). Note that these SLs are present in the secondary structure of the genomic 5' UTR RNA ([39,40,52,55] and ref. therein). Note that the 29-nt long sequence upstream from the Tat initiator AUG is mostly unstructured and thus could serve as a landing pad for the ribosomes. ΔG's for the Tat UTR1 and UTR2, indicated on the right, reveal a high degree of stability (see methods and ref. [52]).