Figure 1.

SL1 constructs and the kissing-loop model of dimer maturation. (a) Stem-loop SL1 of the HIV-1 packaging signal and its fragments used in this study. SL1-fl RNA corresponds to the full-length 35-nt SL1 RNA with two terminal base pairs (shown in low case) reversed in order to optimize the in vitro transcription yield. SL1-s RNA includes the palindromic loop and the upper stem of SL1 but not the G-rich internal loop; two G:C base pairs were added to the bottom of the lower stem to increase its stability. SL1-gril RNA consists of the stems and the G-rich internal loop of SL1 with an apical UACG loop added to reduce dimerization during folding and a dangling G residue added at the 5’ end to increase the transcription yield. Broken boxes enclose wild-type residues from SL1; non-wild-type residues are shown in low case and indicated with an asterisk. Two additional constructs were used in this study: SL1-yf consisted of the sequence SL1-fl with the three flanking purines (adenines) being replaced by pyrimidines (uracils), and SL1-yb consisted of SL1-fl with the GRIL purines all replaced with pyrimidines (two cytosines and two uracils). (b) A two-step model of SL1 dimerization. A metastable kissing dimer (top) is formed using the self-complementary sequence in the apical loops of SL1 monomers and it can be converted into a more stable extended dimer (bottom) by heat or viral NCp7 protein.