RNA secondary structure of SL1 and position of the SD2-nucleotide deletion in the SIV leader. Secondary structure of the SIVmac239 SL1 RNA element was predicted by free energy minimization and adapted from published information [6, 28, 48]. All nucleotide deletions are relative to the transcriptional initiation site (1+) based on the sequence of the wild type clone of SIVmac239. The DIS palindrome is shown in bold, the A423G compensatory mutation is highlighted. Below is a diagram of the location of the various compensatory mutations generated in different cell lines. Asterisks denote substitutions selected in CEMx174 cells, Bullets denote substitutions selected in C8166 cells.